******************************************************************************** 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/74/74.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 28730 1.0000 500 47585 1.0000 500 37877 1.0000 500 5668 1.0000 500 38642 1.0000 500 48529 1.0000 500 39079 1.0000 500 48668 1.0000 500 9927 1.0000 500 49040 1.0000 500 7562 1.0000 500 4821 1.0000 500 33480 1.0000 500 38757 1.0000 500 48961 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/74/74.seqs.fa -oc motifs/74 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.275 C 0.233 G 0.216 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.233 G 0.216 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 134 E-value = 3.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:28:6:::95: pos.-specific C 4:2:a:::31:: probability G ::5:::a:5:32 matrix T 5a12:4:a2:28 bits 2.2 * * 2.0 * * 1.8 * * ** 1.5 * * ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** * * (14.9 bits) 0.9 * ***** * * 0.7 * ******* * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTGACAGTGAAT consensus C C T C GG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 28730 422 1.44e-07 GACCTCAATA TTGACAGTGAAT TTCGTTTGGG 47585 25 7.91e-07 GTAAACGATT CTGACTGTGAGT TTTGTATCGG 7562 190 1.40e-06 ATCTGCGTAT TTGACAGTTAAT TTTAAAGAAT 48668 32 2.45e-06 CTTTACATGG TTCACAGTCAAT CGCTGCCACG 39079 180 2.45e-06 TTGCTTTGTC TTCACAGTCAAT ATGCGACTGA 5668 131 2.45e-06 TATCTACACT CTGACAGTCAAG TCGAACCGGA 49040 401 3.24e-06 GGATTTGCTC ATGACTGTGAAT GACAGATAGT 38757 432 5.49e-06 TCAAAAGTTG CTGACTGTCAAG GTGAGGTGAT 48529 394 1.42e-05 CAGTGATTTA CTAACAGTTAGT GATAGCTAAT 33480 370 2.33e-05 ATCAGATTTT TTTACAGTGATT GCGCCGAGGA 37877 400 2.33e-05 CAACAAAACG CTGTCTGTGATT TTCAGAGATG 4821 97 6.12e-05 TTGGACGACC ATATCTGTGAGT TCTTTTCAGG 48961 444 7.28e-05 GTATTGCGGT TTCACAGTTCGG TAAGAACGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28730 1.4e-07 421_[+1]_67 47585 7.9e-07 24_[+1]_464 7562 1.4e-06 189_[+1]_299 48668 2.4e-06 31_[+1]_457 39079 2.4e-06 179_[+1]_309 5668 2.4e-06 130_[+1]_358 49040 3.2e-06 400_[+1]_88 38757 5.5e-06 431_[+1]_57 48529 1.4e-05 393_[+1]_95 33480 2.3e-05 369_[+1]_119 37877 2.3e-05 399_[+1]_89 4821 6.1e-05 96_[+1]_392 48961 7.3e-05 443_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 28730 ( 422) TTGACAGTGAAT 1 47585 ( 25) CTGACTGTGAGT 1 7562 ( 190) TTGACAGTTAAT 1 48668 ( 32) TTCACAGTCAAT 1 39079 ( 180) TTCACAGTCAAT 1 5668 ( 131) CTGACAGTCAAG 1 49040 ( 401) ATGACTGTGAAT 1 38757 ( 432) CTGACTGTCAAG 1 48529 ( 394) CTAACAGTTAGT 1 33480 ( 370) TTTACAGTGATT 1 37877 ( 400) CTGTCTGTGATT 1 4821 ( 97) ATATCTGTGAGT 1 48961 ( 444) TTCACAGTTCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7335 bayes= 9.66888 E= 3.4e-001 -84 72 -1035 74 -1035 -1035 -1035 186 -84 -1 132 -184 162 -1035 -1035 -84 -1035 210 -1035 -1035 116 -1035 -1035 48 -1035 -1035 221 -1035 -1035 -1035 -1035 186 -1035 40 109 -26 175 -160 -1035 -1035 97 -1035 51 -84 -1035 -1035 9 148 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 3.4e-001 0.153846 0.384615 0.000000 0.461538 0.000000 0.000000 0.000000 1.000000 0.153846 0.230769 0.538462 0.076923 0.846154 0.000000 0.000000 0.153846 0.000000 1.000000 0.000000 0.000000 0.615385 0.000000 0.000000 0.384615 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.307692 0.461538 0.230769 0.923077 0.076923 0.000000 0.000000 0.538462 0.000000 0.307692 0.153846 0.000000 0.000000 0.230769 0.769231 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[GC]AC[AT]GT[GCT]A[AG][TG] -------------------------------------------------------------------------------- Time 2.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 3 llr = 54 E-value = 9.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::3:::::::: pos.-specific C a7:73::a3:7::a: probability G :3a3:a7:7a:a::a matrix T ::::7:::::3:a:: bits 2.2 * * * * * * ** 2.0 * * * * * * ** 1.8 * * * * * **** 1.5 * * * * * **** Relative 1.3 **** * *** **** Entropy 1.1 *************** (26.2 bits) 0.9 *************** 0.7 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCGCTGGCGGCGTCG consensus G GC A C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 4821 447 1.28e-09 GCTTGGCGGA CCGCTGGCCGCGTCG CGACTCGGAC 39079 105 1.93e-09 GTCGAGACTT CCGCTGGCGGTGTCG CATCATAAGC 7562 435 1.29e-08 AAAACCTGCT CGGGCGACGGCGTCG AACGTAGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4821 1.3e-09 446_[+2]_39 39079 1.9e-09 104_[+2]_381 7562 1.3e-08 434_[+2]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=3 4821 ( 447) CCGCTGGCCGCGTCG 1 39079 ( 105) CCGCTGGCGGTGTCG 1 7562 ( 435) CGGGCGACGGCGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7290 bayes= 11.6938 E= 9.5e+002 -823 210 -823 -823 -823 151 62 -823 -823 -823 221 -823 -823 151 62 -823 -823 51 -823 127 -823 -823 221 -823 28 -823 162 -823 -823 210 -823 -823 -823 51 162 -823 -823 -823 221 -823 -823 151 -823 27 -823 -823 221 -823 -823 -823 -823 186 -823 210 -823 -823 -823 -823 221 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3 E= 9.5e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[CG]G[CG][TC]G[GA]C[GC]G[CT]GTCG -------------------------------------------------------------------------------- Time 4.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 13 llr = 125 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 21:6:2:1:8:9 pos.-specific C ::8254::a:9: probability G 2:21122::2:1 matrix T 69:25389::1: bits 2.2 * 2.0 * 1.8 * * 1.5 ** ** ** Relative 1.3 ** ** ** Entropy 1.1 ** ****** (13.8 bits) 0.9 ** ****** 0.7 *** * ****** 0.4 ***** ****** 0.2 ************ 0.0 ------------ Multilevel TTCACCTTCACA consensus G TTG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48529 210 8.35e-07 AAAATATCGT TTCATGTTCACA TCAGACCGAT 33480 158 1.16e-06 GGCAACAATG TTCATCGTCACA GTTTGTTTTC 5668 73 1.16e-06 TTCCGGCCGA GTCACTTTCACA GGCCTCCGAT 48961 81 1.84e-06 AAAGTGTCTT TTCCTCTTCACA ACGTGGAACC 4821 374 8.16e-06 GTGTGCGCAG TTCTCATTCACA TTTACGTGAA 47585 384 8.16e-06 TCTATCCTTC GTCCTTTTCACA TCACGTTTAC 28730 463 1.10e-05 TCTTTCGATA GTCACATTCGCA ACAGAGAGAA 49040 212 3.18e-05 AGCAAGAAAC ATCACCTACACA TCCGTGTATG 9927 242 3.18e-05 TAAAAATCAA ATCATTGTCGCA TGTACCGTAC 7562 285 4.49e-05 TTTTATCAAG TACGCCTTCACA TCTATACTTT 38757 362 6.14e-05 CTGCATCCAC TTGACGTTCACG CCGTCAGGAA 48668 110 6.14e-05 TGACCACTCT TTGAGTTTCGCA CGCTGAGGTG 37877 36 8.26e-05 TGTTGTACTA TTCTTCGTCATA CAAAGAGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48529 8.3e-07 209_[+3]_279 33480 1.2e-06 157_[+3]_331 5668 1.2e-06 72_[+3]_416 48961 1.8e-06 80_[+3]_408 4821 8.2e-06 373_[+3]_115 47585 8.2e-06 383_[+3]_105 28730 1.1e-05 462_[+3]_26 49040 3.2e-05 211_[+3]_277 9927 3.2e-05 241_[+3]_247 7562 4.5e-05 284_[+3]_204 38757 6.1e-05 361_[+3]_127 48668 6.1e-05 109_[+3]_379 37877 8.3e-05 35_[+3]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=13 48529 ( 210) TTCATGTTCACA 1 33480 ( 158) TTCATCGTCACA 1 5668 ( 73) GTCACTTTCACA 1 48961 ( 81) TTCCTCTTCACA 1 4821 ( 374) TTCTCATTCACA 1 47585 ( 384) GTCCTTTTCACA 1 28730 ( 463) GTCACATTCGCA 1 49040 ( 212) ATCACCTACACA 1 9927 ( 242) ATCATTGTCGCA 1 7562 ( 285) TACGCCTTCACA 1 38757 ( 362) TTGACGTTCACG 1 48668 ( 110) TTGAGTTTCGCA 1 37877 ( 36) TTCTTCGTCATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7335 bayes= 9.66888 E= 1.0e+003 -84 -1035 9 116 -184 -1035 -1035 174 -1035 186 -49 -1035 116 -60 -149 -84 -1035 99 -149 74 -84 72 -49 16 -1035 -1035 9 148 -184 -1035 -1035 174 -1035 210 -1035 -1035 148 -1035 9 -1035 -1035 198 -1035 -184 175 -1035 -149 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 1.0e+003 0.153846 0.000000 0.230769 0.615385 0.076923 0.000000 0.000000 0.923077 0.000000 0.846154 0.153846 0.000000 0.615385 0.153846 0.076923 0.153846 0.000000 0.461538 0.076923 0.461538 0.153846 0.384615 0.153846 0.307692 0.000000 0.000000 0.230769 0.769231 0.076923 0.000000 0.000000 0.923077 0.000000 1.000000 0.000000 0.000000 0.769231 0.000000 0.230769 0.000000 0.000000 0.923077 0.000000 0.076923 0.923077 0.000000 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG]TCA[CT][CT][TG]TC[AG]CA -------------------------------------------------------------------------------- Time 6.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28730 1.34e-05 421_[+1(1.44e-07)]_29_\ [+3(1.10e-05)]_26 47585 2.84e-05 24_[+1(7.91e-07)]_347_\ [+3(8.16e-06)]_105 37877 1.26e-02 35_[+3(8.26e-05)]_352_\ [+1(2.33e-05)]_89 5668 2.81e-05 72_[+3(1.16e-06)]_46_[+1(2.45e-06)]_\ 358 38642 9.89e-01 500 48529 1.72e-04 74_[+1(6.54e-05)]_123_\ [+3(8.35e-07)]_172_[+1(1.42e-05)]_95 39079 8.97e-08 104_[+2(1.93e-09)]_60_\ [+1(2.45e-06)]_108_[+1(4.80e-05)]_189 48668 1.68e-03 31_[+1(2.45e-06)]_66_[+3(6.14e-05)]_\ 379 9927 8.29e-02 241_[+3(3.18e-05)]_247 49040 1.60e-04 211_[+3(3.18e-05)]_177_\ [+1(3.24e-06)]_88 7562 2.70e-08 189_[+1(1.40e-06)]_83_\ [+3(4.49e-05)]_138_[+2(1.29e-08)]_51 4821 2.16e-08 96_[+1(6.12e-05)]_265_\ [+3(8.16e-06)]_61_[+2(1.28e-09)]_39 33480 4.22e-04 157_[+3(1.16e-06)]_200_\ [+1(2.33e-05)]_119 38757 3.14e-03 361_[+3(6.14e-05)]_58_\ [+1(5.49e-06)]_57 48961 4.05e-04 80_[+3(1.84e-06)]_160_\ [+3(2.14e-05)]_179_[+1(7.28e-05)]_45 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************