******************************************************************************** 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/257/257.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42871 1.0000 500 47187 1.0000 500 47353 1.0000 500 54940 1.0000 500 43386 1.0000 500 32656 1.0000 500 54143 1.0000 500 40942 1.0000 500 44822 1.0000 500 34810 1.0000 500 12587 1.0000 500 42546 1.0000 500 45178 1.0000 500 33977 1.0000 500 38280 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/257/257.seqs.fa -oc motifs/257 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.252 C 0.252 G 0.239 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.252 G 0.239 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 11 llr = 151 E-value = 1.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 935669162::5851:63::: pos.-specific C 1:1:2:5:2521124:126:3 probability G :354115:65841359322a7 matrix T :5::1::4:::1:::1:42:: bits 2.1 * 1.9 * 1.7 * * * * 1.4 * * * * * Relative 1.2 * * * * ** Entropy 1.0 * * * * ** * * ** (19.8 bits) 0.8 * * * **** * ** ** 0.6 * ** ****** ***** *** 0.4 ***************** *** 0.2 ***************** *** 0.0 --------------------- Multilevel ATAAAACAGGGAAAGGATCGG consensus AGG GT C G GC GA C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 47353 29 6.12e-11 ATACAAGGAG ATGGAAGAGCGGAAGGAACGG GTACAGAAGC 42546 22 2.32e-08 CAACGCTGGC ATAGAACAACGAAAGGGTTGG AAAGCTGACA 38280 335 3.25e-08 GGTCCAACCA ATAGAAGAGCGACACGATCGC CGAACGAGGG 47187 459 3.25e-08 TTCTAGATCG AGGACACTGGCAAGGGATCGG CAACTTTGGC 45178 245 1.11e-07 ATAGGTAAAT AGAATAATGGGGAAGGACCGG GCAACAAGTC 43386 252 3.20e-07 TCCGATACTT AAGAAAGTAGGAAGCGGTTGC CTGTATGTAG 40942 341 4.40e-07 AACCCCGACA ATGACACTGGCAACCGAGGGG GTCGTGGGGG 12587 318 7.43e-07 ACGTCTTTCC CGCAAAGAGCGTAAGGAACGC AATCAGAACG 33977 203 9.84e-07 TTGATTGGCG AAAAGAGAGGGGGGGGGGGGG GGGGGGCGTC 44822 205 1.46e-06 TTTAATTTTG AAAAAACACCGCAAATAACGG TAAACATCGA 32656 224 1.66e-06 GAATTTATGA ATGGAGCACGGGACCGCCCGG TGTTGGATGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47353 6.1e-11 28_[+1]_451 42546 2.3e-08 21_[+1]_458 38280 3.3e-08 334_[+1]_145 47187 3.3e-08 458_[+1]_21 45178 1.1e-07 244_[+1]_235 43386 3.2e-07 251_[+1]_228 40942 4.4e-07 340_[+1]_139 12587 7.4e-07 317_[+1]_162 33977 9.8e-07 202_[+1]_277 44822 1.5e-06 204_[+1]_275 32656 1.7e-06 223_[+1]_256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=11 47353 ( 29) ATGGAAGAGCGGAAGGAACGG 1 42546 ( 22) ATAGAACAACGAAAGGGTTGG 1 38280 ( 335) ATAGAAGAGCGACACGATCGC 1 47187 ( 459) AGGACACTGGCAAGGGATCGG 1 45178 ( 245) AGAATAATGGGGAAGGACCGG 1 43386 ( 252) AAGAAAGTAGGAAGCGGTTGC 1 40942 ( 341) ATGACACTGGCAACCGAGGGG 1 12587 ( 318) CGCAAAGAGCGTAAGGAACGC 1 33977 ( 203) AAAAGAGAGGGGGGGGGGGGG 1 44822 ( 205) AAAAAACACCGCAAATAACGG 1 32656 ( 224) ATGGAGCACGGGACCGCCCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 9.70772 E= 1.0e+001 185 -147 -1010 -1010 12 -1010 19 82 85 -147 93 -1010 134 -1010 61 -1010 134 -47 -139 -150 185 -1010 -139 -1010 -147 85 93 -1010 134 -1010 -1010 50 -47 -47 141 -1010 -1010 85 119 -1010 -1010 -47 178 -1010 85 -147 61 -150 170 -147 -139 -1010 111 -47 19 -1010 -147 53 119 -1010 -1010 -1010 193 -150 134 -147 19 -1010 12 -47 -39 50 -1010 134 -39 -50 -1010 -1010 207 -1010 -1010 11 161 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 1.0e+001 0.909091 0.090909 0.000000 0.000000 0.272727 0.000000 0.272727 0.454545 0.454545 0.090909 0.454545 0.000000 0.636364 0.000000 0.363636 0.000000 0.636364 0.181818 0.090909 0.090909 0.909091 0.000000 0.090909 0.000000 0.090909 0.454545 0.454545 0.000000 0.636364 0.000000 0.000000 0.363636 0.181818 0.181818 0.636364 0.000000 0.000000 0.454545 0.545455 0.000000 0.000000 0.181818 0.818182 0.000000 0.454545 0.090909 0.363636 0.090909 0.818182 0.090909 0.090909 0.000000 0.545455 0.181818 0.272727 0.000000 0.090909 0.363636 0.545455 0.000000 0.000000 0.000000 0.909091 0.090909 0.636364 0.090909 0.272727 0.000000 0.272727 0.181818 0.181818 0.363636 0.000000 0.636364 0.181818 0.181818 0.000000 0.000000 1.000000 0.000000 0.000000 0.272727 0.727273 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[TAG][AG][AG]AA[CG][AT]G[GC]G[AG]A[AG][GC]G[AG][TA]CG[GC] -------------------------------------------------------------------------------- Time 2.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 11 llr = 134 E-value = 2.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :17:4:::a152::61 pos.-specific C :5:912:5:5:1:72: probability G 133::831:4:72:29 matrix T 92:15:75::5:83:: bits 2.1 * 1.9 * 1.7 * * 1.4 * * * * * Relative 1.2 * ** ** * * * Entropy 1.0 * ** ** * **** * (17.6 bits) 0.8 * ** ** * **** * 0.6 * ************** 0.4 * ************** 0.2 **************** 0.0 ---------------- Multilevel TCACTGTCACTGTCAG consensus GG A GT GA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 38280 245 7.62e-10 CGGTTTTACT TCACTGTCACAGTCAG TGAGTGAGTT 32656 317 7.62e-10 CTGTCCGTAC TCACTGTCACAGTCAG TGTCGTTACA 44822 365 2.12e-08 CCATATCAAA TCACAGTTACTGTTAG TCTTTGTAAC 40942 132 9.00e-07 GACTGGACAG TGACAGTGAGAGTCCG CGAAGAAAAG 54940 31 1.38e-06 TATGAAGAAT TTACAGTTAGAATCCG TCTTACGAGA 54143 82 2.56e-06 GAGCTACCCG TAGCTCGTACAGTCAG GTGGGCAAGC 47187 133 2.93e-06 GAGTGGCCTA TCGCCGGCAGTGGCAG CCGCCGTTGT 43386 18 3.38e-06 GATCGGGCTA GGACTGGTAGTGGCAG ATCGCTTGCG 42546 419 5.96e-06 TTAGGTTATG TTACAGTTACTATTAA TTGGTGTTGC 34810 239 5.96e-06 CATCCGGGTT TCACTGTCAATCTTGG TAATATTTCT 45178 216 7.13e-06 TTGGTCGCGG TGGTTCTCACTGTCGG TCAATAGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38280 7.6e-10 244_[+2]_240 32656 7.6e-10 316_[+2]_168 44822 2.1e-08 364_[+2]_120 40942 9e-07 131_[+2]_353 54940 1.4e-06 30_[+2]_454 54143 2.6e-06 81_[+2]_403 47187 2.9e-06 132_[+2]_352 43386 3.4e-06 17_[+2]_467 42546 6e-06 418_[+2]_66 34810 6e-06 238_[+2]_246 45178 7.1e-06 215_[+2]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=11 38280 ( 245) TCACTGTCACAGTCAG 1 32656 ( 317) TCACTGTCACAGTCAG 1 44822 ( 365) TCACAGTTACTGTTAG 1 40942 ( 132) TGACAGTGAGAGTCCG 1 54940 ( 31) TTACAGTTAGAATCCG 1 54143 ( 82) TAGCTCGTACAGTCAG 1 47187 ( 133) TCGCCGGCAGTGGCAG 1 43386 ( 18) GGACTGGTAGTGGCAG 1 42546 ( 419) TTACAGTTACTATTAA 1 34810 ( 239) TCACTGTCAATCTTGG 1 45178 ( 216) TGGTTCTCACTGTCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7275 bayes= 9.72269 E= 2.9e+001 -1010 -1010 -139 182 -147 85 19 -50 153 -1010 19 -1010 -1010 185 -1010 -150 53 -147 -1010 108 -1010 -47 178 -1010 -1010 -1010 19 150 -1010 85 -139 82 199 -1010 -1010 -1010 -147 111 61 -1010 85 -1010 -1010 108 -47 -147 161 -1010 -1010 -1010 -39 167 -1010 153 -1010 8 134 -47 -39 -1010 -147 -1010 193 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 2.9e+001 0.000000 0.000000 0.090909 0.909091 0.090909 0.454545 0.272727 0.181818 0.727273 0.000000 0.272727 0.000000 0.000000 0.909091 0.000000 0.090909 0.363636 0.090909 0.000000 0.545455 0.000000 0.181818 0.818182 0.000000 0.000000 0.000000 0.272727 0.727273 0.000000 0.454545 0.090909 0.454545 1.000000 0.000000 0.000000 0.000000 0.090909 0.545455 0.363636 0.000000 0.454545 0.000000 0.000000 0.545455 0.181818 0.090909 0.727273 0.000000 0.000000 0.000000 0.181818 0.818182 0.000000 0.727273 0.000000 0.272727 0.636364 0.181818 0.181818 0.000000 0.090909 0.000000 0.909091 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CG][AG]C[TA]G[TG][CT]A[CG][TA]GT[CT]AG -------------------------------------------------------------------------------- Time 3.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 11 llr = 131 E-value = 3.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:::::::::1:2::8 pos.-specific C 21::55:4:::a5341 probability G :1:253:3522:3611 matrix T 68a8:3a4587::15: bits 2.1 * 1.9 * * * 1.7 * * * 1.4 * * * Relative 1.2 ** * * * Entropy 1.0 **** * ** * * (17.2 bits) 0.8 **** * **** * * 0.6 ***** * ******** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TTTTGCTCGTTCCGTA consensus CG TT GCC sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 54143 143 1.13e-09 GCCCCCCTTT TTTTCCTCGTTCCGTA CGGAACACCC 47187 198 7.57e-08 ACGTGAACGC TTTTGCTGTTTCCCCA AGACATGGTA 34810 215 4.91e-07 CACTCAGACA TTTTCCTGTTTCACCA TCCGGGTTTC 38280 277 1.18e-06 AGTTTCGAAG TTTGGGTCTTTCGCTA GAGGTGTCCA 40942 466 1.29e-06 ACACTACAAC ATTTGTTTGGTCGGTA ATTTCCGATT 42871 448 1.41e-06 TCGGCATTGT TGTTCCTTTGTCCGTA GTCGAGAAGC 47353 224 2.16e-06 TACAATGAAT TTTTGCTTGTGCGTCA TAGGCCATGT 33977 165 3.66e-06 ATGTATTTGA ATTTCTTTTTGCAGCA TCGTACATCC 43386 38 3.66e-06 TGGCAGATCG CTTGCGTCGTTCCGGA ACGCTGCTCA 32656 29 4.52e-06 CGGATTGTGG TCTTGTTGGTTCCGTG TCTTGGTGGG 45178 420 8.45e-06 GCATCGCACT CTTTGGTCGTACCGTC TCGTCCGACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54143 1.1e-09 142_[+3]_342 47187 7.6e-08 197_[+3]_287 34810 4.9e-07 214_[+3]_270 38280 1.2e-06 276_[+3]_208 40942 1.3e-06 465_[+3]_19 42871 1.4e-06 447_[+3]_37 47353 2.2e-06 223_[+3]_261 33977 3.7e-06 164_[+3]_320 43386 3.7e-06 37_[+3]_447 32656 4.5e-06 28_[+3]_456 45178 8.5e-06 419_[+3]_65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=11 54143 ( 143) TTTTCCTCGTTCCGTA 1 47187 ( 198) TTTTGCTGTTTCCCCA 1 34810 ( 215) TTTTCCTGTTTCACCA 1 38280 ( 277) TTTGGGTCTTTCGCTA 1 40942 ( 466) ATTTGTTTGGTCGGTA 1 42871 ( 448) TGTTCCTTTGTCCGTA 1 47353 ( 224) TTTTGCTTGTGCGTCA 1 33977 ( 165) ATTTCTTTTTGCAGCA 1 43386 ( 38) CTTGCGTCGTTCCGGA 1 32656 ( 29) TCTTGTTGGTTCCGTG 1 45178 ( 420) CTTTGGTCGTACCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7275 bayes= 9.72269 E= 3.8e+003 -47 -47 -1010 130 -1010 -147 -139 167 -1010 -1010 -1010 196 -1010 -1010 -39 167 -1010 85 119 -1010 -1010 85 19 8 -1010 -1010 -1010 196 -1010 53 19 50 -1010 -1010 119 82 -1010 -1010 -39 167 -147 -1010 -39 150 -1010 199 -1010 -1010 -47 111 19 -1010 -1010 11 141 -150 -1010 53 -139 108 170 -147 -139 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 3.8e+003 0.181818 0.181818 0.000000 0.636364 0.000000 0.090909 0.090909 0.818182 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.181818 0.818182 0.000000 0.454545 0.545455 0.000000 0.000000 0.454545 0.272727 0.272727 0.000000 0.000000 0.000000 1.000000 0.000000 0.363636 0.272727 0.363636 0.000000 0.000000 0.545455 0.454545 0.000000 0.000000 0.181818 0.818182 0.090909 0.000000 0.181818 0.727273 0.000000 1.000000 0.000000 0.000000 0.181818 0.545455 0.272727 0.000000 0.000000 0.272727 0.636364 0.090909 0.000000 0.363636 0.090909 0.545455 0.818182 0.090909 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TTTT[GC][CGT]T[CTG][GT]TTC[CG][GC][TC]A -------------------------------------------------------------------------------- Time 5.73 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42871 1.22e-02 447_[+3(1.41e-06)]_37 47187 3.39e-10 132_[+2(2.93e-06)]_49_\ [+3(7.57e-08)]_245_[+1(3.25e-08)]_21 47353 4.39e-09 28_[+1(6.12e-11)]_45_[+1(1.18e-05)]_\ 108_[+3(2.16e-06)]_261 54940 1.18e-03 30_[+2(1.38e-06)]_183_\ [+1(8.66e-05)]_250 43386 1.13e-07 17_[+2(3.38e-06)]_4_[+3(3.66e-06)]_\ 198_[+1(3.20e-07)]_228 32656 2.72e-10 28_[+3(4.52e-06)]_179_\ [+1(1.66e-06)]_72_[+2(7.62e-10)]_22_[+2(8.03e-05)]_130 54143 1.00e-07 81_[+2(2.56e-06)]_45_[+3(1.13e-09)]_\ 342 40942 1.75e-08 131_[+2(9.00e-07)]_193_\ [+1(4.40e-07)]_104_[+3(1.29e-06)]_19 44822 1.39e-06 204_[+1(1.46e-06)]_139_\ [+2(2.12e-08)]_120 34810 4.28e-05 214_[+3(4.91e-07)]_8_[+2(5.96e-06)]_\ 246 12587 9.57e-03 317_[+1(7.43e-07)]_130_\ [+1(2.17e-05)]_11 42546 4.59e-06 21_[+1(2.32e-08)]_376_\ [+2(5.96e-06)]_66 45178 1.83e-07 215_[+2(7.13e-06)]_13_\ [+1(1.11e-07)]_154_[+3(8.45e-06)]_65 33977 1.61e-05 164_[+3(3.66e-06)]_22_\ [+1(9.84e-07)]_277 38280 1.95e-12 244_[+2(7.62e-10)]_16_\ [+3(1.18e-06)]_42_[+1(3.25e-08)]_145 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************