******************************************************************************** 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/290/290.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 24439 1.0000 500 42704 1.0000 500 32099 1.0000 500 46504 1.0000 500 28215 1.0000 500 54813 1.0000 500 47913 1.0000 500 38893 1.0000 500 43369 1.0000 500 43397 1.0000 500 43519 1.0000 500 49216 1.0000 500 45791 1.0000 500 42895 1.0000 500 48709 1.0000 500 37020 1.0000 500 36595 1.0000 500 47052 1.0000 500 37840 1.0000 500 50561 1.0000 500 49538 1.0000 500 47680 1.0000 500 45457 1.0000 500 46117 1.0000 500 49747 1.0000 500 44798 1.0000 500 43921 1.0000 500 45006 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/290/290.seqs.fa -oc motifs/290 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.234 G 0.223 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.234 G 0.223 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 15 llr = 166 E-value = 1.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::917:::9:1 pos.-specific C :29:5::1a:91 probability G 7:112:a1:113 matrix T 38::33:9::16 bits 2.2 * * 1.9 * * 1.7 * * * 1.5 ** * ** Relative 1.3 * ** ***** Entropy 1.1 **** ****** (16.0 bits) 0.9 **** ****** 0.6 **** ****** 0.4 **** ******* 0.2 ************ 0.0 ------------ Multilevel GTCACAGTCACT consensus TC TT G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46504 271 5.97e-08 GACTTTCAGG GTCACAGTCACT CAAAAGACGT 38893 233 1.78e-07 TCACTATCAT GTCATAGTCACT TATAGACACA 36595 272 4.20e-07 CCACTGCCAA TTCACAGTCACT CACTGCCAGC 47680 330 5.73e-07 GAAAAAAACG GTCACTGTCACG GTCAGTCCAT 49747 274 6.44e-07 TAAGATTGCG GTCATTGTCACT TACGATCACT 42895 133 1.37e-06 AATGACACAT TTCACTGTCACT CTCTTTGGCC 43397 225 1.74e-06 CGAGCAGTAT GTCACAGTCGCT CGTCGTAGCT 43921 157 4.01e-06 ACGACCAACC GCCACAGTCACC TCTTCTGACC 49216 483 5.10e-06 GCAGAAACAA GTCAGAGTCATT GCAATA 45457 149 6.36e-06 AACTTGCGAC GTCAGAGGCACG CTTACGTTAA 42704 478 6.36e-06 GCTTGTGTCA TTCACAGTCAGT AAACACAATA 37840 417 9.87e-06 CGTCTCTCTG GCCATAGCCACT GGATCATGGT 50561 213 1.47e-05 GACCGCTGCG GTCGGTGTCACG ACAAAAGAGG 48709 256 2.11e-05 CCGAAATTCG GTGAAAGTCACG GACCATCACG 28215 315 2.11e-05 CCCCATTGCT TCCATAGTCACA GAGCACACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46504 6e-08 270_[+1]_218 38893 1.8e-07 232_[+1]_256 36595 4.2e-07 271_[+1]_217 47680 5.7e-07 329_[+1]_159 49747 6.4e-07 273_[+1]_215 42895 1.4e-06 132_[+1]_356 43397 1.7e-06 224_[+1]_264 43921 4e-06 156_[+1]_332 49216 5.1e-06 482_[+1]_6 45457 6.4e-06 148_[+1]_340 42704 6.4e-06 477_[+1]_11 37840 9.9e-06 416_[+1]_72 50561 1.5e-05 212_[+1]_276 48709 2.1e-05 255_[+1]_233 28215 2.1e-05 314_[+1]_174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=15 46504 ( 271) GTCACAGTCACT 1 38893 ( 233) GTCATAGTCACT 1 36595 ( 272) TTCACAGTCACT 1 47680 ( 330) GTCACTGTCACG 1 49747 ( 274) GTCATTGTCACT 1 42895 ( 133) TTCACTGTCACT 1 43397 ( 225) GTCACAGTCGCT 1 43921 ( 157) GCCACAGTCACC 1 49216 ( 483) GTCAGAGTCATT 1 45457 ( 149) GTCAGAGGCACG 1 42704 ( 478) TTCACAGTCAGT 1 37840 ( 417) GCCATAGCCACT 1 50561 ( 213) GTCGGTGTCACG 1 48709 ( 256) GTGAAAGTCACG 1 28215 ( 315) TCCATAGTCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13692 bayes= 10.5074 E= 1.7e-004 -1055 -1055 172 -4 -1055 -23 -1055 154 -1055 200 -174 -1055 179 -1055 -174 -1055 -201 100 -16 -4 145 -1055 -1055 -4 -1055 -1055 216 -1055 -1055 -181 -174 166 -1055 210 -1055 -1055 179 -1055 -174 -1055 -1055 189 -174 -204 -201 -181 26 113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.7e-004 0.000000 0.000000 0.733333 0.266667 0.000000 0.200000 0.000000 0.800000 0.000000 0.933333 0.066667 0.000000 0.933333 0.000000 0.066667 0.000000 0.066667 0.466667 0.200000 0.266667 0.733333 0.000000 0.000000 0.266667 0.000000 0.000000 1.000000 0.000000 0.000000 0.066667 0.066667 0.866667 0.000000 1.000000 0.000000 0.000000 0.933333 0.000000 0.066667 0.000000 0.000000 0.866667 0.066667 0.066667 0.066667 0.066667 0.266667 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][TC]CA[CTG][AT]GTCAC[TG] -------------------------------------------------------------------------------- Time 7.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 19 llr = 199 E-value = 4.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :52111:1::22111: pos.-specific C 113:673::3:3:2:6 probability G 8513::7:115327:: matrix T 1:5642:996328:94 bits 2.2 1.9 1.7 1.5 * * Relative 1.3 *** * Entropy 1.1 * **** * ** (15.1 bits) 0.9 ** ******* **** 0.6 ** ******** **** 0.4 ** ******** **** 0.2 *********** **** 0.0 ---------------- Multilevel GATTCCGTTTGCTGTC consensus GCGTTC CTG C T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 28215 195 1.59e-08 TGGATCCTAT GGTTTCGTTCGGTGTC AAAAATGTCT 49538 419 8.49e-08 CTTGGTCGTG GATTTCGTTTTGTGTT ATTTTGCAAG 36595 392 3.10e-07 AGGGGACACT GGCTCCGTTCATTGTC TCCCTGTTCC 46117 252 8.30e-07 TTTCTTCAAT TGTTCCGTTTTCTGTT CAAATCCTGT 43369 9 2.20e-06 GATCATTT GGCTCTGTTCTATGTT CACTGGTCAT 45791 215 2.68e-06 GCACACAACC GGTTCCGATTGAGGTC TTTTGGGTGC 44798 174 2.96e-06 GTTGCCACTC GAATTCGTTCGCTATC GGAGCTCGAC 38893 341 3.58e-06 TTCTGGGAAT CGCGCCGTTCACTGTC ATCAACTTCA 43921 418 3.93e-06 CTATCGCATG GATTCCCTTGTCTGTT TGCATCTCGT 47913 297 3.93e-06 ATCTCTAGAA GGAGCCCTTTGTTCTT TAAATTATTG 47052 215 4.31e-06 ACTCCAGAAG GACGCACTTTGCTGTC CTGTCGATCA 48709 339 5.16e-06 AGAGCGGTAG GGTACTGTTTGGTCTC GAGCGTGTGT 50561 172 1.10e-05 GATTCACTAA TGTGTCGTTCGGTATC CATTCGATTC 42895 190 1.19e-05 TGTCAAACTT GACTCCGTGTGGAGTC GTATTCGATA 54813 371 1.19e-05 GCAGTAACAA GATTCTGTTTACTGAC GTATTCAGTG 47680 364 1.88e-05 GAAAGCGTCC GAGTTCCATTGGTGTT CGCATATAGT 37020 93 3.07e-05 AGTATGATAT GACGTTGTTTTAGCTC TAAAATCGAC 42704 456 4.82e-05 CGAACCGACC GAAGTCCTTTTTGCTT GTGTCATTCA 45006 478 5.44e-05 CTACGCCCGT CCTTACGTTTGTTGTT GGGCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28215 1.6e-08 194_[+2]_290 49538 8.5e-08 418_[+2]_66 36595 3.1e-07 391_[+2]_93 46117 8.3e-07 251_[+2]_233 43369 2.2e-06 8_[+2]_476 45791 2.7e-06 214_[+2]_270 44798 3e-06 173_[+2]_311 38893 3.6e-06 340_[+2]_144 43921 3.9e-06 417_[+2]_67 47913 3.9e-06 296_[+2]_188 47052 4.3e-06 214_[+2]_270 48709 5.2e-06 338_[+2]_146 50561 1.1e-05 171_[+2]_313 42895 1.2e-05 189_[+2]_295 54813 1.2e-05 370_[+2]_114 47680 1.9e-05 363_[+2]_121 37020 3.1e-05 92_[+2]_392 42704 4.8e-05 455_[+2]_29 45006 5.4e-05 477_[+2]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=19 28215 ( 195) GGTTTCGTTCGGTGTC 1 49538 ( 419) GATTTCGTTTTGTGTT 1 36595 ( 392) GGCTCCGTTCATTGTC 1 46117 ( 252) TGTTCCGTTTTCTGTT 1 43369 ( 9) GGCTCTGTTCTATGTT 1 45791 ( 215) GGTTCCGATTGAGGTC 1 44798 ( 174) GAATTCGTTCGCTATC 1 38893 ( 341) CGCGCCGTTCACTGTC 1 43921 ( 418) GATTCCCTTGTCTGTT 1 47913 ( 297) GGAGCCCTTTGTTCTT 1 47052 ( 215) GACGCACTTTGCTGTC 1 48709 ( 339) GGTACTGTTTGGTCTC 1 50561 ( 172) TGTGTCGTTCGGTATC 1 42895 ( 190) GACTCCGTGTGGAGTC 1 54813 ( 371) GATTCTGTTTACTGAC 1 47680 ( 364) GAGTTCCATTGGTGTT 1 37020 ( 93) GACGTTGTTTTAGCTC 1 42704 ( 456) GAAGTCCTTTTTGCTT 1 45006 ( 478) CCTTACGTTTGTTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 9.67432 E= 4.5e+002 -1089 -115 182 -138 82 -215 109 -1089 -77 43 -208 79 -235 -1089 50 120 -235 131 -1089 43 -235 166 -1089 -38 -1089 17 172 -1089 -135 -1089 -1089 171 -1089 -1089 -208 179 -1089 43 -208 120 -77 -1089 124 20 -77 43 50 -38 -235 -1089 -50 152 -135 -15 162 -1089 -235 -1089 -1089 179 -1089 131 -1089 62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 19 E= 4.5e+002 0.000000 0.105263 0.789474 0.105263 0.473684 0.052632 0.473684 0.000000 0.157895 0.315789 0.052632 0.473684 0.052632 0.000000 0.315789 0.631579 0.052632 0.578947 0.000000 0.368421 0.052632 0.736842 0.000000 0.210526 0.000000 0.263158 0.736842 0.000000 0.105263 0.000000 0.000000 0.894737 0.000000 0.000000 0.052632 0.947368 0.000000 0.315789 0.052632 0.631579 0.157895 0.000000 0.526316 0.315789 0.157895 0.315789 0.315789 0.210526 0.052632 0.000000 0.157895 0.789474 0.105263 0.210526 0.684211 0.000000 0.052632 0.000000 0.000000 0.947368 0.000000 0.578947 0.000000 0.421053 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AG][TC][TG][CT][CT][GC]TT[TC][GT][CGT]T[GC]T[CT] -------------------------------------------------------------------------------- Time 14.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 3 llr = 66 E-value = 3.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::a::::::::7:a73::a pos.-specific C ::::a:::::337:3:a:: probability G a3:a:a37aa7:3::7:a: matrix T :7::::73::::::::::: bits 2.2 * *** ** ** 1.9 * **** ** * *** 1.7 * **** ** * *** 1.5 * **** ** * *** Relative 1.3 * **** *** ** *** Entropy 1.1 ******************* (31.8 bits) 0.9 ******************* 0.6 ******************* 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel GTAGCGTGGGGACAAGCGA consensus G GT CCG CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 45791 58 2.27e-11 GGACGACGCC GGAGCGTGGGGCCAAGCGA GATAGGGTTG 47052 397 3.66e-11 ACGGCACCCA GTAGCGTGGGCACACGCGA ATGGCCTTGT 46504 319 2.60e-10 TAGGTTTAGG GTAGCGGTGGGAGAAACGA AAGAATGACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45791 2.3e-11 57_[+3]_424 47052 3.7e-11 396_[+3]_85 46504 2.6e-10 318_[+3]_163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=3 45791 ( 58) GGAGCGTGGGGCCAAGCGA 1 47052 ( 397) GTAGCGTGGGCACACGCGA 1 46504 ( 319) GTAGCGGTGGGAGAAACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 13496 bayes= 11.7938 E= 3.6e+003 -823 -823 216 -823 -823 -823 58 128 189 -823 -823 -823 -823 -823 216 -823 -823 209 -823 -823 -823 -823 216 -823 -823 -823 58 128 -823 -823 158 28 -823 -823 216 -823 -823 -823 216 -823 -823 51 158 -823 131 51 -823 -823 -823 151 58 -823 189 -823 -823 -823 131 51 -823 -823 31 -823 158 -823 -823 209 -823 -823 -823 -823 216 -823 189 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 3 E= 3.6e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TG]AGCG[TG][GT]GG[GC][AC][CG]A[AC][GA]CGA -------------------------------------------------------------------------------- Time 21.01 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24439 5.78e-01 500 42704 2.65e-03 455_[+2(4.82e-05)]_6_[+1(6.36e-06)]_\ 11 32099 9.60e-02 500 46504 1.88e-10 270_[+1(5.97e-08)]_36_\ [+3(2.60e-10)]_163 28215 1.04e-05 194_[+2(1.59e-08)]_104_\ [+1(2.11e-05)]_37_[+2(3.74e-05)]_121 54813 6.80e-02 370_[+2(1.19e-05)]_114 47913 2.21e-02 296_[+2(3.93e-06)]_188 38893 5.32e-06 232_[+1(1.78e-07)]_96_\ [+2(3.58e-06)]_144 43369 1.57e-03 8_[+2(2.20e-06)]_476 43397 3.03e-03 224_[+1(1.74e-06)]_264 43519 5.98e-01 500 49216 2.48e-02 482_[+1(5.10e-06)]_6 45791 3.25e-09 57_[+3(2.27e-11)]_138_\ [+2(2.68e-06)]_270 42895 5.52e-05 43_[+1(2.40e-06)]_77_[+1(1.37e-06)]_\ 45_[+2(1.19e-05)]_295 48709 2.41e-04 255_[+1(2.11e-05)]_71_\ [+2(5.16e-06)]_146 37020 1.48e-01 92_[+2(3.07e-05)]_392 36595 1.41e-06 271_[+1(4.20e-07)]_108_\ [+2(3.10e-07)]_93 47052 3.93e-09 214_[+2(4.31e-06)]_166_\ [+3(3.66e-11)]_85 37840 2.45e-02 416_[+1(9.87e-06)]_72 50561 3.73e-04 171_[+2(1.10e-05)]_25_\ [+1(1.47e-05)]_276 49538 1.16e-03 418_[+2(8.49e-08)]_66 47680 1.52e-05 17_[+3(8.65e-05)]_293_\ [+1(5.73e-07)]_22_[+2(1.88e-05)]_121 45457 1.62e-02 148_[+1(6.36e-06)]_340 46117 4.67e-03 251_[+2(8.30e-07)]_233 49747 1.45e-03 273_[+1(6.44e-07)]_215 44798 2.22e-02 173_[+2(2.96e-06)]_311 43921 1.58e-04 76_[+1(3.16e-05)]_68_[+1(4.01e-06)]_\ 249_[+2(3.93e-06)]_67 45006 8.63e-03 477_[+2(5.44e-05)]_7 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************