******************************************************************************** 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/130/130.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 24474 1.0000 500 9164 1.0000 500 43144 1.0000 500 8230 1.0000 500 37018 1.0000 500 48306 1.0000 500 48322 1.0000 500 15323 1.0000 500 25331 1.0000 500 49091 1.0000 500 42274 1.0000 500 49172 1.0000 500 40626 1.0000 500 49829 1.0000 500 41287 1.0000 500 50425 1.0000 500 44382 1.0000 500 19244 1.0000 500 12188 1.0000 500 45854 1.0000 500 44485 1.0000 500 34991 1.0000 500 49307 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/130/130.seqs.fa -oc motifs/130 -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= 23 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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.244 G 0.225 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.244 G 0.225 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 22 llr = 197 E-value = 9.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 31::a142::a6 pos.-specific C :6:3:81::2:2 probability G 3::4:::8:4:2 matrix T 43a3::5:a4:: bits 2.1 1.9 * 1.7 * * * * 1.5 * * ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** * (12.9 bits) 0.9 * ** ** * 0.6 ** ***** ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCTGACTGTGAA consensus AT T A T sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 8230 62 3.18e-07 CCTCGAGAAA ACTGACTGTGAA TGCAACATAA 9164 314 6.43e-07 GTATAGAGCA TCTGACAGTTAA TTCCGAATTC 41287 114 1.50e-06 TTCACAACGG TCTTACTGTTAA TTTGTACGTC 40626 112 1.50e-06 TTCACAACGG TCTTACTGTTAA TTTGTACGTC 25331 400 3.22e-06 GTGGTGTGGT GTTGACTGTGAA CTCGATGGTC 37018 187 3.98e-06 AATATAAGAG ACTGACTGTGAG GCAGTCAAAC 44382 199 4.53e-06 CGAGTACTGC ACTGACTGTGAC TGTGCACGCC 50425 281 6.52e-06 AGTACGAATA TCTGACAGTTAC CGTACTGTCG 45854 362 1.78e-05 GTTCTCTTAC TCTTAATGTGAA ATAGCGTTTC 34991 210 2.40e-05 AAACTTGGTC GTTCACAGTCAA TCAGAGCAAG 48322 321 2.40e-05 ACCGCGCTTA GTTGACCGTGAA GGCCTTTTTC 24474 487 2.90e-05 TATCACCAAG AATCACTGTTAA CA 19244 96 4.22e-05 TGACATATGG TCTCACAATCAA GAAGATGCAT 49307 221 5.02e-05 CAGAAAGGCC ATTCACAATGAA TTCTAAGTGA 49829 437 5.41e-05 GTTGAAATTT TATCACAGTCAA CAAATTCAAG 43144 458 5.96e-05 GAGTGCGGCA GCTTACTATTAG ATTGGGGAGA 44485 367 9.48e-05 GGCTTTTTGT GCTTACCGTCAC TCTTCGCTCG 15323 146 1.50e-04 AAATGAAAAT TCTGAAAATGAG CTTTTCCCAC 48306 338 1.50e-04 CGTACTCACA ATTCACAGTTCA TCGACGGAGA 42274 164 1.67e-04 ACAAGTAGTA GCTTATAGTTAG AATCAAAAAC 49091 153 1.76e-04 TGCGCCGGCC ACAGAATGTGAA ATGGCTTATT 49172 419 2.33e-04 CCTACAGCCA TTTTGCTGTTAC CTGCTCAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8230 3.2e-07 61_[+1]_427 9164 6.4e-07 313_[+1]_175 41287 1.5e-06 113_[+1]_375 40626 1.5e-06 111_[+1]_377 25331 3.2e-06 399_[+1]_89 37018 4e-06 186_[+1]_302 44382 4.5e-06 198_[+1]_290 50425 6.5e-06 280_[+1]_208 45854 1.8e-05 361_[+1]_127 34991 2.4e-05 209_[+1]_279 48322 2.4e-05 320_[+1]_168 24474 2.9e-05 486_[+1]_2 19244 4.2e-05 95_[+1]_393 49307 5e-05 220_[+1]_268 49829 5.4e-05 436_[+1]_52 43144 6e-05 457_[+1]_31 44485 9.5e-05 366_[+1]_122 15323 0.00015 145_[+1]_343 48306 0.00015 337_[+1]_151 42274 0.00017 163_[+1]_325 49091 0.00018 152_[+1]_336 49172 0.00023 418_[+1]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=22 8230 ( 62) ACTGACTGTGAA 1 9164 ( 314) TCTGACAGTTAA 1 41287 ( 114) TCTTACTGTTAA 1 40626 ( 112) TCTTACTGTTAA 1 25331 ( 400) GTTGACTGTGAA 1 37018 ( 187) ACTGACTGTGAG 1 44382 ( 199) ACTGACTGTGAC 1 50425 ( 281) TCTGACAGTTAC 1 45854 ( 362) TCTTAATGTGAA 1 34991 ( 210) GTTCACAGTCAA 1 48322 ( 321) GTTGACCGTGAA 1 24474 ( 487) AATCACTGTTAA 1 19244 ( 96) TCTCACAATCAA 1 49307 ( 221) ATTCACAATGAA 1 49829 ( 437) TATCACAGTCAA 1 43144 ( 458) GCTTACTATTAG 1 44485 ( 367) GCTTACCGTCAC 1 15323 ( 146) TCTGAAAATGAG 1 48306 ( 338) ATTCACAGTTCA 1 42274 ( 164) GCTTATAGTTAG 1 49091 ( 153) ACAGAATGTGAA 1 49172 ( 419) TTTTGCTGTTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 9.35071 E= 9.0e-002 28 -1110 27 60 -152 138 -1110 2 -252 -1110 -1110 183 -1110 16 86 24 187 -1110 -231 -1110 -94 175 -1110 -256 64 -142 -1110 89 -52 -1110 186 -1110 -1110 -1110 -1110 189 -1110 -42 86 60 187 -242 -1110 -1110 128 -42 -31 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 22 E= 9.0e-002 0.318182 0.000000 0.272727 0.409091 0.090909 0.636364 0.000000 0.272727 0.045455 0.000000 0.000000 0.954545 0.000000 0.272727 0.409091 0.318182 0.954545 0.000000 0.045455 0.000000 0.136364 0.818182 0.000000 0.045455 0.409091 0.090909 0.000000 0.500000 0.181818 0.000000 0.818182 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.409091 0.409091 0.954545 0.045455 0.000000 0.000000 0.636364 0.181818 0.181818 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TAG][CT]T[GTC]AC[TA]GT[GT]AA -------------------------------------------------------------------------------- Time 5.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 115 E-value = 3.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::282::5::25:8::528: pos.-specific C ::a2:82::2a3:7:322:2: probability G a3:72:8a:8:553:7738:8 matrix T :7::::::5:::::2:2:::2 bits 2.1 * * 1.9 * * * * 1.7 * * * * 1.5 * * ** ** * * Relative 1.3 * * **** ** ** *** Entropy 1.1 *** **** ** **** *** (27.7 bits) 0.9 *********** ***** *** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTCGACGGAGCGACAGGAGAG consensus G T CGG C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41287 214 3.86e-13 TTCCCTTCCC GTCGACGGAGCGACAGGAGAG ACTTGCGCCT 40626 212 3.86e-13 TTCCCTTCCC GTCGACGGAGCGACAGGAGAG ACTTGCGCCT 12188 476 2.89e-09 GTGACGGCAT GGCGACGGTGCAAGTCGCGAG ACAT 49307 62 3.52e-09 GCGGGGACGA GTCGACCGTGCCGCACCGGCG CGGGTCGGTG 9164 28 5.02e-09 AAATAGCTAT GGCAAAGGAGCCGGAGTGGAG GCAAGAGGAA 34991 338 1.38e-08 TTCGCTGCTC GTCCGCGGTCCGGCAGGAAAT CACTGCCAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41287 3.9e-13 213_[+2]_266 40626 3.9e-13 211_[+2]_268 12188 2.9e-09 475_[+2]_4 49307 3.5e-09 61_[+2]_418 9164 5e-09 27_[+2]_452 34991 1.4e-08 337_[+2]_142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 41287 ( 214) GTCGACGGAGCGACAGGAGAG 1 40626 ( 212) GTCGACGGAGCGACAGGAGAG 1 12188 ( 476) GGCGACGGTGCAAGTCGCGAG 1 49307 ( 62) GTCGACCGTGCCGCACCGGCG 1 9164 ( 28) GGCAAAGGAGCCGGAGTGGAG 1 34991 ( 338) GTCCGCGGTCCGGCAGGAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 11.9447 E= 3.8e-001 -923 -923 215 -923 -923 -923 56 131 -923 203 -923 -923 -65 -55 156 -923 167 -923 -44 -923 -65 177 -923 -923 -923 -55 188 -923 -923 -923 215 -923 93 -923 -923 89 -923 -55 188 -923 -923 203 -923 -923 -65 45 115 -923 93 -923 115 -923 -923 145 56 -923 167 -923 -923 -69 -923 45 156 -923 -923 -55 156 -69 93 -55 56 -923 -65 -923 188 -923 167 -55 -923 -923 -923 -923 188 -69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 3.8e-001 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.833333 0.000000 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.666667 0.333333 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.333333 0.666667 0.000000 0.000000 0.166667 0.666667 0.166667 0.500000 0.166667 0.333333 0.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TG]CGACGG[AT]GC[GC][AG][CG]A[GC]G[AG]GAG -------------------------------------------------------------------------------- Time 11.54 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 94 E-value = 3.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::8::3:::a8:3::aaa pos.-specific C 8::8:::3::3::3::::::: probability G 3::3a::83::a::a:8a::: matrix T :aa::3a:5a8::::83:::: bits 2.1 * * * * 1.9 ** * * * ** * **** 1.7 ** * * * ** * **** 1.5 ** * * * ** * **** Relative 1.3 ***** ** * ** * ***** Entropy 1.1 ******** ************ (33.9 bits) 0.9 ******** ************ 0.6 ******** ************ 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CTTCGATGTTTGAAGTGGAAA consensus G G T CA C C AT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41287 39 2.55e-13 TGAAAATAGC CTTCGATGTTTGAAGTGGAAA AGGGCGGGAT 40626 37 2.55e-13 TGAAAATAGC CTTCGATGTTTGAAGTGGAAA AGGGCGGGAT 44485 288 4.58e-11 GACCAAGACC GTTCGTTGGTTGAAGAGGAAA GGTTACTCTA 49091 435 1.49e-10 GCTTCGGTAG CTTGGATCATCGACGTTGAAA GCCACTGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41287 2.5e-13 38_[+3]_441 40626 2.5e-13 36_[+3]_443 44485 4.6e-11 287_[+3]_192 49091 1.5e-10 434_[+3]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 41287 ( 39) CTTCGATGTTTGAAGTGGAAA 1 40626 ( 37) CTTCGATGTTTGAAGTGGAAA 1 44485 ( 288) GTTCGTTGGTTGAAGAGGAAA 1 49091 ( 435) CTTGGATCATCGACGTTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 11.4299 E= 3.0e+000 -865 162 15 -865 -865 -865 -865 189 -865 -865 -865 189 -865 162 15 -865 -865 -865 215 -865 152 -865 -865 -11 -865 -865 -865 189 -865 4 173 -865 -7 -865 15 89 -865 -865 -865 189 -865 4 -865 148 -865 -865 215 -865 193 -865 -865 -865 152 4 -865 -865 -865 -865 215 -865 -7 -865 -865 148 -865 -865 173 -11 -865 -865 215 -865 193 -865 -865 -865 193 -865 -865 -865 193 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.0e+000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG]TT[CG]G[AT]T[GC][TAG]T[TC]GA[AC]G[TA][GT]GAAA -------------------------------------------------------------------------------- Time 16.87 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24474 7.33e-02 419_[+1(6.46e-05)]_55_\ [+1(2.90e-05)]_2 9164 1.76e-07 27_[+2(5.02e-09)]_265_\ [+1(6.43e-07)]_69_[+1(3.60e-05)]_94 43144 1.38e-01 457_[+1(5.96e-05)]_31 8230 4.89e-04 61_[+1(3.18e-07)]_427 37018 1.33e-02 186_[+1(3.98e-06)]_302 48306 1.03e-01 500 48322 1.92e-02 320_[+1(2.40e-05)]_168 15323 5.01e-02 500 25331 1.41e-02 399_[+1(3.22e-06)]_89 49091 8.86e-07 434_[+3(1.49e-10)]_45 42274 4.97e-01 500 49172 1.20e-01 500 40626 2.38e-20 36_[+3(2.55e-13)]_54_[+1(1.50e-06)]_\ 88_[+2(3.86e-13)]_268 49829 9.94e-02 436_[+1(5.41e-05)]_52 41287 2.38e-20 38_[+3(2.55e-13)]_54_[+1(1.50e-06)]_\ 88_[+2(3.86e-13)]_266 50425 4.59e-02 248_[+1(6.95e-05)]_20_\ [+1(6.52e-06)]_208 44382 1.16e-03 114_[+2(8.96e-05)]_63_\ [+1(4.53e-06)]_290 19244 1.27e-01 95_[+1(4.22e-05)]_393 12188 7.01e-05 475_[+2(2.89e-09)]_4 45854 1.31e-02 361_[+1(1.78e-05)]_127 44485 1.33e-07 287_[+3(4.58e-11)]_58_\ [+1(9.48e-05)]_122 34991 7.79e-06 209_[+1(2.40e-05)]_116_\ [+2(1.38e-08)]_142 49307 6.50e-06 61_[+2(3.52e-09)]_138_\ [+1(5.02e-05)]_268 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************