******************************************************************************** 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/135/135.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 51305 1.0000 500 37067 1.0000 500 7342 1.0000 500 38736 1.0000 500 54926 1.0000 500 43482 1.0000 500 15595 1.0000 500 49047 1.0000 500 35185 1.0000 500 36013 1.0000 500 31811 1.0000 500 43044 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/135/135.seqs.fa -oc motifs/135 -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 0.259 C 0.261 G 0.220 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.260 G 0.220 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 8 llr = 93 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::1::1:: pos.-specific C 6a14:5:::5a: probability G 3::1159:1::a matrix T 1:959::a94:: bits 2.2 * 2.0 * * ** 1.7 * * ** 1.5 * * *** ** Relative 1.3 ** * *** ** Entropy 1.1 ** ***** ** (16.7 bits) 0.9 ** ***** ** 0.7 ********* ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCTTTCGTTCCG consensus G C G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 15595 350 3.78e-07 GCAGTAGCAG CCTCTCGTTCCG ATCCGTCACT 43044 447 6.11e-07 CTCTCAGTAA GCTTTCGTTCCG TTGACCACTA 49047 415 1.04e-06 GCAAACCTTT GCTCTGGTTTCG CAATCGACGA 36013 80 1.55e-06 TGTACTGTTT CCTTTGGTGCCG AGTGGGGCGT 35185 193 1.55e-06 AAGAGACAAC CCTCTGGTTACG GAAAGGTCTA 31811 16 3.54e-06 CAATTTGTAG CCCTTCGTTTCG AAACGGTTGA 54926 195 7.01e-06 GAGTTTTGTT CCTGGGGTTTCG ATAGCTGCAA 7342 128 9.88e-06 GAGGATCCAA TCTTTCATTCCG TCATATGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15595 3.8e-07 349_[+1]_139 43044 6.1e-07 446_[+1]_42 49047 1e-06 414_[+1]_74 36013 1.6e-06 79_[+1]_409 35185 1.6e-06 192_[+1]_296 31811 3.5e-06 15_[+1]_473 54926 7e-06 194_[+1]_294 7342 9.9e-06 127_[+1]_361 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=8 15595 ( 350) CCTCTCGTTCCG 1 43044 ( 447) GCTTTCGTTCCG 1 49047 ( 415) GCTCTGGTTTCG 1 36013 ( 80) CCTTTGGTGCCG 1 35185 ( 193) CCTCTGGTTACG 1 31811 ( 16) CCCTTCGTTTCG 1 54926 ( 195) CCTGGGGTTTCG 1 7342 ( 128) TCTTTCATTCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 9.51668 E= 2.3e+002 -965 126 18 -105 -965 194 -965 -965 -965 -106 -965 175 -965 53 -82 94 -965 -965 -82 175 -965 94 118 -965 -105 -965 199 -965 -965 -965 -965 194 -965 -965 -82 175 -105 94 -965 53 -965 194 -965 -965 -965 -965 218 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 2.3e+002 0.000000 0.625000 0.250000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.375000 0.125000 0.500000 0.000000 0.000000 0.125000 0.875000 0.000000 0.500000 0.500000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.125000 0.500000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]CT[TC]T[CG]GTT[CT]CG -------------------------------------------------------------------------------- Time 1.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 5 llr = 84 E-value = 8.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2a:4242:8:a::a:: pos.-specific C :8::::4:6::6::::82 probability G 6:8:8:462824:a8:28 matrix T 42::26:::2::::2::: bits 2.2 * 2.0 * ** * 1.7 * ** * 1.5 * ** * Relative 1.3 **** ** ****** Entropy 1.1 ***** * ********* (24.3 bits) 0.9 ****** * ********* 0.7 ****** *********** 0.4 ****************** 0.2 ****************** 0.0 ------------------ Multilevel GCGAGTCGCGACAGGACG consensus TTA TAGAATGG T GC sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 54926 368 2.05e-10 TCATCGTGAT GCGAGAGACGAGAGGACG GGCTCACACA 35185 372 5.58e-09 CTCGTCGTTC GCGAGTCGCGAGAGGAGC GACGTTTCCC 43044 355 8.97e-09 TCCGGGCAAA GCAAGACAGGACAGGACG TTCATATGGA 36013 265 3.62e-08 CTCCAAGGCA TTGATTGGCTACAGGACG CCGTCGTCCA 49047 20 4.40e-08 TTACATCCAT TCGAGTAGAGGCAGTACG GACAGCGAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54926 2.1e-10 367_[+2]_115 35185 5.6e-09 371_[+2]_111 43044 9e-09 354_[+2]_128 36013 3.6e-08 264_[+2]_218 49047 4.4e-08 19_[+2]_463 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=5 54926 ( 368) GCGAGAGACGAGAGGACG 1 35185 ( 372) GCGAGTCGCGAGAGGAGC 1 43044 ( 355) GCAAGACAGGACAGGACG 1 36013 ( 265) TTGATTGGCTACAGGACG 1 49047 ( 20) TCGAGTAGAGGCAGTACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 5796 bayes= 10.4294 E= 8.9e+002 -897 -897 144 62 -897 162 -897 -38 -37 -897 186 -897 195 -897 -897 -897 -897 -897 186 -38 63 -897 -897 120 -37 62 86 -897 63 -897 144 -897 -37 120 -14 -897 -897 -897 186 -38 162 -897 -14 -897 -897 120 86 -897 195 -897 -897 -897 -897 -897 218 -897 -897 -897 186 -38 195 -897 -897 -897 -897 162 -14 -897 -897 -38 186 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 5 E= 8.9e+002 0.000000 0.000000 0.600000 0.400000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.400000 0.000000 0.000000 0.600000 0.200000 0.400000 0.400000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 0.800000 0.000000 0.200000 0.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][CT][GA]A[GT][TA][CGA][GA][CAG][GT][AG][CG]AG[GT]A[CG][GC] -------------------------------------------------------------------------------- Time 3.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 12 llr = 122 E-value = 8.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :12::311:3:322: pos.-specific C 1262:29:71::231 probability G 821:a::92:92238 matrix T 1628:6::2715531 bits 2.2 * 2.0 * 1.7 * * * 1.5 * ** * Relative 1.3 * ** ** * * Entropy 1.1 * ** ** * * (14.7 bits) 0.9 * ** ** * * 0.7 * ******** * 0.4 ************ * 0.2 ************* * 0.0 --------------- Multilevel GTCTGTCGCTGTTTG consensus A A A C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 7342 42 1.34e-09 ACAGAAATCA GTCTGTCGCTGTTGG GGCTCAAATG 49047 264 8.49e-07 GCGATTTGTT GTCTGTCACTGTGTG AATGCGCGGA 43044 173 9.74e-07 CAGTCTGCCT GTCTGCCGTAGTTTG TGTGGCTCCC 38736 117 2.28e-06 CCGCTAGTTC GATTGTCGCTGGTGG GGGGTAGTTG 51305 63 4.44e-06 ATCAAGCGCT GCCTGACGCAGAACG ACATCTGACT 35185 100 5.38e-06 CGCCCTGTGT GGTTGCCGTTGTTTG GAATCGGGAA 43482 206 1.57e-05 TGTGCACAAA GCATGTCGCTGATAC TTTATTTTAT 31811 451 1.70e-05 GACGAAAAGG GGATGTCGGTTTTGG TTTCTTTACG 36013 428 1.84e-05 ACCCCAAACT GTCCGACGCCGACCG ACAAACCTTG 15595 377 2.13e-05 TCACTGCGCT CTCCGTCGGTGTGCG ACACCGTACT 54926 455 4.24e-05 GAGAAAGCAG TTCTGTAGCAGACTG CCTGGTCTCA 37067 353 6.21e-05 GCAAAATGAA GTGTGACGCTGGAAT CTTGACAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7342 1.3e-09 41_[+3]_444 49047 8.5e-07 263_[+3]_222 43044 9.7e-07 172_[+3]_313 38736 2.3e-06 116_[+3]_369 51305 4.4e-06 62_[+3]_423 35185 5.4e-06 99_[+3]_386 43482 1.6e-05 205_[+3]_280 31811 1.7e-05 450_[+3]_35 36013 1.8e-05 427_[+3]_58 15595 2.1e-05 376_[+3]_109 54926 4.2e-05 454_[+3]_31 37067 6.2e-05 352_[+3]_133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=12 7342 ( 42) GTCTGTCGCTGTTGG 1 49047 ( 264) GTCTGTCACTGTGTG 1 43044 ( 173) GTCTGCCGTAGTTTG 1 38736 ( 117) GATTGTCGCTGGTGG 1 51305 ( 63) GCCTGACGCAGAACG 1 35185 ( 100) GGTTGCCGTTGTTTG 1 43482 ( 206) GCATGTCGCTGATAC 1 31811 ( 451) GGATGTCGGTTTTGG 1 36013 ( 428) GTCCGACGCCGACCG 1 15595 ( 377) CTCCGTCGGTGTGCG 1 54926 ( 455) TTCTGTAGCAGACTG 1 37067 ( 353) GTGTGACGCTGGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5832 bayes= 9.37009 E= 8.7e+002 -1023 -164 192 -164 -163 -64 -40 117 -64 116 -140 -64 -1023 -64 -1023 168 -1023 -1023 218 -1023 -5 -64 -1023 117 -163 181 -1023 -1023 -163 -1023 206 -1023 -1023 135 -40 -64 -5 -164 -1023 136 -1023 -1023 206 -164 36 -1023 -40 94 -64 -64 -40 94 -64 -6 18 36 -1023 -164 192 -164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 12 E= 8.7e+002 0.000000 0.083333 0.833333 0.083333 0.083333 0.166667 0.166667 0.583333 0.166667 0.583333 0.083333 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.250000 0.166667 0.000000 0.583333 0.083333 0.916667 0.000000 0.000000 0.083333 0.000000 0.916667 0.000000 0.000000 0.666667 0.166667 0.166667 0.250000 0.083333 0.000000 0.666667 0.000000 0.000000 0.916667 0.083333 0.333333 0.000000 0.166667 0.500000 0.166667 0.166667 0.166667 0.500000 0.166667 0.250000 0.250000 0.333333 0.000000 0.083333 0.833333 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GTCTG[TA]CGC[TA]G[TA]T[TCG]G -------------------------------------------------------------------------------- Time 4.66 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 51305 3.33e-02 62_[+3(4.44e-06)]_423 37067 2.59e-01 352_[+3(6.21e-05)]_133 7342 4.22e-07 41_[+3(1.34e-09)]_71_[+1(9.88e-06)]_\ 361 38736 1.14e-02 116_[+3(2.28e-06)]_369 54926 2.47e-09 194_[+1(7.01e-06)]_161_\ [+2(2.05e-10)]_69_[+3(4.24e-05)]_31 43482 6.18e-02 205_[+3(1.57e-05)]_280 15595 1.74e-04 349_[+1(3.78e-07)]_15_\ [+3(2.13e-05)]_109 49047 1.64e-09 19_[+2(4.40e-08)]_226_\ [+3(8.49e-07)]_136_[+1(1.04e-06)]_74 35185 1.94e-09 99_[+3(5.38e-06)]_78_[+1(1.55e-06)]_\ 167_[+2(5.58e-09)]_111 36013 3.37e-08 79_[+1(1.55e-06)]_173_\ [+2(3.62e-08)]_145_[+3(1.84e-05)]_58 31811 2.65e-04 15_[+1(3.54e-06)]_423_\ [+3(1.70e-05)]_35 43044 2.60e-10 172_[+3(9.74e-07)]_149_\ [+1(5.88e-05)]_6_[+2(8.97e-09)]_74_[+1(6.11e-07)]_42 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************