******************************************************************************** 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/86/86.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42514 1.0000 500 46535 1.0000 500 47465 1.0000 500 48819 1.0000 500 15968 1.0000 500 49856 1.0000 500 42586 1.0000 500 43268 1.0000 500 43725 1.0000 500 46718 1.0000 500 46763 1.0000 500 40725 1.0000 500 43726 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/86/86.seqs.fa -oc motifs/86 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.241 G 0.208 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.241 G 0.208 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 124 E-value = 5.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22::27a8:478 pos.-specific C :53a:::2:5:2 probability G 42::83::a2:: matrix T 427:1::1::3: bits 2.3 * 2.0 * * 1.8 * * * 1.6 * * * Relative 1.4 * * * * Entropy 1.1 ***** * * (13.8 bits) 0.9 ******* ** 0.7 ******* ** 0.5 * ********** 0.2 ************ 0.0 ------------ Multilevel GCTCGAAAGCAA consensus TTC G AT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46535 238 5.03e-07 GTTTAGCAAT ACTCGAAAGCAA TGTAAATTCC 47465 156 1.20e-06 AAACGACTCC TCTCGAAAGCTA TTTAGACAGC 43726 296 2.62e-06 AGAGTACATC TGTCGAAAGAAA GTCGGCAGGG 42586 283 3.12e-06 AATCTGGAGT GATCGAAAGAAA CCTATTACAC 15968 469 3.57e-06 GGTGAGCGTG TGTCGGAAGCAA AAGCGACACT 43268 476 4.71e-06 ACCCGAAAAA GCTCAAAAGCAA CCCAACAGTA 46763 449 1.55e-05 AACTCCCACA ATTCGAAAGATA TTGTTTGTCA 49856 71 2.39e-05 CCAAGTACAA ACCCGAAAGGTA AACACGACCG 46718 154 3.61e-05 ATTACCATAT GCCCGGAAGGAC AGTGACAGGA 42514 141 3.85e-05 ACGGCAAATC GTCCGAATGCAA TCCAATCGGA 43725 478 5.15e-05 GCGCAGATTT TTTCTGAAGCAA AACTCATCTC 48819 272 5.52e-05 GTCTTAATTG GCTCAGACGAAA ATGCAGACAG 40725 394 1.88e-04 ATCCGCGTAG TACCGAACGATC CGTCGAGGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46535 5e-07 237_[+1]_251 47465 1.2e-06 155_[+1]_333 43726 2.6e-06 295_[+1]_193 42586 3.1e-06 282_[+1]_206 15968 3.6e-06 468_[+1]_20 43268 4.7e-06 475_[+1]_13 46763 1.6e-05 448_[+1]_40 49856 2.4e-05 70_[+1]_418 46718 3.6e-05 153_[+1]_335 42514 3.8e-05 140_[+1]_348 43725 5.1e-05 477_[+1]_11 48819 5.5e-05 271_[+1]_217 40725 0.00019 393_[+1]_95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 46535 ( 238) ACTCGAAAGCAA 1 47465 ( 156) TCTCGAAAGCTA 1 43726 ( 296) TGTCGAAAGAAA 1 42586 ( 283) GATCGAAAGAAA 1 15968 ( 469) TGTCGGAAGCAA 1 43268 ( 476) GCTCAAAAGCAA 1 46763 ( 449) ATTCGAAAGATA 1 49856 ( 71) ACCCGAAAGGTA 1 46718 ( 154) GCCCGGAAGGAC 1 42514 ( 141) GTCCGAATGCAA 1 43725 ( 478) TTTCTGAAGCAA 1 48819 ( 272) GCTCAGACGAAA 1 40725 ( 394) TACCGAACGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 8.93074 E= 5.2e+001 -26 -1035 89 49 -85 94 -44 -25 -1035 35 -1035 134 -1035 205 -1035 -1035 -85 -1035 188 -183 132 -1035 56 -1035 185 -1035 -1035 -1035 147 -64 -1035 -183 -1035 -1035 226 -1035 47 94 -44 -1035 132 -1035 -1035 17 161 -64 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 5.2e+001 0.230769 0.000000 0.384615 0.384615 0.153846 0.461538 0.153846 0.230769 0.000000 0.307692 0.000000 0.692308 0.000000 1.000000 0.000000 0.000000 0.153846 0.000000 0.769231 0.076923 0.692308 0.000000 0.307692 0.000000 1.000000 0.000000 0.000000 0.000000 0.769231 0.153846 0.000000 0.076923 0.000000 0.000000 1.000000 0.000000 0.384615 0.461538 0.153846 0.000000 0.692308 0.000000 0.000000 0.307692 0.846154 0.153846 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GTA][CT][TC]CG[AG]AAG[CA][AT]A -------------------------------------------------------------------------------- Time 1.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 13 llr = 139 E-value = 5.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 112742:262:a52:: pos.-specific C :142::2712a::81: probability G 7542576112:::::7 matrix T 23::212:24::5:93 bits 2.3 2.0 * 1.8 ** 1.6 ** * Relative 1.4 ** *** Entropy 1.1 ** *** (15.5 bits) 0.9 * *** ****** 0.7 * ***** ****** 0.5 ********* ****** 0.2 ********* ****** 0.0 ---------------- Multilevel GGCAGGGCATCAACTG consensus TTG AACATA T T sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 43726 311 3.28e-10 AAAGAAAGTC GGCAGGGCATCAACTG CGACCAGAAG 43268 131 1.65e-07 CTGCTTGCGC GGGATGCCACCATCTG CCCGTTTCCG 48819 19 1.16e-06 CCAATAGGTC GTCGGGTCACCATCTG TCTAGTACTG 49856 478 1.44e-06 TTCGAACCAG TGGAGGGGTTCAACTG CTCTATG 47465 407 2.89e-06 TTTCTAAGGT GTGGAGGCGGCATCTG GCCACTCGCT 40725 194 9.02e-06 ACAAACACGT GTGAGGTATCCAACTT TTGGCAACAC 46718 372 9.02e-06 CCAATCCATC GTCAATCCATCATCTT CATTTCGTGA 46535 78 9.02e-06 TTCAAAGCGG TGGATGGCAGCAAATT GTGTCTTTTT 42586 345 9.77e-06 CCGACAGGTA AGAAGAGCAACATCTT CAGCTTAATT 43725 344 1.23e-05 CTTGCTCTAA GGAAAAGACACAACTG GTTGGAAATC 15968 105 1.33e-05 GAGTACTTCC TCCAAAGCTTCAACTG TGAGCCTTTT 46763 23 1.66e-05 GCAACTCGAA GAACAGGAAACATCTG CGTCAGAGTC 42514 400 1.66e-05 CTTGGCAGAT GGCCGGCCATCAAACG CCGTGCCGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43726 3.3e-10 310_[+2]_174 43268 1.7e-07 130_[+2]_354 48819 1.2e-06 18_[+2]_466 49856 1.4e-06 477_[+2]_7 47465 2.9e-06 406_[+2]_78 40725 9e-06 193_[+2]_291 46718 9e-06 371_[+2]_113 46535 9e-06 77_[+2]_407 42586 9.8e-06 344_[+2]_140 43725 1.2e-05 343_[+2]_141 15968 1.3e-05 104_[+2]_380 46763 1.7e-05 22_[+2]_462 42514 1.7e-05 399_[+2]_85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=13 43726 ( 311) GGCAGGGCATCAACTG 1 43268 ( 131) GGGATGCCACCATCTG 1 48819 ( 19) GTCGGGTCACCATCTG 1 49856 ( 478) TGGAGGGGTTCAACTG 1 47465 ( 407) GTGGAGGCGGCATCTG 1 40725 ( 194) GTGAGGTATCCAACTT 1 46718 ( 372) GTCAATCCATCATCTT 1 46535 ( 78) TGGATGGCAGCAAATT 1 42586 ( 345) AGAAGAGCAACATCTT 1 43725 ( 344) GGAAAAGACACAACTG 1 15968 ( 105) TCCAAAGCTTCAACTG 1 46763 ( 23) GAACAGGAAACATCTG 1 42514 ( 400) GGCCGGCCATCAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 8.91886 E= 5.4e+001 -185 -1035 173 -25 -185 -164 137 17 -26 68 89 -1035 132 -64 -44 -1035 47 -1035 115 -83 -26 -1035 173 -183 -1035 -6 156 -83 -26 152 -143 -1035 115 -164 -143 -25 -26 -6 -44 49 -1035 205 -1035 -1035 185 -1035 -1035 -1035 96 -1035 -1035 75 -85 181 -1035 -1035 -1035 -164 -1035 175 -1035 -1035 173 17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 13 E= 5.4e+001 0.076923 0.000000 0.692308 0.230769 0.076923 0.076923 0.538462 0.307692 0.230769 0.384615 0.384615 0.000000 0.692308 0.153846 0.153846 0.000000 0.384615 0.000000 0.461538 0.153846 0.230769 0.000000 0.692308 0.076923 0.000000 0.230769 0.615385 0.153846 0.230769 0.692308 0.076923 0.000000 0.615385 0.076923 0.076923 0.230769 0.230769 0.230769 0.153846 0.384615 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.538462 0.000000 0.000000 0.461538 0.153846 0.846154 0.000000 0.000000 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 0.692308 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][GT][CGA]A[GA][GA][GC][CA][AT][TAC]CA[AT]CT[GT] -------------------------------------------------------------------------------- Time 2.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 13 llr = 136 E-value = 2.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :2:3:1:8:2::1:: pos.-specific C ::86:2:1622a:14 probability G 132:5782:35:12: matrix T 95:1512:444:876 bits 2.3 2.0 * 1.8 * 1.6 * * Relative 1.4 * * * * Entropy 1.1 * * * * * ** (15.1 bits) 0.9 * * ***** **** 0.7 ********* ***** 0.5 ********* ***** 0.2 *************** 0.0 --------------- Multilevel TTCCGGGACTGCTTT consensus GGAT T TGT GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 46535 256 5.89e-09 GCAATGTAAA TTCCGGGACGTCTTT CGGCCATCTG 40725 250 7.24e-07 ACGTCCGTTC TGCTGGGACTGCTTC TGTCGATCGT 42514 419 1.47e-06 TCAAACGCCG TGCCGCGATGTCTTC TCGGTCAACG 43726 20 2.03e-06 ATAAAAATGT TACCTGGGTTGCTTT CGATCTTTGT 43725 149 3.07e-06 TTACTGCAGA TTCCTGTATTTCTGT ATCTTGTACT 43268 217 3.07e-06 CACACAACCG TTCCTGTACCGCTGC TCGCTGGTGT 46718 419 3.40e-06 TGGTCGATAT TGCAGCGACTCCTTT TCTTTTGGAT 46763 380 5.41e-06 CTCAAAATTC TTCCTGGACGCCATC AATCACTTTC 48819 113 1.26e-05 TATATGCCTG TTGAGGTGTTGCTTT TCCTACCGTC 15968 167 2.11e-05 ATCTCTCTCG TTCCTTGACAGCGTT CTCTTGAAAA 47465 37 2.11e-05 ATTTTTCTGG TAGAGAGACGTCTTT GATCCCGGAG 42586 230 2.95e-05 CATCTGCCAT TGGATGGCCAGCTGT TGATGGGTTT 49856 48 3.57e-05 GAAACTCACA GTCCGGGATCTCTCC AAGTACAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46535 5.9e-09 255_[+3]_230 40725 7.2e-07 249_[+3]_236 42514 1.5e-06 418_[+3]_67 43726 2e-06 19_[+3]_466 43725 3.1e-06 148_[+3]_337 43268 3.1e-06 216_[+3]_269 46718 3.4e-06 418_[+3]_67 46763 5.4e-06 379_[+3]_106 48819 1.3e-05 112_[+3]_373 15968 2.1e-05 166_[+3]_319 47465 2.1e-05 36_[+3]_449 42586 3e-05 229_[+3]_256 49856 3.6e-05 47_[+3]_438 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=13 46535 ( 256) TTCCGGGACGTCTTT 1 40725 ( 250) TGCTGGGACTGCTTC 1 42514 ( 419) TGCCGCGATGTCTTC 1 43726 ( 20) TACCTGGGTTGCTTT 1 43725 ( 149) TTCCTGTATTTCTGT 1 43268 ( 217) TTCCTGTACCGCTGC 1 46718 ( 419) TGCAGCGACTCCTTT 1 46763 ( 380) TTCCTGGACGCCATC 1 48819 ( 113) TTGAGGTGTTGCTTT 1 15968 ( 167) TTCCTTGACAGCGTT 1 47465 ( 37) TAGAGAGACGTCTTT 1 42586 ( 230) TGGATGGCCAGCTGT 1 49856 ( 48) GTCCGGGATCTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6318 bayes= 8.92184 E= 2.7e+001 -1035 -1035 -143 175 -85 -1035 56 97 -1035 168 15 -1035 15 135 -1035 -183 -1035 -1035 137 75 -185 -64 173 -183 -1035 -1035 188 -25 147 -164 -44 -1035 -1035 135 -1035 49 -85 -64 56 49 -1035 -64 115 49 -1035 205 -1035 -1035 -185 -1035 -143 163 -1035 -164 15 134 -1035 68 -1035 117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 13 E= 2.7e+001 0.000000 0.000000 0.076923 0.923077 0.153846 0.000000 0.307692 0.538462 0.000000 0.769231 0.230769 0.000000 0.307692 0.615385 0.000000 0.076923 0.000000 0.000000 0.538462 0.461538 0.076923 0.153846 0.692308 0.076923 0.000000 0.000000 0.769231 0.230769 0.769231 0.076923 0.153846 0.000000 0.000000 0.615385 0.000000 0.384615 0.153846 0.153846 0.307692 0.384615 0.000000 0.153846 0.461538 0.384615 0.000000 1.000000 0.000000 0.000000 0.076923 0.000000 0.076923 0.846154 0.000000 0.076923 0.230769 0.692308 0.000000 0.384615 0.000000 0.615385 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TG][CG][CA][GT]G[GT]A[CT][TG][GT]CT[TG][TC] -------------------------------------------------------------------------------- Time 4.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42514 1.55e-05 140_[+1(3.85e-05)]_247_\ [+2(1.66e-05)]_3_[+3(1.47e-06)]_67 46535 1.16e-09 77_[+2(9.02e-06)]_119_\ [+1(5.92e-05)]_13_[+1(5.03e-07)]_6_[+3(5.89e-09)]_230 47465 1.61e-06 36_[+3(2.11e-05)]_104_\ [+1(1.20e-06)]_239_[+2(2.89e-06)]_78 48819 1.36e-05 18_[+2(1.16e-06)]_78_[+3(1.26e-05)]_\ 144_[+1(5.52e-05)]_217 15968 1.66e-05 104_[+2(1.33e-05)]_46_\ [+3(2.11e-05)]_287_[+1(3.57e-06)]_20 49856 1.97e-05 47_[+3(3.57e-05)]_8_[+1(2.39e-05)]_\ 395_[+2(1.44e-06)]_7 42586 1.50e-05 229_[+3(2.95e-05)]_38_\ [+1(3.12e-06)]_50_[+2(9.77e-06)]_140 43268 7.29e-08 130_[+2(1.65e-07)]_70_\ [+3(3.07e-06)]_244_[+1(4.71e-06)]_13 43725 2.96e-05 148_[+3(3.07e-06)]_180_\ [+2(1.23e-05)]_118_[+1(5.15e-05)]_11 46718 1.80e-05 153_[+1(3.61e-05)]_206_\ [+2(9.02e-06)]_31_[+3(3.40e-06)]_67 46763 2.21e-05 22_[+2(1.66e-05)]_341_\ [+3(5.41e-06)]_54_[+1(1.55e-05)]_40 40725 1.92e-05 193_[+2(9.02e-06)]_40_\ [+3(7.24e-07)]_236 43726 9.18e-11 19_[+3(2.03e-06)]_261_\ [+1(2.62e-06)]_3_[+2(3.28e-10)]_174 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************