******************************************************************************** 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/293/293.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 37918 1.0000 500 48114 1.0000 500 39635 1.0000 500 49580 1.0000 500 49589 1.0000 500 41210 1.0000 500 34196 1.0000 500 11273 1.0000 500 46231 1.0000 500 12898 1.0000 500 42676 1.0000 500 32260 1.0000 500 45087 1.0000 500 48871 1.0000 500 44467 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/293/293.seqs.fa -oc motifs/293 -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 0.283 C 0.232 G 0.223 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.283 C 0.232 G 0.223 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 15 llr = 140 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::1151::::: pos.-specific C 1111953:::7: probability G :337::15:115 matrix T 9761::55a935 bits 2.2 1.9 * 1.7 * * 1.5 * * ** Relative 1.3 * * ** Entropy 1.1 * * *** * (13.5 bits) 0.9 ** *** ***** 0.6 ****** ***** 0.4 ****** ***** 0.2 ************ 0.0 ------------ Multilevel TTTGCATTTTCT consensus GG CCG TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 34196 332 9.09e-07 TTCCACAATT TTTGCACTTTCT CTTTTCAATA 41210 267 9.09e-07 GACTAGTACA TTTGCACTTTCT ATCGGTTACT 37918 348 1.32e-06 ATTTCAAACG TTGGCATGTTCT CTCGATACCG 44467 76 5.50e-06 AGATATGTCT TGGGCCCGTTCG AGAGTCTAAC 48114 364 1.06e-05 AATGAAATCG TTTGCCTGTTGG AAAGCGAGCG 49589 5 1.26e-05 GTCG TTTCCCTGTTCT TATCATTAGA 46231 287 1.59e-05 TCTAAAATAG TTTGCATGTGCT ATGCCCCAAC 11273 170 1.95e-05 CAGGAGCGTC TCGGCCTTTTCG ATTAGTCCTT 42676 478 2.63e-05 TCAGCCCAAG TTGGCAATTTTG TCTTGCCTGT 12898 253 2.63e-05 GGGTTACCTG TGCGCCTTTTTG GCGAACGTAC 32260 385 3.17e-05 CCAGACTCCC TTTTCCATTTCG ATCTTCAGGA 49580 31 4.01e-05 AGAATTTGAC CTTGCCTGTTTT GATTCCGCCA 48871 211 5.75e-05 ATTGGAACCG TGTGAACGTTCT CGCAAATCGA 45087 35 8.81e-05 ACAAATGGTA TTTACAGTTTCG TAAACCAACT 39635 218 1.48e-04 CGTATCAATC TGCTCACTTTTT CTCAGTCAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34196 9.1e-07 331_[+1]_157 41210 9.1e-07 266_[+1]_222 37918 1.3e-06 347_[+1]_141 44467 5.5e-06 75_[+1]_413 48114 1.1e-05 363_[+1]_125 49589 1.3e-05 4_[+1]_484 46231 1.6e-05 286_[+1]_202 11273 2e-05 169_[+1]_319 42676 2.6e-05 477_[+1]_11 12898 2.6e-05 252_[+1]_236 32260 3.2e-05 384_[+1]_104 49580 4e-05 30_[+1]_458 48871 5.7e-05 210_[+1]_278 45087 8.8e-05 34_[+1]_454 39635 0.00015 217_[+1]_271 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=15 34196 ( 332) TTTGCACTTTCT 1 41210 ( 267) TTTGCACTTTCT 1 37918 ( 348) TTGGCATGTTCT 1 44467 ( 76) TGGGCCCGTTCG 1 48114 ( 364) TTTGCCTGTTGG 1 49589 ( 5) TTTCCCTGTTCT 1 46231 ( 287) TTTGCATGTGCT 1 11273 ( 170) TCGGCCTTTTCG 1 42676 ( 478) TTGGCAATTTTG 1 12898 ( 253) TGCGCCTTTTTG 1 32260 ( 385) TTTTCCATTTCG 1 49580 ( 31) CTTGCCTGTTTT 1 48871 ( 211) TGTGAACGTTCT 1 45087 ( 35) TTTACAGTTTCG 1 39635 ( 218) TGCTCACTTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7335 bayes= 9.60607 E= 1.4e+001 -1055 -180 -1055 183 -1055 -180 26 134 -1055 -80 26 119 -208 -180 172 -98 -208 201 -1055 -1055 92 101 -1055 -1055 -108 52 -174 83 -1055 -1055 106 102 -1055 -1055 -1055 193 -1055 -1055 -174 183 -1055 152 -174 2 -1055 -1055 106 102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.4e+001 0.000000 0.066667 0.000000 0.933333 0.000000 0.066667 0.266667 0.666667 0.000000 0.133333 0.266667 0.600000 0.066667 0.066667 0.733333 0.133333 0.066667 0.933333 0.000000 0.000000 0.533333 0.466667 0.000000 0.000000 0.133333 0.333333 0.066667 0.466667 0.000000 0.000000 0.466667 0.533333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.066667 0.933333 0.000000 0.666667 0.066667 0.266667 0.000000 0.000000 0.466667 0.533333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[TG][TG]GC[AC][TC][TG]TT[CT][TG] -------------------------------------------------------------------------------- Time 2.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 4 llr = 78 E-value = 3.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::33::3::::::3: pos.-specific C 3::a::833:::5385:a:8 probability G :a::a::33aa3:5::a:83 matrix T 8:a::a333::55335:::: bits 2.2 * ** ** ** 1.9 ***** ** ** 1.7 ***** ** ** 1.5 ***** ** ** Relative 1.3 ****** ** * **** Entropy 1.1 ******* ** * ****** (28.2 bits) 0.9 ******* ** * ****** 0.6 ******* ** ******** 0.4 ******* *********** 0.2 ******* *********** 0.0 -------------------- Multilevel TGTCGTCAAGGTCGCCGCGC consensus C TCC ATCTT AG sequence GG G T TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 49580 434 9.83e-13 TTCGCATTCC TGTCGTCGCGGTCGCCGCGC TTTCCTTACG 49589 466 1.21e-09 TCCATCCCAG TGTCGTCTAGGTTGTTGCGG AAGAAGTTCA 48871 8 1.76e-09 CAGAAAA TGTCGTTATGGGTTCTGCGC ATCGCCGTGG 41210 1 2.81e-09 . CGTCGTCCGGGACCCCGCAC ACCCCGTACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49580 9.8e-13 433_[+2]_47 49589 1.2e-09 465_[+2]_15 48871 1.8e-09 7_[+2]_473 41210 2.8e-09 [+2]_480 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=4 49580 ( 434) TGTCGTCGCGGTCGCCGCGC 1 49589 ( 466) TGTCGTCTAGGTTGTTGCGG 1 48871 ( 8) TGTCGTTATGGGTTCTGCGC 1 41210 ( 1) CGTCGTCCGGGACCCCGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7215 bayes= 10.816 E= 3.3e+002 -865 11 -865 151 -865 -865 216 -865 -865 -865 -865 193 -865 211 -865 -865 -865 -865 216 -865 -865 -865 -865 193 -865 169 -865 -7 -18 11 16 -7 -18 11 16 -7 -865 -865 216 -865 -865 -865 216 -865 -18 -865 16 93 -865 111 -865 93 -865 11 116 -7 -865 169 -865 -7 -865 111 -865 93 -865 -865 216 -865 -865 211 -865 -865 -18 -865 175 -865 -865 169 16 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 3.3e+002 0.000000 0.250000 0.000000 0.750000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.500000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]GTCGT[CT][ACGT][ACGT]GG[TAG][CT][GCT][CT][CT]GC[GA][CG] -------------------------------------------------------------------------------- Time 4.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 7 llr = 95 E-value = 5.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 61:::3319::71:3a pos.-specific C 49:1:11411:36::: probability G ::a:a141:3a:3a7: matrix T :::9:413:6:::::: bits 2.2 * * * * 1.9 * * * * 1.7 * * * * * 1.5 ** * * * * Relative 1.3 **** * * *** Entropy 1.1 **** * ** *** (19.6 bits) 0.9 ***** * ** *** 0.6 ***** ******** 0.4 ***** ******** 0.2 **************** 0.0 ---------------- Multilevel ACGTGTGCATGACGGA consensus C AAT G CG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44467 143 3.42e-08 ATATGGGAAC CCGTGTGCAGGCGGGA AATGACTACT 49580 346 1.28e-07 CTCTTTCGGG ACGCGTTCATGACGGA CTCGTGTCAC 45087 256 1.71e-07 GTCGTTCGTG ACGTGTAAACGACGGA GGCCCTGTTG 48871 32 2.06e-07 CTGCGCATCG CCGTGGCCATGACGAA AACCGTCGAA 32260 128 2.81e-07 TTCGCATTCC ACGTGCGGATGCGGGA CAGACTGTTT 11273 418 6.15e-07 CTAGCAACAA CCGTGAGTCTGAAGGA GACGGGAGGA 48114 426 1.31e-06 CCTCTTCATC AAGTGAATAGGACGAA TGAAAGCAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44467 3.4e-08 142_[+3]_342 49580 1.3e-07 345_[+3]_139 45087 1.7e-07 255_[+3]_229 48871 2.1e-07 31_[+3]_453 32260 2.8e-07 127_[+3]_357 11273 6.2e-07 417_[+3]_67 48114 1.3e-06 425_[+3]_59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=7 44467 ( 143) CCGTGTGCAGGCGGGA 1 49580 ( 346) ACGCGTTCATGACGGA 1 45087 ( 256) ACGTGTAAACGACGGA 1 48871 ( 32) CCGTGGCCATGACGAA 1 32260 ( 128) ACGTGCGGATGCGGGA 1 11273 ( 418) CCGTGAGTCTGAAGGA 1 48114 ( 426) AAGTGAATAGGACGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7275 bayes= 9.86371 E= 5.8e+002 102 89 -945 -945 -98 189 -945 -945 -945 -945 216 -945 -945 -70 -945 171 -945 -945 216 -945 2 -70 -64 71 2 -70 94 -88 -98 89 -64 12 160 -70 -945 -945 -945 -70 36 112 -945 -945 216 -945 134 30 -945 -945 -98 130 36 -945 -945 -945 216 -945 2 -945 168 -945 182 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 5.8e+002 0.571429 0.428571 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.285714 0.142857 0.142857 0.428571 0.285714 0.142857 0.428571 0.142857 0.142857 0.428571 0.142857 0.285714 0.857143 0.142857 0.000000 0.000000 0.000000 0.142857 0.285714 0.571429 0.000000 0.000000 1.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.142857 0.571429 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC]CGTG[TA][GA][CT]A[TG]G[AC][CG]G[GA]A -------------------------------------------------------------------------------- Time 5.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37918 1.90e-02 347_[+1(1.32e-06)]_141 48114 1.92e-04 363_[+1(1.06e-05)]_50_\ [+3(1.31e-06)]_59 39635 3.62e-01 500 49580 3.71e-13 30_[+1(4.01e-05)]_303_\ [+3(1.28e-07)]_72_[+2(9.83e-13)]_47 49589 6.53e-07 4_[+1(1.26e-05)]_449_[+2(1.21e-09)]_\ 15 41210 1.07e-07 [+2(2.81e-09)]_246_[+1(9.09e-07)]_\ 11_[+1(4.29e-05)]_199 34196 1.36e-03 331_[+1(9.09e-07)]_157 11273 1.38e-04 169_[+1(1.95e-05)]_236_\ [+3(6.15e-07)]_67 46231 3.06e-02 286_[+1(1.59e-05)]_202 12898 2.57e-02 252_[+1(2.63e-05)]_236 42676 1.60e-01 477_[+1(2.63e-05)]_11 32260 5.68e-05 127_[+3(2.81e-07)]_241_\ [+1(3.17e-05)]_104 45087 7.48e-05 34_[+1(8.81e-05)]_209_\ [+3(1.71e-07)]_229 48871 9.08e-10 7_[+2(1.76e-09)]_4_[+3(2.06e-07)]_\ 163_[+1(5.75e-05)]_278 44467 7.17e-06 75_[+1(5.50e-06)]_55_[+3(3.42e-08)]_\ 342 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************