******************************************************************************** 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/416/416.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46928 1.0000 500 51183 1.0000 500 40017 1.0000 500 23658 1.0000 500 41423 1.0000 500 54986 1.0000 500 54987 1.0000 500 46929 1.0000 500 47937 1.0000 500 55031 1.0000 500 52498 1.0000 500 49272 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/416/416.seqs.fa -oc motifs/416 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.235 G 0.214 T 0.280 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.235 G 0.214 T 0.280 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 9 llr = 146 E-value = 2.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1:6:21:312416:::::14 pos.-specific C 14a:9:1:28119:9:4:774 probability G 84:318:81163:3:a:a:2: matrix T 1::1::823:11:11:6:3:1 bits 2.2 * * 2.0 * * * 1.8 * * * 1.6 * * * ** * Relative 1.3 * ** * * ** * Entropy 1.1 * * ** * * * ** ** (23.4 bits) 0.9 * * **** * * ****** 0.7 ******** * ********* 0.4 ******** ** ********* 0.2 ******** ************ 0.0 --------------------- Multilevel GCCACGTGACGACACGTGCCA consensus G G A TT AG G C TGC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46929 219 4.92e-11 GCGCGTGGTA GCCACGTTACGGCACGTGCCC TATTTTAACC 55031 347 1.85e-09 AAGCTTTGAA GCCGCATGTCAGCACGTGTCC ACGTCCTGCG 41423 136 3.17e-09 TGCTTCCGAT GGCGGGTGTGGACACGTGCCA ACCGACCAGG 49272 212 1.57e-08 CAAGATACTC TCCACGCGCCGCCACGCGCCA TACACCGAGA 54986 315 2.40e-08 AGAACCTAGT GGCACGTGACCGAGCGCGTGC AATCCACGCG 52498 211 2.60e-08 GAAAAAATGA GGCGCGTGTCTTCTCGTGCGA CATCGTGTGC 23658 321 3.05e-08 GAGTTTCCTT GACACGTGCCAACGTGTGTCC GTTCTAGCAT 54987 368 9.15e-08 CACACGATGT CGCACGAGAAGACACGCGCCT CATTTTTTCT 46928 348 1.19e-07 CACTATCAAC GCCTCATTGCGACGCGCGCAA AACCGGGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46929 4.9e-11 218_[+1]_261 55031 1.9e-09 346_[+1]_133 41423 3.2e-09 135_[+1]_344 49272 1.6e-08 211_[+1]_268 54986 2.4e-08 314_[+1]_165 52498 2.6e-08 210_[+1]_269 23658 3.1e-08 320_[+1]_159 54987 9.2e-08 367_[+1]_112 46928 1.2e-07 347_[+1]_132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=9 46929 ( 219) GCCACGTTACGGCACGTGCCC 1 55031 ( 347) GCCGCATGTCAGCACGTGTCC 1 41423 ( 136) GGCGGGTGTGGACACGTGCCA 1 49272 ( 212) TCCACGCGCCGCCACGCGCCA 1 54986 ( 315) GGCACGTGACCGAGCGCGTGC 1 52498 ( 211) GGCGCGTGTCTTCTCGTGCGA 1 23658 ( 321) GACACGTGCCAACGTGTGTCC 1 54987 ( 368) CGCACGAGAAGACACGCGCCT 1 46928 ( 348) GCCTCATTGCGACGCGCGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.7255 E= 2.2e-005 -982 -108 186 -133 -128 92 105 -982 -982 209 -982 -982 104 -982 64 -133 -982 192 -94 -982 -28 -982 186 -982 -128 -108 -982 147 -982 -982 186 -33 30 -8 -94 25 -128 172 -94 -982 -28 -108 138 -133 71 -108 64 -133 -128 192 -982 -982 104 -982 64 -133 -982 192 -982 -133 -982 -982 222 -982 -982 92 -982 99 -982 -982 222 -982 -982 150 -982 25 -128 150 5 -982 71 92 -982 -133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 2.2e-005 0.000000 0.111111 0.777778 0.111111 0.111111 0.444444 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.000000 0.333333 0.111111 0.000000 0.888889 0.111111 0.000000 0.222222 0.000000 0.777778 0.000000 0.111111 0.111111 0.000000 0.777778 0.000000 0.000000 0.777778 0.222222 0.333333 0.222222 0.111111 0.333333 0.111111 0.777778 0.111111 0.000000 0.222222 0.111111 0.555556 0.111111 0.444444 0.111111 0.333333 0.111111 0.111111 0.888889 0.000000 0.000000 0.555556 0.000000 0.333333 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.444444 0.000000 0.555556 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.111111 0.666667 0.222222 0.000000 0.444444 0.444444 0.000000 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[CG]C[AG]C[GA]T[GT][ATC]C[GA][AG]C[AG]CG[TC]G[CT][CG][AC] -------------------------------------------------------------------------------- Time 1.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 12 llr = 131 E-value = 1.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :938:328:2:4418 pos.-specific C 3:51311:31::5:: probability G 71::8:3:74a6:93 matrix T ::22:643:3::1:: bits 2.2 * 2.0 * 1.8 * * 1.6 * * * Relative 1.3 ** * * * * Entropy 1.1 ** * ** ** ** (15.8 bits) 0.9 ** ** ** ** ** 0.7 ** *** ** ***** 0.4 ****** ** ***** 0.2 *************** 0.0 --------------- Multilevel GACAGTTAGGGGCGA consensus C A CAGTCT AA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 46929 96 1.26e-07 CTGCTAACCT GACTGTGAGGGGAGA TCGTGCTAGA 49272 370 2.43e-07 GTGCCTCTCG GACAGTTTGAGGCGA TTTAGGCACA 55031 191 4.80e-07 AGATTTTAAA GAAAGAAACGGGCGA CTAACTCGTT 23658 45 6.26e-07 TGCTGGCTTT CACCGTTAGGGGCGA GCTGACGGAT 47937 144 1.02e-06 TAGCGAGATA GACAGTGTGAGAAGA TTGGCGAATT 46928 455 1.44e-06 TAGATGCCTT CAAAGATACTGGAGA TTGGAACAAT 52498 321 5.06e-06 TCAATGTGCT GGTAGTTAGTGACGA AAGAAAGAAC 41423 204 6.49e-06 AAGTCCGCGT GATTCTTACGGGCGA ACGTAGGCGA 54986 209 1.18e-05 AAGTTCCGGA GACACAATGGGAAGG AGTTCTATAT 40017 352 1.35e-05 CCGTCGACAG CACAGACAGCGGAGG ATTGCGAATT 51183 357 1.98e-05 TAAAGCCGTC CAAAGCGAGTGATGA ATGCGAAGCT 54987 132 3.43e-05 TGTACCAAAG GAAACTGACTGACAG TGAGTTCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46929 1.3e-07 95_[+2]_390 49272 2.4e-07 369_[+2]_116 55031 4.8e-07 190_[+2]_295 23658 6.3e-07 44_[+2]_441 47937 1e-06 143_[+2]_342 46928 1.4e-06 454_[+2]_31 52498 5.1e-06 320_[+2]_165 41423 6.5e-06 203_[+2]_282 54986 1.2e-05 208_[+2]_277 40017 1.4e-05 351_[+2]_134 51183 2e-05 356_[+2]_129 54987 3.4e-05 131_[+2]_354 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=12 46929 ( 96) GACTGTGAGGGGAGA 1 49272 ( 370) GACAGTTTGAGGCGA 1 55031 ( 191) GAAAGAAACGGGCGA 1 23658 ( 45) CACCGTTAGGGGCGA 1 47937 ( 144) GACAGTGTGAGAAGA 1 46928 ( 455) CAAAGATACTGGAGA 1 52498 ( 321) GGTAGTTAGTGACGA 1 41423 ( 204) GATTCTTACGGGCGA 1 54986 ( 209) GACACAATGGGAAGG 1 40017 ( 352) CACAGACAGCGGAGG 1 51183 ( 357) CAAAGCGAGTGATGA 1 54987 ( 132) GAAACTGACTGACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5832 bayes= 10.023 E= 1.3e+000 -1023 50 164 -1023 176 -1023 -136 -1023 30 109 -1023 -75 147 -150 -1023 -75 -1023 9 181 -1023 30 -150 -1023 106 -70 -150 64 57 147 -1023 -1023 -16 -1023 50 164 -1023 -70 -150 96 25 -1023 -1023 222 -1023 62 -1023 145 -1023 62 109 -1023 -174 -170 -1023 210 -1023 147 -1023 22 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 12 E= 1.3e+000 0.000000 0.333333 0.666667 0.000000 0.916667 0.000000 0.083333 0.000000 0.333333 0.500000 0.000000 0.166667 0.750000 0.083333 0.000000 0.166667 0.000000 0.250000 0.750000 0.000000 0.333333 0.083333 0.000000 0.583333 0.166667 0.083333 0.333333 0.416667 0.750000 0.000000 0.000000 0.250000 0.000000 0.333333 0.666667 0.000000 0.166667 0.083333 0.416667 0.333333 0.000000 0.000000 1.000000 0.000000 0.416667 0.000000 0.583333 0.000000 0.416667 0.500000 0.000000 0.083333 0.083333 0.000000 0.916667 0.000000 0.750000 0.000000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC]A[CA]A[GC][TA][TG][AT][GC][GT]G[GA][CA]G[AG] -------------------------------------------------------------------------------- Time 2.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 130 E-value = 8.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 9:62:2272:::a31:::711 pos.-specific C :1:2182124:9:332:a123 probability G 1:32::1:23:1:::7::27: matrix T :9139:4232a::361a:::6 bits 2.2 2.0 * 1.8 * * ** 1.6 *** ** Relative 1.3 ** ** *** ** Entropy 1.1 ** ** *** ** (20.8 bits) 0.9 ** ** *** *** * 0.7 *** ** * *** ******* 0.4 *** ** * ************ 0.2 *** ** * ************ 0.0 --------------------- Multilevel ATATTCTATCTCAATGTCAGT consensus GA AATAG CCC GCC sequence C C CT T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 47937 314 2.54e-10 GTATGCCGCA ATATTCCATGTCATTGTCAGC AGATTCATTT 52498 439 7.73e-09 TGCGAGGAGA ATATTAGAACTCACTGTCAGT CAGTTTCCTT 40017 284 3.89e-08 CGCGTGTGGG ATGATCTTGCTGATTGTCAGT TTCAGAGAAA 54986 260 4.77e-08 GCTAATGTAA ATACTATAGCTCACTTTCAGC CCTTTTGAGT 51183 281 7.73e-08 CTCTCCGTCG ATGGTCCACGTCAACCTCCGT ACCGATCTCG 23658 266 3.84e-07 TATTGGTCCT ACGCTCTCATTCAATGTCGGT GTGTCTGAAG 49272 99 4.70e-07 TTAAGCTTGC ATTTTCATTTTCACCGTCGCT CATTTTTTTT 46929 277 5.02e-07 TGAGTGGTCA ATAGTCTATCTCATACTCAAA ACAGCTTAAG 41423 272 7.71e-07 GCATCTTTAC GTAACCAACGTCAACGTCACC TGTACGAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47937 2.5e-10 313_[+3]_166 52498 7.7e-09 438_[+3]_41 40017 3.9e-08 283_[+3]_196 54986 4.8e-08 259_[+3]_220 51183 7.7e-08 280_[+3]_199 23658 3.8e-07 265_[+3]_214 49272 4.7e-07 98_[+3]_381 46929 5e-07 276_[+3]_203 41423 7.7e-07 271_[+3]_208 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 47937 ( 314) ATATTCCATGTCATTGTCAGC 1 52498 ( 439) ATATTAGAACTCACTGTCAGT 1 40017 ( 284) ATGATCTTGCTGATTGTCAGT 1 54986 ( 260) ATACTATAGCTCACTTTCAGC 1 51183 ( 281) ATGGTCCACGTCAACCTCCGT 1 23658 ( 266) ACGCTCTCATTCAATGTCGGT 1 49272 ( 99) ATTTTCATTTTCACCGTCGCT 1 46929 ( 277) ATAGTCTATCTCATACTCAAA 1 41423 ( 272) GTAACCAACGTCAACGTCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 9.45417 E= 8.2e+000 171 -982 -94 -982 -982 -108 -982 167 104 -982 64 -133 -28 -8 5 25 -982 -108 -982 167 -28 172 -982 -982 -28 -8 -94 67 130 -108 -982 -33 -28 -8 5 25 -982 92 64 -33 -982 -982 -982 184 -982 192 -94 -982 188 -982 -982 -982 30 50 -982 25 -128 50 -982 99 -982 -8 164 -133 -982 -982 -982 184 -982 209 -982 -982 130 -108 5 -982 -128 -8 164 -982 -128 50 -982 99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 8.2e+000 0.888889 0.000000 0.111111 0.000000 0.000000 0.111111 0.000000 0.888889 0.555556 0.000000 0.333333 0.111111 0.222222 0.222222 0.222222 0.333333 0.000000 0.111111 0.000000 0.888889 0.222222 0.777778 0.000000 0.000000 0.222222 0.222222 0.111111 0.444444 0.666667 0.111111 0.000000 0.222222 0.222222 0.222222 0.222222 0.333333 0.000000 0.444444 0.333333 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.111111 0.333333 0.000000 0.555556 0.000000 0.222222 0.666667 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.111111 0.222222 0.000000 0.111111 0.222222 0.666667 0.000000 0.111111 0.333333 0.000000 0.555556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AT[AG][TACG]T[CA][TAC][AT][TACG][CGT]TCA[ACT][TC][GC]TC[AG][GC][TC] -------------------------------------------------------------------------------- Time 3.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46928 1.16e-06 347_[+1(1.19e-07)]_86_\ [+2(1.44e-06)]_31 51183 2.97e-05 280_[+3(7.73e-08)]_55_\ [+2(1.98e-05)]_129 40017 1.10e-05 283_[+3(3.89e-08)]_47_\ [+2(1.35e-05)]_134 23658 3.41e-10 44_[+2(6.26e-07)]_206_\ [+3(3.84e-07)]_34_[+1(3.05e-08)]_159 41423 7.00e-10 135_[+1(3.17e-09)]_47_\ [+2(6.49e-06)]_53_[+3(7.71e-07)]_208 54986 6.02e-10 208_[+2(1.18e-05)]_36_\ [+3(4.77e-08)]_34_[+1(2.40e-08)]_165 54987 7.94e-05 131_[+2(3.43e-05)]_221_\ [+1(9.15e-08)]_112 46929 2.34e-13 95_[+2(1.26e-07)]_108_\ [+1(4.92e-11)]_37_[+3(5.02e-07)]_135_[+3(6.06e-05)]_47 47937 1.69e-08 143_[+2(1.02e-06)]_155_\ [+3(2.54e-10)]_166 55031 4.35e-08 190_[+2(4.80e-07)]_141_\ [+1(1.85e-09)]_133 52498 5.41e-11 210_[+1(2.60e-08)]_89_\ [+2(5.06e-06)]_103_[+3(7.73e-09)]_41 49272 9.20e-11 98_[+3(4.70e-07)]_92_[+1(1.57e-08)]_\ 137_[+2(2.43e-07)]_116 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************