******************************************************************************** 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/169/169.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 25000 1.0000 500 47291 1.0000 500 22113 1.0000 500 39038 1.0000 500 43359 1.0000 500 43922 1.0000 500 20547 1.0000 500 33111 1.0000 500 46625 1.0000 500 45492 1.0000 500 34098 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/169/169.seqs.fa -oc motifs/169 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.243 G 0.244 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.243 G 0.244 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 13 sites = 11 llr = 114 E-value = 7.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :12:4:2::2168 pos.-specific C :::4:9::186:: probability G 29:541:7::24: matrix T 8:823:839:1:2 bits 2.0 1.8 1.6 * * 1.4 * * ** Relative 1.2 *** ***** * Entropy 1.0 *** ***** ** (14.9 bits) 0.8 *** ***** ** 0.6 **** ******** 0.4 ************* 0.2 ************* 0.0 ------------- Multilevel TGTGACTGTCCAA consensus CG T G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 22113 141 7.43e-08 ACCGTAACCG TGTCACTGTCCAA CGATCGGTAT 47291 144 8.80e-08 GTGAACATGT TGTGGCTGTCCGA TATCCGGATA 25000 223 1.17e-07 GTCCTCTTGA TGTGACTGTCCGA TATTTTCCAG 46625 325 3.13e-06 GGAATCAAGG TGAGACTGTCGAA CACAACTGGC 39038 312 7.21e-06 ACCCGTGAAT TGTTTCTTTCGAA TGGGACTCGC 43359 209 7.64e-06 GAAGCTCTTG TGTGACTGTACGT CCAACATCGG 43922 116 9.99e-06 ATGGATGTAT GGATGCTGTCCAA AGGATACAGG 45492 30 1.36e-05 TGCGATCGCC GGTGTCATTCCAA TCCGTCGTCT 34098 349 2.73e-05 TACTTGGTAG TATCGCATTCCAA ACATATCTCA 33111 383 5.54e-05 AACTTTTCGC TGTCGCTGCAAAA AGACGTCCGC 20547 163 9.10e-05 TGTGTGTGTG TGTCTGTGTCTGT TGTCTTCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22113 7.4e-08 140_[+1]_347 47291 8.8e-08 143_[+1]_344 25000 1.2e-07 222_[+1]_265 46625 3.1e-06 324_[+1]_163 39038 7.2e-06 311_[+1]_176 43359 7.6e-06 208_[+1]_279 43922 1e-05 115_[+1]_372 45492 1.4e-05 29_[+1]_458 34098 2.7e-05 348_[+1]_139 33111 5.5e-05 382_[+1]_105 20547 9.1e-05 162_[+1]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=11 22113 ( 141) TGTCACTGTCCAA 1 47291 ( 144) TGTGGCTGTCCGA 1 25000 ( 223) TGTGACTGTCCGA 1 46625 ( 325) TGAGACTGTCGAA 1 39038 ( 312) TGTTTCTTTCGAA 1 43359 ( 209) TGTGACTGTACGT 1 43922 ( 116) GGATGCTGTCCAA 1 45492 ( 30) GGTGTCATTCCAA 1 34098 ( 349) TATCGCATTCCAA 1 33111 ( 383) TGTCGCTGCAAAA 1 20547 ( 163) TGTCTGTGTCTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 5368 bayes= 8.92778 E= 7.0e+001 -1010 -1010 -42 167 -150 -1010 190 -1010 -50 -1010 -1010 167 -1010 58 90 -50 50 -1010 58 9 -1010 191 -142 -1010 -50 -1010 -1010 167 -1010 -1010 158 9 -1010 -141 -1010 183 -50 175 -1010 -1010 -150 139 -42 -149 131 -1010 58 -1010 167 -1010 -1010 -50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 11 E= 7.0e+001 0.000000 0.000000 0.181818 0.818182 0.090909 0.000000 0.909091 0.000000 0.181818 0.000000 0.000000 0.818182 0.000000 0.363636 0.454545 0.181818 0.363636 0.000000 0.363636 0.272727 0.000000 0.909091 0.090909 0.000000 0.181818 0.000000 0.000000 0.818182 0.000000 0.000000 0.727273 0.272727 0.000000 0.090909 0.000000 0.909091 0.181818 0.818182 0.000000 0.000000 0.090909 0.636364 0.181818 0.090909 0.636364 0.000000 0.363636 0.000000 0.818182 0.000000 0.000000 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGT[GC][AGT]CT[GT]TCC[AG]A -------------------------------------------------------------------------------- Time 1.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 4 llr = 77 E-value = 4.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::53::8:385:a: pos.-specific C a:3a3:853aa::::3::a probability G :35:8a::5::3:83:a:: matrix T :83:::3:::::a::3::: bits 2.0 * * * ** * *** 1.8 * * * ** * *** 1.6 * * * ** * *** 1.4 * * * ** * *** Relative 1.2 ** **** ****** *** Entropy 1.0 ** ***** ****** *** (27.9 bits) 0.8 ** ***** ****** *** 0.6 *************** *** 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel CTGCGGCAGCCATGAAGAC consensus GC C TCA G AGC sequence T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 47291 235 1.05e-10 CAAAATGCTT CTCCGGCCGCCATGACGAC TGACCATGAT 20547 68 2.44e-10 TGTTGTTCTA CTGCGGCAGCCATGGTGAC GATGGACGCA 43359 339 3.06e-09 AGCATAAAGT CTTCCGCAACCATAAAGAC TTTCCTTCTG 33111 25 3.35e-09 GGCGATGCGG CGGCGGTCCCCGTGAAGAC GGCCCAATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47291 1e-10 234_[+2]_247 20547 2.4e-10 67_[+2]_414 43359 3.1e-09 338_[+2]_143 33111 3.4e-09 24_[+2]_457 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=4 47291 ( 235) CTCCGGCCGCCATGACGAC 1 20547 ( 68) CTGCGGCAGCCATGGTGAC 1 43359 ( 339) CTTCCGCAACCATAAAGAC 1 33111 ( 25) CGGCGGTCCCCGTGAAGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 5302 bayes= 10.3712 E= 4.9e+002 -865 204 -865 -865 -865 -865 4 155 -865 4 103 -4 -865 204 -865 -865 -865 4 162 -865 -865 -865 203 -865 -865 163 -865 -4 96 104 -865 -865 -4 4 103 -865 -865 204 -865 -865 -865 204 -865 -865 154 -865 4 -865 -865 -865 -865 196 -4 -865 162 -865 154 -865 4 -865 96 4 -865 -4 -865 -865 203 -865 196 -865 -865 -865 -865 204 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 4 E= 4.9e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TG][GCT]C[GC]G[CT][AC][GAC]CC[AG]T[GA][AG][ACT]GAC -------------------------------------------------------------------------------- Time 2.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 9 llr = 101 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 34:::6:::::7 pos.-specific C 3:::::6::11: probability G 32::a:::8:93 matrix T :3aa:44a29:: bits 2.0 *** * 1.8 *** * 1.6 *** * * 1.4 *** * ** Relative 1.2 *** **** Entropy 1.0 ********** (16.1 bits) 0.8 ********** 0.6 ********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AATTGACTGTGA consensus CT TT T G sequence GG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46625 428 1.91e-07 TCATATGACA AATTGACTGTGA GTGAGCTACG 45492 452 7.09e-07 GTTCACAGGC AATTGATTGTGA AAAGAAGACC 47291 126 1.10e-06 TTTTTTGTCA GTTTGTCTGTGA ACATGTTGTG 39038 355 1.67e-06 CGTCCTTGAC CGTTGACTGTGA GCGACTGCGG 25000 297 3.29e-06 ATAGCAAGGC GTTTGTCTGTGG GTCAGTATTT 43359 291 5.46e-06 TTGACGACGA CATTGTTTTTGA TGGAACCTGC 43922 262 1.18e-05 ACACGTTGGT ATTTGTTTTTGG CTGGCGTCCT 22113 350 1.18e-05 TACATTGGTA GGTTGACTGCGA CAACCAATCC 33111 168 1.41e-05 GGTAGAACGG CATTGATTGTCG TTGCAACGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46625 1.9e-07 427_[+3]_61 45492 7.1e-07 451_[+3]_37 47291 1.1e-06 125_[+3]_363 39038 1.7e-06 354_[+3]_134 25000 3.3e-06 296_[+3]_192 43359 5.5e-06 290_[+3]_198 43922 1.2e-05 261_[+3]_227 22113 1.2e-05 349_[+3]_139 33111 1.4e-05 167_[+3]_321 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=9 46625 ( 428) AATTGACTGTGA 1 45492 ( 452) AATTGATTGTGA 1 47291 ( 126) GTTTGTCTGTGA 1 39038 ( 355) CGTTGACTGTGA 1 25000 ( 297) GTTTGTCTGTGG 1 43359 ( 291) CATTGTTTTTGA 1 43922 ( 262) ATTTGTTTTTGG 1 22113 ( 350) GGTTGACTGCGA 1 33111 ( 168) CATTGATTGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.3553 E= 1.3e+002 37 46 45 -982 79 -982 -13 38 -982 -982 -982 196 -982 -982 -982 196 -982 -982 203 -982 111 -982 -982 79 -982 119 -982 79 -982 -982 -982 196 -982 -982 167 -21 -982 -112 -982 179 -982 -112 187 -982 137 -982 45 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 1.3e+002 0.333333 0.333333 0.333333 0.000000 0.444444 0.000000 0.222222 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.000000 0.555556 0.000000 0.444444 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.888889 0.000000 0.666667 0.000000 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [ACG][ATG]TTG[AT][CT]T[GT]TG[AG] -------------------------------------------------------------------------------- Time 3.35 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25000 8.54e-06 222_[+1(1.17e-07)]_61_\ [+3(3.29e-06)]_192 47291 7.30e-13 125_[+3(1.10e-06)]_6_[+1(8.80e-08)]_\ 78_[+2(1.05e-10)]_247 22113 5.04e-06 140_[+1(7.43e-08)]_196_\ [+3(1.18e-05)]_139 39038 2.35e-04 311_[+1(7.21e-06)]_30_\ [+3(1.67e-06)]_134 43359 4.94e-09 208_[+1(7.64e-06)]_69_\ [+3(5.46e-06)]_36_[+2(3.06e-09)]_143 43922 4.49e-04 115_[+1(9.99e-06)]_133_\ [+3(1.18e-05)]_227 20547 2.81e-07 67_[+2(2.44e-10)]_70_[+1(7.84e-05)]_\ 331 33111 7.81e-08 24_[+2(3.35e-09)]_124_\ [+3(1.41e-05)]_203_[+1(5.54e-05)]_105 46625 3.34e-06 324_[+1(3.13e-06)]_90_\ [+3(1.91e-07)]_61 45492 8.46e-05 29_[+1(1.36e-05)]_409_\ [+3(7.09e-07)]_37 34098 6.54e-02 348_[+1(2.73e-05)]_139 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************