******************************************************************************** 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/189/189.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17228 1.0000 500 1550 1.0000 500 8659 1.0000 500 42854 1.0000 500 43103 1.0000 500 43112 1.0000 500 54621 1.0000 500 46726 1.0000 500 47327 1.0000 500 47418 1.0000 500 54844 1.0000 500 38977 1.0000 500 25521 1.0000 500 49332 1.0000 500 52561 1.0000 500 49631 1.0000 500 52603 1.0000 500 10499 1.0000 500 33295 1.0000 500 55206 1.0000 500 17109 1.0000 500 44638 1.0000 500 44036 1.0000 500 45320 1.0000 500 46088 1.0000 500 45792 1.0000 500 33579 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/189/189.seqs.fa -oc motifs/189 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.245 G 0.235 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.245 G 0.235 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 133 E-value = 5.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::1:31::::::::2 pos.-specific C 14:6539:5:121::: probability G 8172:::1:a:791a6 matrix T 153154:95:91:9:2 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 ** ** *** Relative 1.3 * ** ** *** Entropy 1.0 * * * ***** *** (19.2 bits) 0.8 * * * ********* 0.6 *** * ********** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GTGCCTCTCGTGGTGG consensus CTGTA T C A sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 1550 485 1.37e-09 ATCCCTTAGC GCGCCTCTTGTGGTGG 43103 128 5.63e-08 TGAAATGGTC GTGGCTCTCGTCGTGG TGCTGCCATG 49332 89 6.55e-08 CAGCTGCTTG GTGCTACTCGTTGTGG ACTAGTTAGT 47327 323 1.41e-07 TTACTACAAC GTTCTTCTTGTGGGGG TTTTGCATTC 45792 405 1.55e-07 GTGTGCATTG GTGTTCCTTGTGGTGT GGTGTGTTGT 44036 143 2.95e-07 GGAACGAGCC GCGCCTCTCGTGCTGA CCGAGAATGA 10499 444 8.76e-07 CGACCAATCC TCGCCACTCGCGGTGG CCGAAGCCCT 46088 139 1.38e-06 TTGGACGATT CTGACACTTGTGGTGA CGGAGTTTTC 49631 169 1.92e-06 GGGAAGCGGT GCTGTCATCGTGGTGT GGTCGTTCCT 52561 477 2.56e-06 GCCCCACGAT GGTCTCCGTGTCGTGG GCTGTGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1550 1.4e-09 484_[+1] 43103 5.6e-08 127_[+1]_357 49332 6.5e-08 88_[+1]_396 47327 1.4e-07 322_[+1]_162 45792 1.5e-07 404_[+1]_80 44036 3e-07 142_[+1]_342 10499 8.8e-07 443_[+1]_41 46088 1.4e-06 138_[+1]_346 49631 1.9e-06 168_[+1]_316 52561 2.6e-06 476_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 1550 ( 485) GCGCCTCTTGTGGTGG 1 43103 ( 128) GTGGCTCTCGTCGTGG 1 49332 ( 89) GTGCTACTCGTTGTGG 1 47327 ( 323) GTTCTTCTTGTGGGGG 1 45792 ( 405) GTGTTCCTTGTGGTGT 1 44036 ( 143) GCGCCTCTCGTGCTGA 1 10499 ( 444) TCGCCACTCGCGGTGG 1 46088 ( 139) CTGACACTTGTGGTGA 1 49631 ( 169) GCTGTCATCGTGGTGT 1 52561 ( 477) GGTCTCCGTGTCGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 10.6054 E= 5.5e+001 -997 -129 177 -137 -997 71 -123 95 -997 -997 158 21 -138 129 -23 -137 -997 103 -997 95 20 29 -997 62 -138 188 -997 -997 -997 -997 -123 179 -997 103 -997 95 -997 -997 209 -997 -997 -129 -997 179 -997 -29 158 -137 -997 -129 194 -997 -997 -997 -123 179 -997 -997 209 -997 -39 -997 135 -38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 5.5e+001 0.000000 0.100000 0.800000 0.100000 0.000000 0.400000 0.100000 0.500000 0.000000 0.000000 0.700000 0.300000 0.100000 0.600000 0.200000 0.100000 0.000000 0.500000 0.000000 0.500000 0.300000 0.300000 0.000000 0.400000 0.100000 0.900000 0.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.200000 0.700000 0.100000 0.000000 0.100000 0.900000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.600000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[TC][GT][CG][CT][TAC]CT[CT]GT[GC]GTG[GAT] -------------------------------------------------------------------------------- Time 6.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 12 llr = 131 E-value = 9.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3:1:1:1:335 pos.-specific C :::::::1::63 probability G :3::9::8171: matrix T a5a919a19::3 bits 2.1 1.9 * * * 1.7 * * * * 1.5 * ***** * Relative 1.3 * ***** * Entropy 1.0 * ***** ** (15.8 bits) 0.8 * ******** 0.6 * ********* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTGTTGTGCA consensus A AAC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 33579 93 4.56e-07 TCAGATATCA TTTTGTTGTGCT TGTGCATTAC 1550 259 4.56e-07 TGGGAAGCCA TTTTGTTGTGCT GTGCAGCCCT 45792 20 6.38e-07 CGGACTGCTT TGTTGTTGTGCC TCGACTGACC 46726 388 1.32e-06 TCTACCTATC TATTGTTGTACA ACCCTGGATA 17109 254 2.46e-06 GACAGGAGGT TTTTGTTATGCA GATGATTCAC 47327 136 3.04e-06 TTGTGCGGAT TATTGTTGTGGA AACTACGCAA 33295 301 8.15e-06 TACTTAAGCA TTTTGTTCTAAA TGAACATATG 49332 458 8.15e-06 GTCGCCGAGC TTTTGTTGGGAT CTTCGATATC 52603 24 9.46e-06 TACCAGTGTA TGTTGATGTGCC GTACCTCGTA 55206 230 1.21e-05 ACAAAATATA TATTGTTTTACA TTTAAAGTCC 38977 243 1.21e-05 TCAACAAGAA TTTTTTTGTAAA GGTATTGAAA 47418 356 1.48e-05 GCTTCAAACC TGTAGTTGTGAC AAAGGCCCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33579 4.6e-07 92_[+2]_396 1550 4.6e-07 258_[+2]_230 45792 6.4e-07 19_[+2]_469 46726 1.3e-06 387_[+2]_101 17109 2.5e-06 253_[+2]_235 47327 3e-06 135_[+2]_353 33295 8.1e-06 300_[+2]_188 49332 8.1e-06 457_[+2]_31 52603 9.5e-06 23_[+2]_465 55206 1.2e-05 229_[+2]_259 38977 1.2e-05 242_[+2]_246 47418 1.5e-05 355_[+2]_133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=12 33579 ( 93) TTTTGTTGTGCT 1 1550 ( 259) TTTTGTTGTGCT 1 45792 ( 20) TGTTGTTGTGCC 1 46726 ( 388) TATTGTTGTACA 1 17109 ( 254) TTTTGTTATGCA 1 47327 ( 136) TATTGTTGTGGA 1 33295 ( 301) TTTTGTTCTAAA 1 49332 ( 458) TTTTGTTGGGAT 1 52603 ( 24) TGTTGATGTGCC 1 55206 ( 230) TATTGTTTTACA 1 38977 ( 243) TTTTTTTGTAAA 1 47418 ( 356) TGTAGTTGTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 10.5501 E= 9.0e+002 -1023 -1023 -1023 195 -6 -1023 9 95 -1023 -1023 -1023 195 -165 -1023 -1023 182 -1023 -1023 197 -164 -165 -1023 -1023 182 -1023 -1023 -1023 195 -165 -155 168 -164 -1023 -1023 -149 182 35 -1023 151 -1023 35 125 -149 -1023 94 3 -1023 -5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 9.0e+002 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.083333 0.000000 0.000000 0.916667 0.000000 0.000000 0.916667 0.083333 0.083333 0.000000 0.000000 0.916667 0.000000 0.000000 0.000000 1.000000 0.083333 0.083333 0.750000 0.083333 0.000000 0.000000 0.083333 0.916667 0.333333 0.000000 0.666667 0.000000 0.333333 0.583333 0.083333 0.000000 0.500000 0.250000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[TAG]TTGTTGT[GA][CA][ACT] -------------------------------------------------------------------------------- Time 11.88 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 6 llr = 92 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a3:2:a:::::a2::: pos.-specific C ::::::8238::3:2: probability G :7:3::285:a:2588 matrix T ::a5a:::22::35:2 bits 2.1 * 1.9 * * ** ** 1.7 * * ** ** 1.5 * * **** *** ** Relative 1.3 * * **** *** ** Entropy 1.0 *** **** *** *** (22.2 bits) 0.8 *** **** *** *** 0.6 ************ *** 0.4 ************ *** 0.2 ************ *** 0.0 ---------------- Multilevel AGTTTACGGCGACGGG consensus A G C TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44036 322 1.48e-09 GCACGAGTAC AGTGTACGGCGATGGG AGCAGCACAC 52603 88 9.00e-09 TTTATAGTTC AGTTTACGCCGAATGG CTGTTTAATA 43103 93 3.71e-08 ATGCAATGAT AGTGTAGGCCGACTGG CGACGCAAGT 33295 183 4.59e-08 AGCTACTAGC AATTTACGGTGACTGG TTAGAAAAAT 33579 482 8.51e-08 AGTTGCCTAC AATTTACGGCGAGGCG CCC 8659 386 4.77e-07 TTTTGAGGCA AGTATACCTCGATGGT AGGAAGAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44036 1.5e-09 321_[+3]_163 52603 9e-09 87_[+3]_397 43103 3.7e-08 92_[+3]_392 33295 4.6e-08 182_[+3]_302 33579 8.5e-08 481_[+3]_3 8659 4.8e-07 385_[+3]_99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=6 44036 ( 322) AGTGTACGGCGATGGG 1 52603 ( 88) AGTTTACGCCGAATGG 1 43103 ( 93) AGTGTAGGCCGACTGG 1 33295 ( 183) AATTTACGGTGACTGG 1 33579 ( 482) AATTTACGGCGAGGCG 1 8659 ( 386) AGTATACCTCGATGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 10.7499 E= 1.6e+003 193 -923 -923 -923 35 -923 151 -923 -923 -923 -923 194 -65 -923 51 95 -923 -923 -923 194 193 -923 -923 -923 -923 177 -49 -923 -923 -55 183 -923 -923 45 109 -64 -923 177 -923 -64 -923 -923 209 -923 193 -923 -923 -923 -65 45 -49 36 -923 -923 109 95 -923 -55 183 -923 -923 -923 183 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 1.6e+003 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.333333 0.500000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.333333 0.500000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.166667 0.333333 0.000000 0.000000 0.500000 0.500000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.833333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[GA]T[TG]TACG[GC]CGA[CT][GT]GG -------------------------------------------------------------------------------- Time 17.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17228 7.12e-01 500 1550 2.43e-08 258_[+2(4.56e-07)]_214_\ [+1(1.37e-09)] 8659 8.23e-04 385_[+3(4.77e-07)]_99 42854 3.19e-01 224_[+3(8.33e-05)]_260 43103 4.60e-08 92_[+3(3.71e-08)]_19_[+1(5.63e-08)]_\ 357 43112 7.73e-01 500 54621 4.61e-01 500 46726 1.43e-03 387_[+2(1.32e-06)]_101 47327 1.10e-05 135_[+2(3.04e-06)]_175_\ [+1(1.41e-07)]_162 47418 7.16e-03 355_[+2(1.48e-05)]_133 54844 8.17e-01 500 38977 7.68e-02 242_[+2(1.21e-05)]_246 25521 6.09e-01 500 49332 8.28e-06 88_[+1(6.55e-08)]_353_\ [+2(8.15e-06)]_31 52561 1.07e-02 476_[+1(2.56e-06)]_8 49631 1.14e-02 168_[+1(1.92e-06)]_316 52603 2.77e-06 23_[+2(9.46e-06)]_52_[+3(9.00e-09)]_\ 397 10499 1.63e-02 443_[+1(8.76e-07)]_41 33295 1.28e-05 182_[+3(4.59e-08)]_102_\ [+2(8.15e-06)]_188 55206 4.00e-02 229_[+2(1.21e-05)]_259 17109 2.12e-02 253_[+2(2.46e-06)]_235 44638 9.99e-01 500 44036 4.04e-09 142_[+1(2.95e-07)]_163_\ [+3(1.48e-09)]_163 45320 9.24e-01 500 46088 1.77e-03 138_[+1(1.38e-06)]_346 45792 3.46e-06 19_[+2(6.38e-07)]_373_\ [+1(1.55e-07)]_80 33579 1.61e-06 92_[+2(4.56e-07)]_377_\ [+3(8.51e-08)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************