******************************************************************************** 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/383/383.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42498 1.0000 500 42762 1.0000 500 42948 1.0000 500 9316 1.0000 500 8982 1.0000 500 13553 1.0000 500 52367 1.0000 500 43422 1.0000 500 18199 1.0000 500 49277 1.0000 500 40147 1.0000 500 1719 1.0000 500 50516 1.0000 500 44433 1.0000 500 45221 1.0000 500 45782 1.0000 500 46213 1.0000 500 42656 1.0000 500 49030 1.0000 500 48696 1.0000 500 47686 1.0000 500 50027 1.0000 500 47875 1.0000 500 46302 1.0000 500 47701 1.0000 500 50575 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/383/383.seqs.fa -oc motifs/383 -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= 26 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= 13000 N= 26 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.257 G 0.229 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.257 G 0.229 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 11 llr = 161 E-value = 2.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 75596:68:852:75:2:7a8 pos.-specific C 151::9::7:145::729::: probability G 1:21413231:5232:512:2 matrix T 1:2:::1::14:3:431:1:: bits 2.1 1.9 * 1.7 * 1.5 * * * * Relative 1.3 * * * * * ** Entropy 1.1 * *** *** * * * ** (21.1 bits) 0.9 * ******* * * **** 0.6 ** *********** * **** 0.4 ** ****************** 0.2 ********************* 0.0 --------------------- Multilevel AAAAACAACAAGCAACGCAAA consensus C G G G TCTGTT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50516 286 3.75e-10 TAGTACCAAC AATAACAACAACCGTCGCAAA AGTACACACC 46213 58 7.98e-09 AGGGAAGGGG ACAAGCGGGATCCAACGCAAA CGACTCGCCG 50575 366 1.24e-08 GTTAACAGGA TCAAGCAACAAGTATTGCAAA AGACGTCTCT 42762 358 5.46e-08 TACGATCCTT ACAAACAACACGTGACCCGAA TTGCGTGCAC 45221 348 7.13e-08 CCGCGAAGCC AAAAGCAACAACGATTACTAA AAAATGGATG 1719 372 7.13e-08 AGGTGTCGAG GAAAACAACAAGCGACGGAAG AACCAGAGAA 47686 433 7.78e-08 GCGAACGAAA AAGAGCAGCGTACAACGCAAA CGAAGCAATC 18199 222 2.76e-07 GGCCGAACTT AACAAGAAGAAGGAACTCAAA TCCGTAGATC 44433 77 3.18e-07 AACTCCCGAC CCAAACGAGATCCAGCACGAA AGAAGGAACA 9316 187 3.66e-07 TCTCAAGGCA ACGAACTACTTGTATCCCAAA CACGTCGAAG 48696 397 4.48e-07 GTTGTTGATA AATGACGACAAACAGTGCAAG GCTACCGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50516 3.8e-10 285_[+1]_194 46213 8e-09 57_[+1]_422 50575 1.2e-08 365_[+1]_114 42762 5.5e-08 357_[+1]_122 45221 7.1e-08 347_[+1]_132 1719 7.1e-08 371_[+1]_108 47686 7.8e-08 432_[+1]_47 18199 2.8e-07 221_[+1]_258 44433 3.2e-07 76_[+1]_403 9316 3.7e-07 186_[+1]_293 48696 4.5e-07 396_[+1]_83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=11 50516 ( 286) AATAACAACAACCGTCGCAAA 1 46213 ( 58) ACAAGCGGGATCCAACGCAAA 1 50575 ( 366) TCAAGCAACAAGTATTGCAAA 1 42762 ( 358) ACAAACAACACGTGACCCGAA 1 45221 ( 348) AAAAGCAACAACGATTACTAA 1 1719 ( 372) GAAAACAACAAGCGACGGAAG 1 47686 ( 433) AAGAGCAGCGTACAACGCAAA 1 18199 ( 222) AACAAGAAGAAGGAACTCAAA 1 44433 ( 77) CCAAACGAGATCCAGCACGAA 1 9316 ( 187) ACGAACTACTTGTATCCCAAA 1 48696 ( 397) AATGACGACAAACAGTGCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12480 bayes= 10.502 E= 2.0e+000 151 -149 -133 -151 110 82 -1010 -1010 110 -149 -33 -51 183 -1010 -133 -1010 132 -1010 67 -1010 -1010 182 -133 -1010 132 -1010 25 -151 168 -1010 -33 -1010 -1010 150 25 -1010 168 -1010 -133 -151 110 -149 -1010 49 -49 50 99 -1010 -1010 109 -33 7 151 -1010 25 -1010 84 -1010 -33 49 -1010 150 -1010 7 -49 -50 125 -151 -1010 182 -133 -1010 151 -1010 -33 -151 197 -1010 -1010 -1010 168 -1010 -33 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 2.0e+000 0.727273 0.090909 0.090909 0.090909 0.545455 0.454545 0.000000 0.000000 0.545455 0.090909 0.181818 0.181818 0.909091 0.000000 0.090909 0.000000 0.636364 0.000000 0.363636 0.000000 0.000000 0.909091 0.090909 0.000000 0.636364 0.000000 0.272727 0.090909 0.818182 0.000000 0.181818 0.000000 0.000000 0.727273 0.272727 0.000000 0.818182 0.000000 0.090909 0.090909 0.545455 0.090909 0.000000 0.363636 0.181818 0.363636 0.454545 0.000000 0.000000 0.545455 0.181818 0.272727 0.727273 0.000000 0.272727 0.000000 0.454545 0.000000 0.181818 0.363636 0.000000 0.727273 0.000000 0.272727 0.181818 0.181818 0.545455 0.090909 0.000000 0.909091 0.090909 0.000000 0.727273 0.000000 0.181818 0.090909 1.000000 0.000000 0.000000 0.000000 0.818182 0.000000 0.181818 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AC]AA[AG]C[AG]A[CG]A[AT][GC][CT][AG][AT][CT]GCAAA -------------------------------------------------------------------------------- Time 6.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 9 llr = 108 E-value = 4.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 91a28:929:a: pos.-specific C :9:7:a:4:9:a probability G 1::1:::11::: matrix T ::::2:12:1:: bits 2.1 1.9 * * ** 1.7 * * ** 1.5 *** ** **** Relative 1.3 *** *** **** Entropy 1.1 *** *** **** (17.3 bits) 0.9 ******* **** 0.6 ******* **** 0.4 ******* **** 0.2 ************ 0.0 ------------ Multilevel ACACACACACAC consensus AT A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43422 387 7.92e-08 GGTCCTCTAG ACACACACACAC ACACACACAC 45221 394 2.38e-07 CCAAAAAGAG ACACACATACAC CTTGCCAAGT 42498 437 2.38e-07 CCTACAGACA ACACACATACAC ACTCCCGACA 18199 315 4.68e-07 TTCCTTGGCC ACACTCACACAC GATCAAGTTA 50027 457 1.16e-06 TTGCATGTAT ACACACACATAC ATACGTGACA 46213 464 1.90e-06 TGTACCGGGA AAACACAAACAC CTTTTATAGA 50575 332 5.01e-06 TCTTGCTGGG ACAGACTCACAC AAAAGGGGTG 47875 486 7.50e-06 AGCAGATAGA ACAAACAGGCAC ACT 47701 328 1.07e-05 GCGCAAGCAA GCAATCAAACAC ACAATTGATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43422 7.9e-08 386_[+2]_102 45221 2.4e-07 393_[+2]_95 42498 2.4e-07 436_[+2]_52 18199 4.7e-07 314_[+2]_174 50027 1.2e-06 456_[+2]_32 46213 1.9e-06 463_[+2]_25 50575 5e-06 331_[+2]_157 47875 7.5e-06 485_[+2]_3 47701 1.1e-05 327_[+2]_161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=9 43422 ( 387) ACACACACACAC 1 45221 ( 394) ACACACATACAC 1 42498 ( 437) ACACACATACAC 1 18199 ( 315) ACACTCACACAC 1 50027 ( 457) ACACACACATAC 1 46213 ( 464) AAACACAAACAC 1 50575 ( 332) ACAGACTCACAC 1 47875 ( 486) ACAAACAGGCAC 1 47701 ( 328) GCAATCAAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 12714 bayes= 11.3116 E= 4.6e+001 180 -982 -104 -982 -119 179 -982 -982 197 -982 -982 -982 -20 138 -104 -982 161 -982 -982 -22 -982 196 -982 -982 180 -982 -982 -122 -20 79 -104 -22 180 -982 -104 -982 -982 179 -982 -122 197 -982 -982 -982 -982 196 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 4.6e+001 0.888889 0.000000 0.111111 0.000000 0.111111 0.888889 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.666667 0.111111 0.000000 0.777778 0.000000 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.222222 0.444444 0.111111 0.222222 0.888889 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ACA[CA][AT]CA[CAT]ACAC -------------------------------------------------------------------------------- Time 12.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 171 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:222::::2237::1::82: pos.-specific C ::2:2::821522:::69111 probability G 5:23:2222322:96921228 matrix T 5a45688:7524114:2::52 bits 2.1 1.9 * 1.7 * * * 1.5 * * * * Relative 1.3 * *** * * * Entropy 1.1 * *** *** ** * (18.9 bits) 0.9 * **** **** ** * 0.6 ** ***** ******* * 0.4 ** ****** ******* * 0.2 ** ******** ********* 0.0 --------------------- Multilevel GTTTTTTCTTCTAGGGCCATG consensus T AGAG G GAAC T T A sequence GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50575 193 3.33e-10 GGGTTTACGA GTTTTTTCTTCAAGGGCCACG AAAACGTTCC 18199 333 7.81e-08 ACACGATCAA GTTATTTCTCGACGGGCCAAG CTCAAAGTGC 42498 23 8.70e-08 TTTGTTACGC TTTTCTTCTGCAAGGGCCCGG TGTGGAGGAA 47686 198 1.19e-07 CGCCTTTTTT TTAATTTCTTCGAGGGGCATC GAAAAGCTCC 50516 215 1.32e-07 TATTCGTTGG TTCGTTTCCTATAGTGCCATT CTAGTCGAGT 52367 222 2.86e-07 TATCTTTTCG GTAGAGTCTGATCGGGTCAAG GCGGTCGAGA 50027 238 3.75e-07 CCGTTAGCCT ATGTATTCTTGCCGTGCCATG GCGTAATTGA 45221 1 4.87e-07 . TTGAAGTGCGCTAGGGTCATG ATATGCGCTA 42656 342 1.01e-06 ACGCGTTGCT TTGTCTTGTATTATGGCCATG GCTGACTTGT 47701 424 1.18e-06 GGATTGTTAG GTTGTTTGTTTTTGTGCCGGG TTTGAGTTTG 9316 13 1.27e-06 GACGAGTTCG GTTTTGGCTTCCAGTGCGGTG CTTGCCTTTC 49277 284 1.47e-06 TGTATAGCTA GTATTTTCGAAGAGGAGCATG TTTAATTATG 44433 220 2.41e-06 TACCTTACGT TTCGTTGCGGCAAGTGTCAAT TGACACTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50575 3.3e-10 192_[+3]_287 18199 7.8e-08 332_[+3]_147 42498 8.7e-08 22_[+3]_457 47686 1.2e-07 197_[+3]_282 50516 1.3e-07 214_[+3]_265 52367 2.9e-07 221_[+3]_258 50027 3.7e-07 237_[+3]_242 45221 4.9e-07 [+3]_479 42656 1e-06 341_[+3]_138 47701 1.2e-06 423_[+3]_56 9316 1.3e-06 12_[+3]_467 49277 1.5e-06 283_[+3]_196 44433 2.4e-06 219_[+3]_260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 50575 ( 193) GTTTTTTCTTCAAGGGCCACG 1 18199 ( 333) GTTATTTCTCGACGGGCCAAG 1 42498 ( 23) TTTTCTTCTGCAAGGGCCCGG 1 47686 ( 198) TTAATTTCTTCGAGGGGCATC 1 50516 ( 215) TTCGTTTCCTATAGTGCCATT 1 52367 ( 222) GTAGAGTCTGATCGGGTCAAG 1 50027 ( 238) ATGTATTCTTGCCGTGCCATG 1 45221 ( 1) TTGAAGTGCGCTAGGGTCATG 1 42656 ( 342) TTGTCTTGTATTATGGCCATG 1 47701 ( 424) GTTGTTTGTTTTTGTGCCGGG 1 9316 ( 13) GTTTTGGCTTCCAGTGCGGTG 1 49277 ( 284) GTATTTTCGAAGAGGAGCATG 1 44433 ( 220) TTCGTTGCGGCAAGTGTCAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12480 bayes= 10.4364 E= 1.8e+002 -172 -1035 101 83 -1035 -1035 -1035 194 -14 -74 1 57 -14 -1035 42 83 -14 -74 -1035 124 -1035 -1035 1 157 -1035 -1035 -57 170 -1035 158 1 -1035 -1035 -74 -57 141 -73 -174 42 83 -14 85 -57 -75 27 -74 -57 57 144 -15 -1035 -175 -1035 -1035 201 -175 -1035 -1035 142 57 -172 -1035 201 -1035 -1035 126 -57 -17 -1035 185 -157 -1035 159 -174 -57 -1035 -14 -174 -57 105 -1035 -174 175 -75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 1.8e+002 0.076923 0.000000 0.461538 0.461538 0.000000 0.000000 0.000000 1.000000 0.230769 0.153846 0.230769 0.384615 0.230769 0.000000 0.307692 0.461538 0.230769 0.153846 0.000000 0.615385 0.000000 0.000000 0.230769 0.769231 0.000000 0.000000 0.153846 0.846154 0.000000 0.769231 0.230769 0.000000 0.000000 0.153846 0.153846 0.692308 0.153846 0.076923 0.307692 0.461538 0.230769 0.461538 0.153846 0.153846 0.307692 0.153846 0.153846 0.384615 0.692308 0.230769 0.000000 0.076923 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 0.615385 0.384615 0.076923 0.000000 0.923077 0.000000 0.000000 0.615385 0.153846 0.230769 0.000000 0.923077 0.076923 0.000000 0.769231 0.076923 0.153846 0.000000 0.230769 0.076923 0.153846 0.538462 0.000000 0.076923 0.769231 0.153846 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT]T[TAG][TGA][TA][TG]T[CG]T[TG][CA][TA][AC]G[GT]G[CT]CA[TA]G -------------------------------------------------------------------------------- Time 18.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42498 3.12e-07 22_[+3(8.70e-08)]_149_\ [+2(4.33e-05)]_232_[+2(2.38e-07)]_52 42762 1.14e-03 357_[+1(5.46e-08)]_122 42948 2.39e-01 500 9316 1.48e-05 12_[+3(1.27e-06)]_153_\ [+1(3.66e-07)]_293 8982 9.36e-01 500 13553 5.24e-01 500 52367 2.74e-03 221_[+3(2.86e-07)]_258 43422 8.28e-04 334_[+2(4.55e-05)]_12_\ [+2(2.96e-05)]_16_[+2(7.92e-08)]_2_[+2(1.16e-06)]_88 18199 4.62e-10 221_[+1(2.76e-07)]_72_\ [+2(4.68e-07)]_6_[+3(7.81e-08)]_147 49277 1.25e-03 111_[+1(8.78e-05)]_151_\ [+3(1.47e-06)]_196 40147 4.22e-01 500 1719 5.94e-04 371_[+1(7.13e-08)]_108 50516 1.67e-09 214_[+3(1.32e-07)]_50_\ [+1(3.75e-10)]_194 44433 1.89e-05 76_[+1(3.18e-07)]_122_\ [+3(2.41e-06)]_260 45221 3.84e-10 [+3(4.87e-07)]_326_[+1(7.13e-08)]_\ 25_[+2(2.38e-07)]_95 45782 7.99e-02 213_[+3(5.30e-05)]_266 46213 6.40e-07 57_[+1(7.98e-09)]_385_\ [+2(1.90e-06)]_25 42656 3.62e-03 341_[+3(1.01e-06)]_138 49030 3.87e-01 500 48696 2.60e-03 396_[+1(4.48e-07)]_83 47686 4.16e-07 197_[+3(1.19e-07)]_214_\ [+1(7.78e-08)]_47 50027 9.86e-06 237_[+3(3.75e-07)]_198_\ [+2(1.16e-06)]_32 47875 4.17e-02 485_[+2(7.50e-06)]_3 46302 6.83e-01 500 47701 1.76e-04 327_[+2(1.07e-05)]_84_\ [+3(1.18e-06)]_56 50575 1.40e-12 192_[+3(3.33e-10)]_118_\ [+2(5.01e-06)]_22_[+1(1.24e-08)]_114 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************