******************************************************************************** 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/205/205.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42585 1.0000 500 31617 1.0000 500 43161 1.0000 500 36915 1.0000 500 13664 1.0000 500 4049 1.0000 500 48602 1.0000 500 43447 1.0000 500 32836 1.0000 500 4048 1.0000 500 708 1.0000 500 26853 1.0000 500 11894 1.0000 500 20143 1.0000 500 42464 1.0000 500 31625 1.0000 500 43117 1.0000 500 50332 1.0000 500 49518 1.0000 500 48919 1.0000 500 35961 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/205/205.seqs.fa -oc motifs/205 -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= 21 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= 10500 N= 21 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.246 G 0.224 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.246 G 0.224 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 20 llr = 189 E-value = 5.0e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6::19:5:1587 pos.-specific C :4:3:a1::222 probability G :1371::a:411 matrix T 567:::5:a::2 bits 2.2 * 1.9 * * 1.7 * ** 1.5 ** ** Relative 1.3 ** ** Entropy 1.1 * ** ** (13.6 bits) 0.9 ****** ** * 0.6 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ATTGACTGTAAA consensus TCGC A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 20143 450 2.12e-07 GCCGTTCTTG ATTGACTGTAAA TCGCGTGCAT 31617 67 2.12e-07 CCCTCTGTGT TTTGACTGTGAA TCCGCAGACA 26853 37 7.98e-07 TGTTGATCGA TCTGACTGTGAA TGTAACTTTT 49518 208 2.93e-06 ATACCATATT ACGGACTGTAAA CTCGCATTTC 43447 181 3.32e-06 GACAGTGAGT ACGGACAGTGAA CCGGGACAGA 43117 454 3.85e-06 CTCTATCGTA TCGGACAGTGAA AATCGCTCCC 48602 379 3.85e-06 ACGGTCGGGA ATTGACAGTGAT AGAATCCAAC 4049 15 5.76e-06 AGACGACGAA ATTGACAGTACA AAATCATGAA 4048 15 8.23e-06 AGACGACGAA ATTGACAGTAGA AAATCATGCA 36915 10 1.04e-05 CAGAATTCG ATTCACAGTCAA AATCCCATTG 42585 362 1.04e-05 CAATGAATCG ATTAACAGTAAA ATCAATTTGA 35961 383 1.31e-05 GAATGGAACA ATTCACTGTAAC GTGTAGTACA 48919 323 1.31e-05 CAGAAACGGC TTTGACTGTGAG AGAATTTCTT 32836 141 1.45e-05 TCTACCGCGT TCGCACAGTGAA GTGGAGAAAT 42464 235 5.10e-05 CTCGTTCGAT ACTAACTGTGAC TTCAATTGTC 11894 216 1.10e-04 ATGACGAGCG TCTGGCCGTAAA CCTTCATTCT 50332 284 1.16e-04 CCGTTCTTTT TTGGACTGTCGT AAAGATAAGT 31625 110 1.57e-04 TTTATTTAGA TTGGACAGAACA GCTGATTGGT 13664 10 1.80e-04 ATAAATCAT TGTCACTGTCAT TACTTTCCGC 43161 442 1.89e-04 TGATCTTGTT ATTCGCTGTACC TTTTCTGTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20143 2.1e-07 449_[+1]_39 31617 2.1e-07 66_[+1]_422 26853 8e-07 36_[+1]_452 49518 2.9e-06 207_[+1]_281 43447 3.3e-06 180_[+1]_308 43117 3.9e-06 453_[+1]_35 48602 3.9e-06 378_[+1]_110 4049 5.8e-06 14_[+1]_474 4048 8.2e-06 14_[+1]_474 36915 1e-05 9_[+1]_479 42585 1e-05 361_[+1]_127 35961 1.3e-05 382_[+1]_106 48919 1.3e-05 322_[+1]_166 32836 1.5e-05 140_[+1]_348 42464 5.1e-05 234_[+1]_254 11894 0.00011 215_[+1]_273 50332 0.00012 283_[+1]_205 31625 0.00016 109_[+1]_379 13664 0.00018 9_[+1]_479 43161 0.00019 441_[+1]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=20 20143 ( 450) ATTGACTGTAAA 1 31617 ( 67) TTTGACTGTGAA 1 26853 ( 37) TCTGACTGTGAA 1 49518 ( 208) ACGGACTGTAAA 1 43447 ( 181) ACGGACAGTGAA 1 43117 ( 454) TCGGACAGTGAA 1 48602 ( 379) ATTGACAGTGAT 1 4049 ( 15) ATTGACAGTACA 1 4048 ( 15) ATTGACAGTAGA 1 36915 ( 10) ATTCACAGTCAA 1 42585 ( 362) ATTAACAGTAAA 1 35961 ( 383) ATTCACTGTAAC 1 48919 ( 323) TTTGACTGTGAG 1 32836 ( 141) TCGCACAGTGAA 1 42464 ( 235) ACTAACTGTGAC 1 11894 ( 216) TCTGGCCGTAAA 1 50332 ( 284) TTGGACTGTCGT 1 31625 ( 110) TTGGACAGAACA 1 13664 ( 10) TGTCACTGTCAT 1 43161 ( 442) ATTCGCTGTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 10269 bayes= 9.25326 E= 5.0e-004 101 -1097 -1097 81 -1097 51 -216 122 -1097 -1097 42 144 -145 2 154 -1097 172 -1097 -116 -1097 -1097 202 -1097 -1097 72 -230 -1097 96 -1097 -1097 216 -1097 -245 -1097 -1097 188 72 -71 84 -1097 146 -71 -116 -1097 125 -71 -216 -78 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 20 E= 5.0e-004 0.550000 0.000000 0.000000 0.450000 0.000000 0.350000 0.050000 0.600000 0.000000 0.000000 0.300000 0.700000 0.100000 0.250000 0.650000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.450000 0.050000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.050000 0.000000 0.000000 0.950000 0.450000 0.150000 0.400000 0.000000 0.750000 0.150000 0.100000 0.000000 0.650000 0.150000 0.050000 0.150000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][TC][TG][GC]AC[TA]GT[AG]AA -------------------------------------------------------------------------------- Time 3.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 8 llr = 138 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::86a::863658a43:8:11 pos.-specific C 91:::9::48:::::84194: probability G 19:4::a3::453:4:3::56 matrix T ::3::1::::::::3:411:3 bits 2.2 * 1.9 * * * 1.7 * * * 1.5 ** *** * * Relative 1.3 ** *** * * Entropy 1.1 ************** * * (24.9 bits) 0.9 ************** * ** * 0.6 ************** * **** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGAAACGAACAAAAACCACGG consensus TG GCAGGG GAT CT sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 49518 357 6.19e-11 TCGTTTTCCT CGAGACGGACAGAAACCACGG AATGAGGATG 4048 274 1.44e-10 AGCGGTAGTA CGAAACGACCAAAAGCTACGT TGCAGCGTAC 4049 274 1.44e-10 AGCGGTAGTA CGAAACGACCAAAAGCTACGT TGCAGCGTAC 20143 412 2.15e-09 TTTCAACTTC CGTGACGAAAGGAAACTACCG AATCGCTGCC 43161 44 1.39e-08 AAGAGTCCCA CGAAACGAACGAAATCCTTCG TGTCACTGGT 708 361 5.31e-08 AGAGAAGAAC GGAAACGGAAAGAAGAGACAG GAAATATTCA 42464 190 5.90e-08 ACTGAGATAA CCTAACGAACAGGAAACACGA CTGTTGTTTT 13664 465 6.21e-08 AACCGACGTT CGAGATGACCGAGATCGCCCG TCGGAATCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49518 6.2e-11 356_[+2]_123 4048 1.4e-10 273_[+2]_206 4049 1.4e-10 273_[+2]_206 20143 2.1e-09 411_[+2]_68 43161 1.4e-08 43_[+2]_436 708 5.3e-08 360_[+2]_119 42464 5.9e-08 189_[+2]_290 13664 6.2e-08 464_[+2]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=8 49518 ( 357) CGAGACGGACAGAAACCACGG 1 4048 ( 274) CGAAACGACCAAAAGCTACGT 1 4049 ( 274) CGAAACGACCAAAAGCTACGT 1 20143 ( 412) CGTGACGAAAGGAAACTACCG 1 43161 ( 44) CGAAACGAACGAAATCCTTCG 1 708 ( 361) GGAAACGGAAAGAAGAGACAG 1 42464 ( 190) CCTAACGAACAGGAAACACGA 1 13664 ( 465) CGAGATGACCGAGATCGCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10080 bayes= 10.2981 E= 1.5e-001 -965 183 -84 -965 -965 -98 197 -965 146 -965 -965 -4 119 -965 75 -965 187 -965 -965 -965 -965 183 -965 -104 -965 -965 216 -965 146 -965 16 -965 119 61 -965 -965 -13 161 -965 -965 119 -965 75 -965 87 -965 116 -965 146 -965 16 -965 187 -965 -965 -965 46 -965 75 -4 -13 161 -965 -965 -965 61 16 54 146 -98 -965 -104 -965 183 -965 -104 -113 61 116 -965 -113 -965 148 -4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 1.5e-001 0.000000 0.875000 0.125000 0.000000 0.000000 0.125000 0.875000 0.000000 0.750000 0.000000 0.000000 0.250000 0.625000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.625000 0.375000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.500000 0.000000 0.500000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.375000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.375000 0.250000 0.375000 0.750000 0.125000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.125000 0.375000 0.500000 0.000000 0.125000 0.000000 0.625000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CG[AT][AG]ACG[AG][AC][CA][AG][AG][AG]A[AGT][CA][CTG]AC[GC][GT] -------------------------------------------------------------------------------- Time 7.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 6 llr = 107 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:::2:::7:3::3a5: pos.-specific C :78::a7a283a3::3:52 probability G :3::8:::5::::a72::8 matrix T a::a2:2:32::3:32::: bits 2.2 * 1.9 * * * * * * * 1.7 * * * * * * * 1.5 * *** * * * * * Relative 1.3 * **** * * * * * * Entropy 1.1 ****** * *** ** * * (25.8 bits) 0.9 ****** * *** ** *** 0.6 ************ ** *** 0.4 *************** *** 0.2 *************** *** 0.0 ------------------- Multilevel TCCTGCCCGCACAGGAAAG consensus G T C C TC C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 4048 445 6.05e-11 TCGTCCGAAC TCCTGCCCGCCCCGGAACG TCGCCGACCC 4049 445 6.05e-11 TCGTCCGAAC TCCTGCCCGCCCCGGAACG TCGCCGACCC 11894 104 2.48e-09 GTTTCGGAAT TGCTGCTCTCACAGGCACG TAGCGATGAT 32836 357 9.80e-09 CAGAGTAAAC TCCTTCCCCCACTGTCAAG CTGGCATCGA 36915 337 1.61e-08 TTTCGGTACA TGATGCACGCACAGGGAAG AAAGAAACTA 20143 347 3.07e-08 TTTTTCTCTT TCCTGCCCTTACTGTTAAC TTTCGATACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4048 6.1e-11 444_[+3]_37 4049 6.1e-11 444_[+3]_37 11894 2.5e-09 103_[+3]_378 32836 9.8e-09 356_[+3]_125 36915 1.6e-08 336_[+3]_145 20143 3.1e-08 346_[+3]_135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=6 4048 ( 445) TCCTGCCCGCCCCGGAACG 1 4049 ( 445) TCCTGCCCGCCCCGGAACG 1 11894 ( 104) TGCTGCTCTCACAGGCACG 1 32836 ( 357) TCCTTCCCCCACTGTCAAG 1 36915 ( 337) TGATGCACGCACAGGGAAG 1 20143 ( 347) TCCTGCCCTTACTGTTAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 10122 bayes= 11.1671 E= 1.1e+000 -923 -923 -923 196 -923 144 58 -923 -71 176 -923 -923 -923 -923 -923 196 -923 -923 190 -62 -923 202 -923 -923 -71 144 -923 -62 -923 202 -923 -923 -923 -56 116 37 -923 176 -923 -62 129 44 -923 -923 -923 202 -923 -923 29 44 -923 37 -923 -923 216 -923 -923 -923 157 37 29 44 -42 -62 187 -923 -923 -923 87 102 -923 -923 -923 -56 190 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 6 E= 1.1e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 1.000000 0.000000 0.000000 0.166667 0.666667 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.500000 0.333333 0.000000 0.833333 0.000000 0.166667 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.333333 0.333333 0.166667 0.166667 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CG]CTGCCC[GT]C[AC]C[ACT]G[GT][AC]A[AC]G -------------------------------------------------------------------------------- Time 11.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42585 4.76e-02 361_[+1(1.04e-05)]_127 31617 7.46e-04 66_[+1(2.12e-07)]_422 43161 6.22e-05 43_[+2(1.39e-08)]_436 36915 4.82e-06 9_[+1(1.04e-05)]_315_[+3(1.61e-08)]_\ 145 13664 2.17e-04 464_[+2(6.21e-08)]_15 4049 4.70e-15 14_[+1(5.76e-06)]_247_\ [+2(1.44e-10)]_150_[+3(6.05e-11)]_37 48602 2.30e-02 378_[+1(3.85e-06)]_110 43447 2.89e-02 43_[+1(1.93e-05)]_106_\ [+1(6.43e-06)]_7_[+1(3.32e-06)]_163_[+1(6.34e-05)]_133 32836 5.34e-06 140_[+1(1.45e-05)]_204_\ [+3(9.80e-09)]_125 4048 6.60e-15 14_[+1(8.23e-06)]_247_\ [+2(1.44e-10)]_150_[+3(6.05e-11)]_37 708 5.31e-04 360_[+2(5.31e-08)]_119 26853 8.33e-03 36_[+1(7.98e-07)]_452 11894 9.23e-07 103_[+3(2.48e-09)]_378 20143 9.74e-13 346_[+3(3.07e-08)]_46_\ [+2(2.15e-09)]_17_[+1(2.12e-07)]_39 42464 5.23e-05 189_[+2(5.90e-08)]_24_\ [+1(5.10e-05)]_254 31625 1.53e-01 500 43117 6.74e-03 453_[+1(3.85e-06)]_35 50332 1.50e-01 500 49518 6.84e-09 207_[+1(2.93e-06)]_137_\ [+2(6.19e-11)]_123 48919 5.96e-03 19_[+1(2.50e-05)]_291_\ [+1(1.31e-05)]_166 35961 1.11e-02 382_[+1(1.31e-05)]_106 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************