******************************************************************************** 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/320/320.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 47753 1.0000 500 38829 1.0000 500 39074 1.0000 500 41254 1.0000 500 10788 1.0000 500 44788 1.0000 500 41928 1.0000 500 38828 1.0000 500 31810 1.0000 500 44088 1.0000 500 48596 1.0000 500 46724 1.0000 500 37853 1.0000 500 39235 1.0000 500 45614 1.0000 500 33504 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/320/320.seqs.fa -oc motifs/320 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.234 G 0.216 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.234 G 0.216 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 16 llr = 143 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 672::5:21::9 pos.-specific C 3:3:14924:1: probability G 132:8:::6191 matrix T ::4a2116:9:: bits 2.2 2.0 1.8 * 1.5 * * ** Relative 1.3 * * *** Entropy 1.1 * ** * *** (12.9 bits) 0.9 * ** * **** 0.7 ** ** ****** 0.4 ** ********* 0.2 ** ********* 0.0 ------------ Multilevel AATTGACTGTGA consensus CGC C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46724 315 4.63e-07 AAAGAATAAT AATTGACTCTGA ACGCTGCTGT 31810 342 2.06e-06 GATTGACGAA AAGTGCCTCTGA AGGAATCAAA 45614 41 3.44e-06 TGATGATTTT AATTTACTGTGA TAGGGCTCTA 41928 11 4.96e-06 TCCGGCAGAC GGTTGACTGTGA CTGCGAATCC 33504 331 5.94e-06 AATCGTTTCG AAATGACAGTGA GCTGTAAACA 38829 321 7.58e-06 TGGCGAAACA AATTGATTGTGA AACTCTTCTC 37853 40 9.47e-06 ATGCTTTAAT GACTGCCTCTGA GAAGTGTTTT 10788 242 1.03e-05 CCACTGCTGC CACTGCCAGTGA GCCCGCTACA 47753 274 2.62e-05 CCGACATCGA AACTGCCCGGGA GACAAAACAC 44088 322 3.74e-05 TTGGATCATC CGATTACTGTGA TATGAGTCGC 39235 194 5.63e-05 ACCCTACGTC AAGTGTCTGTCA TATATACGTT 39074 378 7.09e-05 AGCGTACTGT AAATTTCTCTGA AAACAAAACT 38828 96 1.08e-04 TGCAACGAAG AAGTGCCCCTGG CATTGTCGAT 48596 131 1.22e-04 TGCACGGTTC CGTTGCCCATGA GCTGGGATGT 44788 233 1.86e-04 GTCATTCCAA CGTTGATTCGGA TTGCATGACG 41254 238 3.40e-04 AAAAGTCCTC AGCTCACAGTCA AATCGATGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46724 4.6e-07 314_[+1]_174 31810 2.1e-06 341_[+1]_147 45614 3.4e-06 40_[+1]_448 41928 5e-06 10_[+1]_478 33504 5.9e-06 330_[+1]_158 38829 7.6e-06 320_[+1]_168 37853 9.5e-06 39_[+1]_449 10788 1e-05 241_[+1]_247 47753 2.6e-05 273_[+1]_215 44088 3.7e-05 321_[+1]_167 39235 5.6e-05 193_[+1]_295 39074 7.1e-05 377_[+1]_111 38828 0.00011 95_[+1]_393 48596 0.00012 130_[+1]_358 44788 0.00019 232_[+1]_256 41254 0.00034 237_[+1]_251 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=16 46724 ( 315) AATTGACTCTGA 1 31810 ( 342) AAGTGCCTCTGA 1 45614 ( 41) AATTTACTGTGA 1 41928 ( 11) GGTTGACTGTGA 1 33504 ( 331) AAATGACAGTGA 1 38829 ( 321) AATTGATTGTGA 1 37853 ( 40) GACTGCCTCTGA 1 10788 ( 242) CACTGCCAGTGA 1 47753 ( 274) AACTGCCCGGGA 1 44088 ( 322) CGATTACTGTGA 1 39235 ( 194) AAGTGTCTGTCA 1 39074 ( 378) AAATTTCTCTGA 1 38828 ( 96) AAGTGCCCCTGG 1 48596 ( 131) CGTTGCCCATGA 1 44788 ( 233) CGTTGATTCGGA 1 41254 ( 238) AGCTCACAGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.66888 E= 1.0e+002 117 9 -79 -1064 131 -1064 53 -1064 -56 9 -20 46 -1064 -1064 -1064 188 -1064 -190 180 -54 85 68 -1064 -112 -1064 190 -1064 -112 -56 -32 -1064 120 -215 68 138 -1064 -1064 -1064 -79 168 -1064 -91 202 -1064 176 -1064 -179 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 1.0e+002 0.625000 0.250000 0.125000 0.000000 0.687500 0.000000 0.312500 0.000000 0.187500 0.250000 0.187500 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.062500 0.750000 0.187500 0.500000 0.375000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.187500 0.187500 0.000000 0.625000 0.062500 0.375000 0.562500 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.125000 0.875000 0.000000 0.937500 0.000000 0.062500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AG][TC]TG[AC]CT[GC]TGA -------------------------------------------------------------------------------- Time 2.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 4 llr = 71 E-value = 3.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::583:5:8a::5: pos.-specific C :::::3::3:3::::: probability G ::aa5::a38::aa3a matrix T aa::::8::3::::3: bits 2.2 ** * ** * 2.0 ** * ** * 1.8 **** * *** * 1.5 **** * *** * Relative 1.3 **** * * *** * Entropy 1.1 ******** ***** * (25.4 bits) 0.9 ******** ***** * 0.7 ******** ***** * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TTGGAATGAGAAGGAG consensus GCA CTC G sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 37853 140 8.81e-10 AAATCATAAA TTGGGATGAGAAGGTG TGAATATCGC 41928 340 4.61e-09 GAAAATTGTC TTGGGCTGCGAAGGAG GTTCCTACCA 33504 115 6.08e-09 AAATTCACTA TTGGAATGAGCAGGGG TGAAAATTAT 38829 143 2.23e-08 GCGACAATAC TTGGAAAGGTAAGGAG TCGTGGGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37853 8.8e-10 139_[+2]_345 41928 4.6e-09 339_[+2]_145 33504 6.1e-09 114_[+2]_370 38829 2.2e-08 142_[+2]_342 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=4 37853 ( 140) TTGGGATGAGAAGGTG 1 41928 ( 340) TTGGGCTGCGAAGGAG 1 33504 ( 115) TTGGAATGAGCAGGGG 1 38829 ( 143) TTGGAAAGGTAAGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7760 bayes= 10.9211 E= 3.6e+002 -865 -865 -865 187 -865 -865 -865 187 -865 -865 221 -865 -865 -865 221 -865 85 -865 121 -865 143 9 -865 -865 -15 -865 -865 146 -865 -865 221 -865 85 9 21 -865 -865 -865 179 -12 143 9 -865 -865 185 -865 -865 -865 -865 -865 221 -865 -865 -865 221 -865 85 -865 21 -12 -865 -865 221 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 3.6e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TTGG[AG][AC][TA]G[ACG][GT][AC]AGG[AGT]G -------------------------------------------------------------------------------- Time 4.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 9 llr = 102 E-value = 8.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:aa74:::9a9 pos.-specific C 3::::19:7::: probability G :a:::::231:: matrix T 4:::3418:::1 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 TGAAAACTCAAA consensus C TT GG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44788 169 2.17e-07 TTGTGGATTA TGAAAACTCAAA TGTTTTAATT 41254 340 5.03e-07 GATTTTAAAA TGAAATCTGAAA ACCGTTCCCC 48596 361 1.30e-06 GATTTATAGT CGAAAACTGAAA CCCACGCGCT 47753 116 1.30e-06 GGGCATAGCT CGAATTCTCAAA CGACGGTTAG 31810 74 3.56e-06 CACTTACCGA CGAAAACGGAAA GACTGTTAAG 37853 423 4.14e-06 ATTATCGTGA AGAAACCTCAAA AATTTTTGAT 39074 292 5.36e-06 GAGGAGATTT TGAAAATTCAAA GTTATTCGAC 44088 472 1.10e-05 AGAATCCTGG AGAATTCTCGAA ACGCGAGTTT 38828 36 1.48e-05 TGTTCCGTAC TGAATTCGCAAT GCCATGCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44788 2.2e-07 168_[+3]_320 41254 5e-07 339_[+3]_149 48596 1.3e-06 360_[+3]_128 47753 1.3e-06 115_[+3]_373 31810 3.6e-06 73_[+3]_415 37853 4.1e-06 422_[+3]_66 39074 5.4e-06 291_[+3]_197 44088 1.1e-05 471_[+3]_17 38828 1.5e-05 35_[+3]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=9 44788 ( 169) TGAAAACTCAAA 1 41254 ( 340) TGAAATCTGAAA 1 48596 ( 361) CGAAAACTGAAA 1 47753 ( 116) CGAATTCTCAAA 1 31810 ( 74) CGAAAACGGAAA 1 37853 ( 423) AGAAACCTCAAA 1 39074 ( 292) TGAAAATTCAAA 1 44088 ( 472) AGAATTCTCGAA 1 38828 ( 36) TGAATTCGCAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.89655 E= 8.0e+002 -32 51 -982 71 -982 -982 221 -982 185 -982 -982 -982 185 -982 -982 -982 126 -982 -982 29 68 -108 -982 71 -982 192 -982 -129 -982 -982 4 151 -982 151 63 -982 168 -982 -96 -982 185 -982 -982 -982 168 -982 -982 -129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 8.0e+002 0.222222 0.333333 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.444444 0.111111 0.000000 0.444444 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 0.222222 0.777778 0.000000 0.666667 0.333333 0.000000 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TCA]GAA[AT][AT]C[TG][CG]AAA -------------------------------------------------------------------------------- Time 6.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47753 2.58e-04 47_[+1(6.56e-05)]_56_[+3(1.30e-06)]_\ 146_[+1(2.62e-05)]_215 38829 1.56e-06 142_[+2(2.23e-08)]_162_\ [+1(7.58e-06)]_168 39074 6.71e-04 291_[+3(5.36e-06)]_74_\ [+1(7.09e-05)]_111 41254 2.12e-03 339_[+3(5.03e-07)]_149 10788 1.50e-02 241_[+1(1.03e-05)]_247 44788 5.85e-04 168_[+3(2.17e-07)]_320 41928 1.01e-06 10_[+1(4.96e-06)]_317_\ [+2(4.61e-09)]_145 38828 5.11e-03 35_[+3(1.48e-05)]_453 31810 1.77e-04 73_[+3(3.56e-06)]_152_\ [+1(4.79e-05)]_92_[+1(2.06e-06)]_147 44088 4.49e-03 321_[+1(3.74e-05)]_138_\ [+3(1.10e-05)]_17 48596 1.21e-03 360_[+3(1.30e-06)]_128 46724 5.22e-03 314_[+1(4.63e-07)]_174 37853 1.49e-09 39_[+1(9.47e-06)]_88_[+2(8.81e-10)]_\ 267_[+3(4.14e-06)]_66 39235 1.22e-01 193_[+1(5.63e-05)]_295 45614 6.05e-03 40_[+1(3.44e-06)]_448 33504 4.56e-07 114_[+2(6.08e-09)]_200_\ [+1(5.94e-06)]_158 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************