******************************************************************************** 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/310/310.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10824 1.0000 500 11717 1.0000 500 21184 1.0000 500 261041 1.0000 500 264926 1.0000 500 4199 1.0000 500 4920 1.0000 500 5043 1.0000 500 5589 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/310/310.seqs.fa -oc motifs/310 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.240 G 0.239 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.240 G 0.239 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 9 llr = 99 E-value = 4.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :9867:86:292 pos.-specific C a1:4:a2:7::8 probability G ::2::::::8:: matrix T ::::3::43:1: bits 2.1 * * 1.9 * * 1.7 * * 1.4 ** * * Relative 1.2 *** ** *** Entropy 1.0 ************ (15.9 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAAAACAACGAC consensus GCT CTTA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 4199 423 7.09e-08 AGGCTCCCGC CAAAACAACGAC GCCAAGGCTT 5043 486 1.35e-07 AAAAAGTTAG CAACACAACGAC GAC 261041 243 1.55e-06 TGACATTAAC CAACACAACAAC ACAAACGACG 11717 281 3.62e-06 TTCCGGCGAG CCACACAACGAC CCTTCCAACT 21184 486 4.75e-06 GAGCAATCTC CAACTCATCAAC ATC 4920 437 6.97e-06 CCCGCGGCAG CAAATCCTTGAC GATCTACTTC 5589 276 1.06e-05 TTGCTGACAT CAGAACCTTGAC CTGGTTGGTT 10824 350 1.23e-05 GTTACCAGTT CAGAACATTGAA GGAACCAATG 264926 290 1.66e-05 CAAATTGAAT CAAATCAACGTA TGCCCTTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4199 7.1e-08 422_[+1]_66 5043 1.4e-07 485_[+1]_3 261041 1.6e-06 242_[+1]_246 11717 3.6e-06 280_[+1]_208 21184 4.7e-06 485_[+1]_3 4920 7e-06 436_[+1]_52 5589 1.1e-05 275_[+1]_213 10824 1.2e-05 349_[+1]_139 264926 1.7e-05 289_[+1]_199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=9 4199 ( 423) CAAAACAACGAC 1 5043 ( 486) CAACACAACGAC 1 261041 ( 243) CAACACAACAAC 1 11717 ( 281) CCACACAACGAC 1 21184 ( 486) CAACTCATCAAC 1 4920 ( 437) CAAATCCTTGAC 1 5589 ( 276) CAGAACCTTGAC 1 10824 ( 350) CAGAACATTGAA 1 264926 ( 290) CAAATCAACGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4401 bayes= 9.78005 E= 4.9e+000 -982 206 -982 -982 175 -111 -982 -982 156 -982 -10 -982 107 89 -982 -982 133 -982 -982 38 -982 206 -982 -982 156 -11 -982 -982 107 -982 -982 79 -982 147 -982 38 -25 -982 170 -982 175 -982 -982 -120 -25 169 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 4.9e+000 0.000000 1.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.555556 0.444444 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.000000 0.666667 0.000000 0.333333 0.222222 0.000000 0.777778 0.000000 0.888889 0.000000 0.000000 0.111111 0.222222 0.777778 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AG][AC][AT]C[AC][AT][CT][GA]A[CA] -------------------------------------------------------------------------------- Time 0.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 9 llr = 107 E-value = 1.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4:86241::::2:: pos.-specific C ::::2:1::211:2: probability G 36a:284:96171:a matrix T 7::2:::9128278: bits 2.1 * * 1.9 * * 1.7 * * * 1.4 * ** * Relative 1.2 ** * ** ** Entropy 1.0 **** * ** * ** (17.2 bits) 0.8 **** * ** ***** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TGGAAGATGGTGTTG consensus GA TCAG C TAC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 21184 141 2.78e-08 GCGGTGTGTG TGGTAGATGGTGTTG CTGATGATGT 261041 478 2.45e-07 GGTTCGTCGT TAGAAGATGGTTATG ACACAAAC 5589 29 3.40e-07 TCGCGAACAA GGGAAAGTGTTGTTG TGATTGTTGT 11717 227 1.05e-06 CGAAGATCGA TGGTCGGTGGTGGTG GCGGTCCGAT 4199 75 1.27e-06 GTGATTCAAC TAGAAACTGCTGTTG CTCAAGATAT 4920 265 2.31e-06 CCGACAAATG GGGACGGTTTTGTTG GATGGAACTT 5043 92 3.35e-06 TTAGGAGGAC GAGAGGGAGGTGATG GCTTGGATTT 264926 435 5.12e-06 ATATTTCTTG TAGAGGATGGCTTCG GCAAATGCAA 10824 220 6.97e-06 AATAATCAAG TGGAAGATGCGCTCG CCAGTGTTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21184 2.8e-08 140_[+2]_345 261041 2.5e-07 477_[+2]_8 5589 3.4e-07 28_[+2]_457 11717 1.1e-06 226_[+2]_259 4199 1.3e-06 74_[+2]_411 4920 2.3e-06 264_[+2]_221 5043 3.3e-06 91_[+2]_394 264926 5.1e-06 434_[+2]_51 10824 7e-06 219_[+2]_266 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=9 21184 ( 141) TGGTAGATGGTGTTG 1 261041 ( 478) TAGAAGATGGTTATG 1 5589 ( 29) GGGAAAGTGTTGTTG 1 11717 ( 227) TGGTCGGTGGTGGTG 1 4199 ( 75) TAGAAACTGCTGTTG 1 4920 ( 265) GGGACGGTTTTGTTG 1 5043 ( 92) GAGAGGGAGGTGATG 1 264926 ( 435) TAGAGGATGGCTTCG 1 10824 ( 220) TGGAAGATGCGCTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4374 bayes= 9.05641 E= 1.9e+001 -982 -982 48 138 75 -982 122 -982 -982 -982 206 -982 156 -982 -982 -21 107 -11 -10 -982 -25 -982 170 -982 75 -111 89 -982 -125 -982 -982 179 -982 -982 189 -120 -982 -11 122 -21 -982 -111 -110 160 -982 -111 148 -21 -25 -982 -110 138 -982 -11 -982 160 -982 -982 206 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.9e+001 0.000000 0.000000 0.333333 0.666667 0.444444 0.000000 0.555556 0.000000 0.000000 0.000000 1.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.555556 0.222222 0.222222 0.000000 0.222222 0.000000 0.777778 0.000000 0.444444 0.111111 0.444444 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.000000 0.888889 0.111111 0.000000 0.222222 0.555556 0.222222 0.000000 0.111111 0.111111 0.777778 0.000000 0.111111 0.666667 0.222222 0.222222 0.000000 0.111111 0.666667 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GA]G[AT][ACG][GA][AG]TG[GCT]T[GT][TA][TC]G -------------------------------------------------------------------------------- Time 1.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 9 llr = 94 E-value = 8.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 14:::::1:::: pos.-specific C :16::::2::49 probability G 6::91:a::32: matrix T 34419a:7a731 bits 2.1 ** * 1.9 ** * 1.7 * ** * 1.4 **** * * Relative 1.2 **** * * Entropy 1.0 ***** ** * (15.1 bits) 0.8 ******** * 0.6 ********** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GACGTTGTTTCC consensus TTT C GT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 11717 321 3.38e-07 AGCAAGATAG GTTGTTGTTTCC ACCTGTTGCT 10824 179 7.85e-07 CAAAGCTCAA GTTGTTGTTTTC TCCTCAACGT 264926 85 2.30e-06 AATGCTTAGT GATGTTGCTTCC ATTGGTAGCT 5043 35 5.53e-06 GTGTCAGTGC TTTGTTGTTGGC GAGCGAAAAA 5589 388 6.17e-06 GCTGTTGATG GCCGTTGTTGTC GGCGGTGAGG 21184 419 8.07e-06 CATCACTGGA TTCGTTGCTGTC TCTCACAAAC 4199 386 1.04e-05 TAATGCGGCC TACTTTGTTTCC CCGACGCCCG 261041 327 2.63e-05 TGGATTCCTT GACGTTGATTCT GTCTACGGCC 4920 151 3.55e-05 ATAACACTCG AACGGTGTTTGC GTCGTGCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11717 3.4e-07 320_[+3]_168 10824 7.8e-07 178_[+3]_310 264926 2.3e-06 84_[+3]_404 5043 5.5e-06 34_[+3]_454 5589 6.2e-06 387_[+3]_101 21184 8.1e-06 418_[+3]_70 4199 1e-05 385_[+3]_103 261041 2.6e-05 326_[+3]_162 4920 3.5e-05 150_[+3]_338 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=9 11717 ( 321) GTTGTTGTTTCC 1 10824 ( 179) GTTGTTGTTTTC 1 264926 ( 85) GATGTTGCTTCC 1 5043 ( 35) TTTGTTGTTGGC 1 5589 ( 388) GCCGTTGTTGTC 1 21184 ( 419) TTCGTTGCTGTC 1 4199 ( 386) TACTTTGTTTCC 1 261041 ( 327) GACGTTGATTCT 1 4920 ( 151) AACGGTGTTTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4401 bayes= 9.0653 E= 8.6e+001 -125 -982 122 38 75 -111 -982 79 -982 121 -982 79 -982 -982 189 -120 -982 -982 -110 179 -982 -982 -982 196 -982 -982 206 -982 -125 -11 -982 138 -982 -982 -982 196 -982 -982 48 138 -982 89 -10 38 -982 189 -982 -120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 8.6e+001 0.111111 0.000000 0.555556 0.333333 0.444444 0.111111 0.000000 0.444444 0.000000 0.555556 0.000000 0.444444 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.222222 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.444444 0.222222 0.333333 0.000000 0.888889 0.000000 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][AT][CT]GTTG[TC]T[TG][CTG]C -------------------------------------------------------------------------------- Time 2.68 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10824 1.51e-06 178_[+3(7.85e-07)]_29_\ [+2(6.97e-06)]_115_[+1(1.23e-05)]_139 11717 4.19e-08 144_[+3(3.43e-05)]_70_\ [+2(1.05e-06)]_39_[+1(3.62e-06)]_28_[+3(3.38e-07)]_168 21184 3.50e-08 140_[+2(2.78e-08)]_44_\ [+2(2.34e-05)]_204_[+3(8.07e-06)]_55_[+1(4.75e-06)]_3 261041 2.70e-07 242_[+1(1.55e-06)]_72_\ [+3(2.63e-05)]_139_[+2(2.45e-07)]_8 264926 3.91e-06 84_[+3(2.30e-06)]_193_\ [+1(1.66e-05)]_133_[+2(5.12e-06)]_51 4199 3.12e-08 74_[+2(1.27e-06)]_296_\ [+3(1.04e-05)]_25_[+1(7.09e-08)]_66 4920 1.01e-05 150_[+3(3.55e-05)]_102_\ [+2(2.31e-06)]_157_[+1(6.97e-06)]_52 5043 7.66e-08 34_[+3(5.53e-06)]_45_[+2(3.35e-06)]_\ 379_[+1(1.35e-07)]_3 5589 5.56e-07 28_[+2(3.40e-07)]_232_\ [+1(1.06e-05)]_100_[+3(6.17e-06)]_101 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************