******************************************************************************** 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/285/285.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9509 1.0000 500 13757 1.0000 500 47951 1.0000 500 49117 1.0000 500 40239 1.0000 500 50169 1.0000 500 843 1.0000 500 10216 1.0000 500 33774 1.0000 500 10742 1.0000 500 10948 1.0000 500 44665 1.0000 500 12384 1.0000 500 44000 1.0000 500 42781 1.0000 500 49973 1.0000 500 43021 1.0000 500 46854 1.0000 500 38073 1.0000 500 50150 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/285/285.seqs.fa -oc motifs/285 -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= 20 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= 10000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.232 G 0.221 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.281 C 0.232 G 0.221 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 20 llr = 187 E-value = 1.8e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3:::a17:3:a7 pos.-specific C 1419:71119:2 probability G 14:2:::9:111 matrix T 62a::2316::: bits 2.2 2.0 1.7 * * 1.5 *** ** Relative 1.3 *** * ** Entropy 1.1 *** * ** (13.5 bits) 0.9 ****** *** 0.7 *********** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel TCTCACAGTCAA consensus AG TT A C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43021 308 1.47e-07 TTTTTTAACC TCTCACAGTCAA CGAAACCCCA 44665 296 1.47e-07 ACGCGCACAA TCTCACAGTCAA GAGTTGTGGG 50150 268 5.43e-07 TGAACAAACG ACTCACAGTCAA GCAATTCGAG 44000 414 7.41e-07 GCATTTCTGT TGTCACAGTCAC AGTCACTGAC 47951 365 1.61e-06 ACGACAGCAT TTTCACAGACAA GCATACTTCG 49117 273 6.93e-06 AGAGCTAGGT ATTCACTGTCAA TCATCGAAGA 9509 12 7.36e-06 AAACACAAGC TGTCACTGACAC GGGATTTGCT 10216 40 9.97e-06 TCCTTTGTTC ATTCATAGTCAA AATGCGCGGT 49973 59 1.11e-05 TGACTGTTAG AGTCATTGTCAA CGAACAATAT 10742 126 1.11e-05 TGGAATCCAT CGTGACAGTCAA AGACCCGGCG 46854 248 2.35e-05 CGTCAAATTG TCTGACAGTGAA AGAGATCGCG 13757 140 2.88e-05 TTCCTTGTCG TCTGACATTCAA CGCATAAGAA 33774 227 3.11e-05 CTGTAAAACA TGTCACCGTCAG AAGCAACCGC 42781 369 3.33e-05 GAGCCAGAAT ACTCACAGCCAG CACGAGAAGT 50169 25 4.08e-05 AGGTTGTTGT TGTCACTGACGA CTCACAAGTT 38073 125 4.87e-05 AATCCTTTGG TCCCACAGACAC GTTTTAGCCC 40239 192 5.76e-05 GGATGGAGGT TGTCAAAGCCAC AGGTGTTGGT 10948 260 1.79e-04 CAATTATACC GGTCATACACAA GAACGGTTCC 843 95 2.20e-04 TTTCTCTCTC CCTCATTGAGAA TCTTCGTGTC 12384 107 2.32e-04 AAAAAAAATT GTTCAAATTCAA AATATTTCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43021 1.5e-07 307_[+1]_181 44665 1.5e-07 295_[+1]_193 50150 5.4e-07 267_[+1]_221 44000 7.4e-07 413_[+1]_75 47951 1.6e-06 364_[+1]_124 49117 6.9e-06 272_[+1]_216 9509 7.4e-06 11_[+1]_477 10216 1e-05 39_[+1]_449 49973 1.1e-05 58_[+1]_430 10742 1.1e-05 125_[+1]_363 46854 2.3e-05 247_[+1]_241 13757 2.9e-05 139_[+1]_349 33774 3.1e-05 226_[+1]_262 42781 3.3e-05 368_[+1]_120 50169 4.1e-05 24_[+1]_464 38073 4.9e-05 124_[+1]_364 40239 5.8e-05 191_[+1]_297 10948 0.00018 259_[+1]_229 843 0.00022 94_[+1]_394 12384 0.00023 106_[+1]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=20 43021 ( 308) TCTCACAGTCAA 1 44665 ( 296) TCTCACAGTCAA 1 50150 ( 268) ACTCACAGTCAA 1 44000 ( 414) TGTCACAGTCAC 1 47951 ( 365) TTTCACAGACAA 1 49117 ( 273) ATTCACTGTCAA 1 9509 ( 12) TGTCACTGACAC 1 10216 ( 40) ATTCATAGTCAA 1 49973 ( 59) AGTCATTGTCAA 1 10742 ( 126) CGTGACAGTCAA 1 46854 ( 248) TCTGACAGTGAA 1 13757 ( 140) TCTGACATTCAA 1 33774 ( 227) TGTCACCGTCAG 1 42781 ( 369) ACTCACAGCCAG 1 50169 ( 25) TGTCACTGACGA 1 38073 ( 125) TCCCACAGACAC 1 40239 ( 192) TGTCAAAGCCAC 1 10948 ( 260) GGTCATACACAA 1 843 ( 95) CCTCATTGAGAA 1 12384 ( 107) GTTCAAATTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9780 bayes= 8.93074 E= 1.8e-005 -17 -121 -114 105 -1097 78 86 -41 -1097 -221 -1097 184 -1097 187 -56 -1097 183 -1097 -1097 -1097 -149 159 -1097 -41 132 -221 -1097 -9 -1097 -221 194 -141 9 -121 -1097 117 -1097 195 -114 -1097 176 -1097 -214 -1097 132 -21 -114 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 20 E= 1.8e-005 0.250000 0.100000 0.100000 0.550000 0.000000 0.400000 0.400000 0.200000 0.000000 0.050000 0.000000 0.950000 0.000000 0.850000 0.150000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.700000 0.000000 0.200000 0.700000 0.050000 0.000000 0.250000 0.000000 0.050000 0.850000 0.100000 0.300000 0.100000 0.000000 0.600000 0.000000 0.900000 0.100000 0.000000 0.950000 0.000000 0.050000 0.000000 0.700000 0.200000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA][CGT]TCA[CT][AT]G[TA]CA[AC] -------------------------------------------------------------------------------- Time 3.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 8 llr = 128 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::61a3:9a51:5:89863a pos.-specific C :9:15::51:14a333:131: probability G 81934:15:::5:36:1111: matrix T ::1:::6:::4:::1::::5: bits 2.2 * 2.0 * 1.7 * * * * 1.5 ** * * * * Relative 1.3 *** * ** * * * Entropy 1.1 *** * *** * ** * (23.1 bits) 0.9 *** * *** * **** * 0.7 ********** ** ***** * 0.4 ******************* * 0.2 ********************* 0.0 --------------------- Multilevel GCGACATCAAAGCAGAAAATA consensus A GG AG TC CCC CA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10216 382 1.70e-11 CTCGTCTATC GCGACATCAAACCCGAAAATA TCGGCTTTGA 50150 185 3.43e-09 GCTGCGTACA GCGCGATCAATGCCGAAAAGA TGTAACGAAG 50169 133 2.04e-08 ACGAGCAGTC GCGACATGAAAGCATCGACTA GCTTGTGCAC 47951 427 2.04e-08 CGACGAAAAC ACGACATCAACGCAGCACATA TCGTGGGAAC 46854 463 3.91e-08 GTTTCGAAAG ACGGCATCAAAACGCAAAAAA GCCACATCTG 10742 326 4.91e-08 CTACAGAGGA GGGAGAAGCATGCACAAAATA CGTAGAAGGT 13757 478 9.18e-08 CCTTGCACTG GCGGAAAGAATCCAGAAGCAA CA 42781 262 1.26e-07 AGCTCTACTA GCTAGAGGAAACCGGAAAGCA TGGGTGTGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10216 1.7e-11 381_[+2]_98 50150 3.4e-09 184_[+2]_295 50169 2e-08 132_[+2]_347 47951 2e-08 426_[+2]_53 46854 3.9e-08 462_[+2]_17 10742 4.9e-08 325_[+2]_154 13757 9.2e-08 477_[+2]_2 42781 1.3e-07 261_[+2]_218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=8 10216 ( 382) GCGACATCAAACCCGAAAATA 1 50150 ( 185) GCGCGATCAATGCCGAAAAGA 1 50169 ( 133) GCGACATGAAAGCATCGACTA 1 47951 ( 427) ACGACATCAACGCAGCACATA 1 46854 ( 463) ACGGCATCAAAACGCAAAAAA 1 10742 ( 326) GGGAGAAGCATGCACAAAATA 1 13757 ( 478) GCGGAAAGAATCCAGAAGCAA 1 42781 ( 262) GCTAGAGGAAACCGGAAAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9600 bayes= 10.2276 E= 2.3e+002 -17 -965 176 -965 -965 191 -82 -965 -965 -965 199 -109 115 -89 18 -965 -117 111 76 -965 183 -965 -965 -965 -17 -965 -82 123 -965 111 118 -965 164 -89 -965 -965 183 -965 -965 -965 83 -89 -965 49 -117 69 118 -965 -965 211 -965 -965 83 11 18 -965 -965 11 150 -109 142 11 -965 -965 164 -965 -82 -965 142 -89 -82 -965 115 11 -82 -965 -17 -89 -82 91 183 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 2.3e+002 0.250000 0.000000 0.750000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.875000 0.125000 0.625000 0.125000 0.250000 0.000000 0.125000 0.500000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.125000 0.625000 0.000000 0.500000 0.500000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.125000 0.000000 0.375000 0.125000 0.375000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.250000 0.625000 0.125000 0.750000 0.250000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.750000 0.125000 0.125000 0.000000 0.625000 0.250000 0.125000 0.000000 0.250000 0.125000 0.125000 0.500000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]CG[AG][CG]A[TA][CG]AA[AT][GC]C[ACG][GC][AC]AA[AC][TA]A -------------------------------------------------------------------------------- Time 7.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 83 E-value = 7.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::53::3:::::::::: pos.-specific C 35a53a3:aa33::3888:8: probability G 8::5::35::58a8:33:::a matrix T :5::8::3:::::38::3a3: bits 2.2 * * ** * * 2.0 * * ** * * * 1.7 * * ** * * * 1.5 * * ** * * * Relative 1.3 * * * ** *** ****** Entropy 1.1 ****** ** ********** (29.9 bits) 0.9 ****** ** ********** 0.7 ****** ************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GCCCTCAGCCGGGGTCCCTCG consensus CT GC CA AC TCGGT T sequence GT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50150 78 5.04e-12 ATCGAGAAAT GCCGTCGGCCGGGGTCGCTCG CAAACCGAAA 843 354 3.19e-10 GCGTTCGACT GCCGCCAACCGCGGTGCCTCG CACGTCTTTC 10742 394 3.99e-10 TCCCCAATAG CTCCTCAGCCCGGGCCCCTTG GCGAGAGCGG 47951 392 8.58e-10 CTTCGTGAAC GTCCTCCTCCAGGTTCCTTCG AGCACGACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50150 5e-12 77_[+3]_402 843 3.2e-10 353_[+3]_126 10742 4e-10 393_[+3]_86 47951 8.6e-10 391_[+3]_88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 50150 ( 78) GCCGTCGGCCGGGGTCGCTCG 1 843 ( 354) GCCGCCAACCGCGGTGCCTCG 1 10742 ( 394) CTCCTCAGCCCGGGCCCCTTG 1 47951 ( 392) GTCCTCCTCCAGGTTCCTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9600 bayes= 11.2282 E= 7.9e+002 -865 11 176 -865 -865 111 -865 91 -865 210 -865 -865 -865 111 118 -865 -865 11 -865 149 -865 210 -865 -865 83 11 18 -865 -17 -865 118 -9 -865 210 -865 -865 -865 210 -865 -865 -17 11 118 -865 -865 11 176 -865 -865 -865 218 -865 -865 -865 176 -9 -865 11 -865 149 -865 169 18 -865 -865 169 18 -865 -865 169 -865 -9 -865 -865 -865 191 -865 169 -865 -9 -865 -865 218 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 7.9e+002 0.000000 0.250000 0.750000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][CT]C[CG][TC]C[ACG][GAT]CC[GAC][GC]G[GT][TC][CG][CG][CT]T[CT]G -------------------------------------------------------------------------------- Time 10.79 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9509 6.59e-03 11_[+1(7.36e-06)]_477 13757 1.30e-05 139_[+1(2.88e-05)]_127_\ [+2(1.64e-05)]_178_[+2(9.18e-08)]_2 47951 1.87e-12 364_[+1(1.61e-06)]_15_\ [+3(8.58e-10)]_14_[+2(2.04e-08)]_53 49117 1.27e-02 272_[+1(6.93e-06)]_216 40239 4.34e-02 191_[+1(5.76e-05)]_297 50169 1.87e-05 24_[+1(4.08e-05)]_96_[+2(2.04e-08)]_\ 287_[+2(5.86e-05)]_39 843 1.68e-06 353_[+3(3.19e-10)]_126 10216 7.77e-09 39_[+1(9.97e-06)]_330_\ [+2(1.70e-11)]_98 33774 6.04e-02 226_[+1(3.11e-05)]_262 10742 1.28e-11 125_[+1(1.11e-05)]_188_\ [+2(4.91e-08)]_47_[+3(3.99e-10)]_86 10948 1.55e-02 60_[+3(1.23e-05)]_419 44665 3.31e-03 295_[+1(1.47e-07)]_193 12384 1.34e-01 500 44000 9.01e-03 51_[+1(9.87e-05)]_200_\ [+1(7.32e-05)]_138_[+1(7.41e-07)]_4_[+1(5.60e-06)]_59 42781 4.66e-05 261_[+2(1.26e-07)]_86_\ [+1(3.33e-05)]_120 49973 4.13e-02 3_[+1(9.87e-05)]_43_[+1(1.11e-05)]_\ 430 43021 8.51e-04 307_[+1(1.47e-07)]_111_\ [+1(1.11e-05)]_58 46854 3.05e-06 247_[+1(2.35e-05)]_203_\ [+2(3.91e-08)]_17 38073 7.91e-02 124_[+1(4.87e-05)]_364 50150 9.52e-16 77_[+3(5.04e-12)]_86_[+2(3.43e-09)]_\ 62_[+1(5.43e-07)]_221 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************