******************************************************************************** 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/492/492.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10207 1.0000 500 11974 1.0000 500 1308 1.0000 500 1495 1.0000 500 23371 1.0000 500 25096 1.0000 500 2552 1.0000 500 262253 1.0000 500 264010 1.0000 500 32716 1.0000 500 6820 1.0000 500 7816 1.0000 500 8490 1.0000 500 8782 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/492/492.seqs.fa -oc motifs/492 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.239 G 0.236 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.239 G 0.236 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 132 E-value = 2.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 397:73:8815: pos.-specific C 7129:39:27:a probability G ::113:12:::: matrix T ::1::4:::25: bits 2.1 * 1.9 * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * *** * Entropy 1.0 ** ** *** * (14.7 bits) 0.8 ** ** ****** 0.6 ***** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAACATCAACAC consensus A GA G TT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 1495 30 3.44e-07 ACCACAACAA CAACAACAACTC ACTTGGCCAA 6820 394 4.47e-07 CGATACGCCC CAACGCCAACAC ATCAACTCTA 7816 25 6.19e-07 CTCTCTTCTT CAACGTCAACTC CTTTCTTCCT 8782 480 1.37e-06 TTCTACAAAT CAACACCAATAC ATCTACAAC 8490 184 5.89e-06 ACTGCATCAA CAACATGAACAC TGGAAGGGAG 23371 10 5.89e-06 TCACTTGCA CAGCAACAACTC CAAGCACATC 264010 12 6.67e-06 GGGACTTTGC AACCATCAACTC ACAGATTCAA 25096 222 1.89e-05 GCCCCTCAAT CAAGACCGACAC CATCATCAGA 10207 344 2.43e-05 TCACAGACAG AAACGTCGATAC ACAGGGTCAT 2552 483 2.58e-05 CGTCGGCCTT CCACACCACCAC GCAACG 1308 432 2.58e-05 GCCAGCAAAG AAACAACACTTC TCACCTTTTC 11974 350 2.58e-05 CATAGAGGAG CATCGTCGACAC ACGCATACAG 32716 466 5.16e-05 CTCTCATATC AACCAACAAATC CTTTTACCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1495 3.4e-07 29_[+1]_459 6820 4.5e-07 393_[+1]_95 7816 6.2e-07 24_[+1]_464 8782 1.4e-06 479_[+1]_9 8490 5.9e-06 183_[+1]_305 23371 5.9e-06 9_[+1]_479 264010 6.7e-06 11_[+1]_477 25096 1.9e-05 221_[+1]_267 10207 2.4e-05 343_[+1]_145 2552 2.6e-05 482_[+1]_6 1308 2.6e-05 431_[+1]_57 11974 2.6e-05 349_[+1]_139 32716 5.2e-05 465_[+1]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 1495 ( 30) CAACAACAACTC 1 6820 ( 394) CAACGCCAACAC 1 7816 ( 25) CAACGTCAACTC 1 8782 ( 480) CAACACCAATAC 1 8490 ( 184) CAACATGAACAC 1 23371 ( 10) CAGCAACAACTC 1 264010 ( 12) AACCATCAACTC 1 25096 ( 222) CAAGACCGACAC 1 10207 ( 344) AAACGTCGATAC 1 2552 ( 483) CCACACCACCAC 1 1308 ( 432) AAACAACACTTC 1 11974 ( 350) CATCGTCGACAC 1 32716 ( 466) AACCAACAAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 9.56922 E= 2.9e-001 26 154 -1035 -1035 185 -163 -1035 -1035 143 -63 -161 -180 -1035 195 -161 -1035 143 -1035 38 -1035 26 37 -1035 51 -1035 195 -161 -1035 158 -1035 -3 -1035 172 -63 -1035 -1035 -173 154 -1035 -22 107 -1035 -1035 78 -1035 207 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 2.9e-001 0.307692 0.692308 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 0.692308 0.153846 0.076923 0.076923 0.000000 0.923077 0.076923 0.000000 0.692308 0.000000 0.307692 0.000000 0.307692 0.307692 0.000000 0.384615 0.000000 0.923077 0.076923 0.000000 0.769231 0.000000 0.230769 0.000000 0.846154 0.153846 0.000000 0.000000 0.076923 0.692308 0.000000 0.230769 0.538462 0.000000 0.000000 0.461538 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]AAC[AG][TAC]C[AG]A[CT][AT]C -------------------------------------------------------------------------------- Time 1.80 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 13 llr = 143 E-value = 4.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::12:91:24::2 pos.-specific C 22::23::6:5::1: probability G 2429::a1:925748 matrix T 558185::311135: bits 2.1 * 1.9 * 1.7 * ** * 1.5 * ** * * Relative 1.3 ** ** * * Entropy 1.0 ** ** * * * (15.9 bits) 0.8 *** **** * * 0.6 **** **** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TTTGTTGACGCGGTG consensus CG C T AATG sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 25096 287 3.95e-08 AGGGGCTGTG TTTGTAGACGCAGTG AAGTGTACAT 262253 37 1.95e-07 TGTGGAGTAT TTGGTCGACGCGGTG GCGAATTCTT 7816 210 4.32e-07 GGATGGAAAC TCTGTAGATGCGGTG CGTCGACAAG 23371 199 1.20e-06 CACTCGCATT GTTGTTGATGCGGCG TTGACGAGGC 6820 88 1.63e-06 AGCATTGATG TTTGCCGATGAGGTG GTTGATTCAT 1308 91 2.88e-06 TAGCAATGCC CGTGCAGACGCGTGG AAGCTTCATT 8782 280 3.13e-06 GCGAAGCACG CGTGTCGACGTGTTG CAACCCAAGA 32716 311 3.43e-06 TGACCGACTG TGTTTTGACGAAGGG GGCTGGTTGT 11974 138 3.43e-06 TCGGTCAGTG TGTGTCGGCGAAGTG ATGGGTTTCC 10207 248 3.43e-06 TATCCTGGTC GTTGTTGACGGTGGG GCGGAGGCGT 2552 65 1.99e-05 GTTGACAAAA GTTGATGACGCATGA CTTGGACGAA 8490 377 2.67e-05 GTGAGCTCTT TGGGTTGATGGGTGA GGCCACCGTG 1495 311 2.99e-05 CTAATTACAC CCTGTTGAATCAGTG ACATAATTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25096 4e-08 286_[+2]_199 262253 2e-07 36_[+2]_449 7816 4.3e-07 209_[+2]_276 23371 1.2e-06 198_[+2]_287 6820 1.6e-06 87_[+2]_398 1308 2.9e-06 90_[+2]_395 8782 3.1e-06 279_[+2]_206 32716 3.4e-06 310_[+2]_175 11974 3.4e-06 137_[+2]_348 10207 3.4e-06 247_[+2]_238 2552 2e-05 64_[+2]_421 8490 2.7e-05 376_[+2]_109 1495 3e-05 310_[+2]_175 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=13 25096 ( 287) TTTGTAGACGCAGTG 1 262253 ( 37) TTGGTCGACGCGGTG 1 7816 ( 210) TCTGTAGATGCGGTG 1 23371 ( 199) GTTGTTGATGCGGCG 1 6820 ( 88) TTTGCCGATGAGGTG 1 1308 ( 91) CGTGCAGACGCGTGG 1 8782 ( 280) CGTGTCGACGTGTTG 1 32716 ( 311) TGTTTTGACGAAGGG 1 11974 ( 138) TGTGTCGGCGAAGTG 1 10207 ( 248) GTTGTTGACGGTGGG 1 2552 ( 65) GTTGATGACGCATGA 1 8490 ( 377) TGGGTTGATGGGTGA 1 1495 ( 311) CCTGTTGAATCAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6804 bayes= 9.56033 E= 4.7e-001 -1035 -5 -3 100 -1035 -63 71 78 -1035 -1035 -62 165 -1035 -1035 197 -180 -173 -63 -1035 151 -15 37 -1035 78 -1035 -1035 208 -1035 185 -1035 -161 -1035 -173 137 -1035 19 -1035 -1035 197 -180 -15 117 -62 -180 59 -1035 119 -180 -1035 -1035 155 19 -1035 -163 71 100 -74 -1035 184 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 13 E= 4.7e-001 0.000000 0.230769 0.230769 0.538462 0.000000 0.153846 0.384615 0.461538 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 0.923077 0.076923 0.076923 0.153846 0.000000 0.769231 0.230769 0.307692 0.000000 0.461538 0.000000 0.000000 1.000000 0.000000 0.923077 0.000000 0.076923 0.000000 0.076923 0.615385 0.000000 0.307692 0.000000 0.000000 0.923077 0.076923 0.230769 0.538462 0.153846 0.076923 0.384615 0.000000 0.538462 0.076923 0.000000 0.000000 0.692308 0.307692 0.000000 0.076923 0.384615 0.538462 0.153846 0.000000 0.846154 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TCG][TG]TGT[TCA]GA[CT]G[CA][GA][GT][TG]G -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 11 llr = 140 E-value = 2.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 25:13:::6:121:1115a pos.-specific C :1:12:151121:2::91: probability G 8:814::2:3:6:166:2: matrix T :5272a9436719733:3: bits 2.1 1.9 * * 1.7 * * * 1.5 * * ** * * * Relative 1.3 * * ** * * * Entropy 1.0 * * ** * * * (18.4 bits) 0.8 * * ** * ***** * 0.6 **** ** ********* * 0.4 **** ************ * 0.2 **** ************** 0.0 ------------------- Multilevel GAGTGTTCATTGTTGGCAA consensus T A TTG TT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 262253 239 2.84e-11 TTCATTCATA GTGTATTCATTGTTGGCAA GTTTGTTTGT 25096 175 1.43e-08 CAAACTTGCG GAGTATCTATTGTTGGCTA GATTAGATCG 8782 34 1.79e-07 ATGAGCACAC GAGGATTCAGCGTTTGCAA AAGTAACGTG 6820 130 3.41e-07 ACCCTTACCT GTGACTTTAGTGTCGGCGA GAGGAAGAAA 264010 97 4.83e-07 GGTACGTTGA GTGCCTTCTTTGTTGACTA TCTCTGTGTG 8490 142 7.33e-07 CAGGGTGAAG ACGTGTTCATTGTTTTCCA GTCATAATAT 1495 403 1.36e-06 TCACCTTGAA GATTGTTGTTTCTTTTCAA CTTCAAGTTT 23371 416 1.47e-06 TTCTTGAGAG GAGTTTTTTTAATGGGCAA TATTGTTAGA 10207 88 2.41e-06 TGTGCACAAG ATGTGTTCCTTTTTGGAAA CGCCAATGAA 32716 121 3.15e-06 CAGTACTTCT GATTGTTTAGCAATGGCGA AGGGCCCAGA 2552 267 3.36e-06 CACATTCACT GTGTTTTGACTGTCATCTA AAGACGAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262253 2.8e-11 238_[+3]_243 25096 1.4e-08 174_[+3]_307 8782 1.8e-07 33_[+3]_448 6820 3.4e-07 129_[+3]_352 264010 4.8e-07 96_[+3]_385 8490 7.3e-07 141_[+3]_340 1495 1.4e-06 402_[+3]_79 23371 1.5e-06 415_[+3]_66 10207 2.4e-06 87_[+3]_394 32716 3.2e-06 120_[+3]_361 2552 3.4e-06 266_[+3]_215 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=11 262253 ( 239) GTGTATTCATTGTTGGCAA 1 25096 ( 175) GAGTATCTATTGTTGGCTA 1 8782 ( 34) GAGGATTCAGCGTTTGCAA 1 6820 ( 130) GTGACTTTAGTGTCGGCGA 1 264010 ( 97) GTGCCTTCTTTGTTGACTA 1 8490 ( 142) ACGTGTTCATTGTTTTCCA 1 1495 ( 403) GATTGTTGTTTCTTTTCAA 1 23371 ( 416) GAGTTTTTTTAATGGGCAA 1 10207 ( 88) ATGTGTTCCTTTTTGGAAA 1 32716 ( 121) GATTGTTTAGCAATGGCGA 1 2552 ( 267) GTGTTTTGACTGTCATCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 6748 bayes= 8.97322 E= 2.3e+001 -49 -1010 179 -1010 83 -139 -1010 75 -1010 -1010 179 -57 -149 -139 -137 143 9 -39 62 -57 -1010 -1010 -1010 189 -1010 -139 -1010 175 -1010 93 -38 43 131 -139 -1010 2 -1010 -139 21 124 -149 -39 -1010 143 -49 -139 143 -156 -149 -1010 -1010 175 -1010 -39 -137 143 -149 -1010 143 2 -149 -1010 143 2 -149 193 -1010 -1010 83 -139 -38 2 196 -1010 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 11 E= 2.3e+001 0.181818 0.000000 0.818182 0.000000 0.454545 0.090909 0.000000 0.454545 0.000000 0.000000 0.818182 0.181818 0.090909 0.090909 0.090909 0.727273 0.272727 0.181818 0.363636 0.181818 0.000000 0.000000 0.000000 1.000000 0.000000 0.090909 0.000000 0.909091 0.000000 0.454545 0.181818 0.363636 0.636364 0.090909 0.000000 0.272727 0.000000 0.090909 0.272727 0.636364 0.090909 0.181818 0.000000 0.727273 0.181818 0.090909 0.636364 0.090909 0.090909 0.000000 0.000000 0.909091 0.000000 0.181818 0.090909 0.727273 0.090909 0.000000 0.636364 0.272727 0.090909 0.000000 0.636364 0.272727 0.090909 0.909091 0.000000 0.000000 0.454545 0.090909 0.181818 0.272727 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT]GT[GA]TT[CT][AT][TG]TGTT[GT][GT]C[AT]A -------------------------------------------------------------------------------- Time 4.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10207 3.96e-06 87_[+3(2.41e-06)]_141_\ [+2(3.43e-06)]_81_[+1(2.43e-05)]_145 11974 9.63e-04 137_[+2(3.43e-06)]_197_\ [+1(2.58e-05)]_139 1308 4.26e-04 90_[+2(2.88e-06)]_326_\ [+1(2.58e-05)]_57 1495 3.61e-07 9_[+1(2.16e-06)]_8_[+1(3.44e-07)]_\ 269_[+2(2.99e-05)]_77_[+3(1.36e-06)]_79 23371 2.77e-07 9_[+1(5.89e-06)]_177_[+2(1.20e-06)]_\ 35_[+2(7.19e-05)]_152_[+3(1.47e-06)]_66 25096 4.93e-10 174_[+3(1.43e-08)]_28_\ [+1(1.89e-05)]_53_[+2(3.95e-08)]_199 2552 2.65e-05 64_[+2(1.99e-05)]_187_\ [+3(3.36e-06)]_197_[+1(2.58e-05)]_6 262253 3.44e-10 36_[+2(1.95e-07)]_187_\ [+3(2.84e-11)]_243 264010 7.00e-05 11_[+1(6.67e-06)]_73_[+3(4.83e-07)]_\ 385 32716 9.77e-06 120_[+3(3.15e-06)]_171_\ [+2(3.43e-06)]_140_[+1(5.16e-05)]_23 6820 9.14e-09 87_[+2(1.63e-06)]_27_[+3(3.41e-07)]_\ 245_[+1(4.47e-07)]_95 7816 3.43e-07 24_[+1(6.19e-07)]_173_\ [+2(4.32e-07)]_30_[+1(2.58e-05)]_120_[+3(4.98e-05)]_95 8490 2.41e-06 141_[+3(7.33e-07)]_23_\ [+1(5.89e-06)]_181_[+2(2.67e-05)]_109 8782 2.56e-08 33_[+3(1.79e-07)]_227_\ [+2(3.13e-06)]_185_[+1(1.37e-06)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************