******************************************************************************** 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/149/149.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10898 1.0000 500 11163 1.0000 500 11169 1.0000 500 11271 1.0000 500 11719 1.0000 500 22148 1.0000 500 24348 1.0000 500 261470 1.0000 500 261878 1.0000 500 268314 1.0000 500 30701 1.0000 500 31771 1.0000 500 36764 1.0000 500 37867 1.0000 500 38656 1.0000 500 4064 1.0000 500 4068 1.0000 500 6486 1.0000 500 6787 1.0000 500 7723 1.0000 500 7955 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/149/149.seqs.fa -oc motifs/149 -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 0.271 C 0.215 G 0.251 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.215 G 0.251 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 9 llr = 161 E-value = 2.7e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :317:392::6147192:66: pos.-specific C 932187:88a29629:4a14a probability G 1:7:::1:1::::1:1::2:: matrix T :3:22:::1:2:::::3:1:: bits 2.2 * * * 2.0 * * * 1.8 * * * * * * 1.6 * * * * * * Relative 1.3 * * ** * * ** * * Entropy 1.1 * ****** ** ** * ** (25.7 bits) 0.9 * * ****** ** ** * ** 0.7 * ******** ***** * ** 0.4 ****************** ** 0.2 ********************* 0.0 --------------------- Multilevel CAGACCACCCACCACACCAAC consensus CCTTA A C AC T GC sequence T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 4068 459 1.31e-12 TAGGATTGAA CAGACCACCCACCACATCAAC CTTCCCCTGC 4064 459 1.31e-12 TAGGATTGAA CAGACCACCCACCACATCAAC CTTCCCCTGC 11169 460 2.75e-10 TCTCACCTTC CCGTCAACCCCCCACAACAAC CACAAATTCA 24348 416 7.41e-10 TACCTCGTCA CTCATCACCCTCCCCACCACC GCCGCCACCG 11719 461 3.37e-09 ACAATTCATC CAAACCACTCTCAACACCACC ACAGAAACAA 6486 455 1.35e-08 GCTCTCCACT CCGCCAACGCACAACATCTCC ATCTCATCCT 268314 476 1.88e-08 CATATGCAAA GTGACCAACCACAGCACCCAC GAAG 261878 408 6.35e-08 CTGACACAGA CTGACAACCCCAACCGACGAC GACGAAGCGG 11163 462 9.82e-08 AATAACACCG CCCTTCGACCACCAAACCGCC GCGGCCTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4068 1.3e-12 458_[+1]_21 4064 1.3e-12 458_[+1]_21 11169 2.7e-10 459_[+1]_20 24348 7.4e-10 415_[+1]_64 11719 3.4e-09 460_[+1]_19 6486 1.3e-08 454_[+1]_25 268314 1.9e-08 475_[+1]_4 261878 6.3e-08 407_[+1]_72 11163 9.8e-08 461_[+1]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=9 4068 ( 459) CAGACCACCCACCACATCAAC 1 4064 ( 459) CAGACCACCCACCACATCAAC 1 11169 ( 460) CCGTCAACCCCCCACAACAAC 1 24348 ( 416) CTCATCACCCTCCCCACCACC 1 11719 ( 461) CAAACCACTCTCAACACCACC 1 6486 ( 455) CCGCCAACGCACAACATCTCC 1 268314 ( 476) GTGACCAACCACAGCACCCAC 1 261878 ( 408) CTGACAACCCCAACCGACGAC 1 11163 ( 462) CCCTTCGACCACCAAACCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10080 bayes= 10.9766 E= 2.7e-007 -982 205 -117 -982 30 63 -982 34 -129 5 141 -982 130 -95 -982 -24 -982 185 -982 -24 30 163 -982 -982 171 -982 -117 -982 -29 185 -982 -982 -982 185 -117 -124 -982 222 -982 -982 103 5 -982 -24 -129 205 -982 -982 71 137 -982 -982 130 5 -117 -982 -129 205 -982 -982 171 -982 -117 -982 -29 105 -982 34 -982 222 -982 -982 103 -95 -17 -124 103 105 -982 -982 -982 222 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 2.7e-007 0.000000 0.888889 0.111111 0.000000 0.333333 0.333333 0.000000 0.333333 0.111111 0.222222 0.666667 0.000000 0.666667 0.111111 0.000000 0.222222 0.000000 0.777778 0.000000 0.222222 0.333333 0.666667 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.222222 0.777778 0.000000 0.000000 0.000000 0.777778 0.111111 0.111111 0.000000 1.000000 0.000000 0.000000 0.555556 0.222222 0.000000 0.222222 0.111111 0.888889 0.000000 0.000000 0.444444 0.555556 0.000000 0.000000 0.666667 0.222222 0.111111 0.000000 0.111111 0.888889 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.222222 0.444444 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.555556 0.111111 0.222222 0.111111 0.555556 0.444444 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ACT][GC][AT][CT][CA]A[CA]CC[ACT]C[CA][AC]CA[CTA]C[AG][AC]C -------------------------------------------------------------------------------- Time 4.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 17 llr = 183 E-value = 4.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 228518282142:951 pos.-specific C 1::3:1:14::4::22 probability G 88229:822961a117 matrix T :::::11:2::4:121 bits 2.2 2.0 * 1.8 * * 1.6 * * * Relative 1.3 * * ** Entropy 1.1 *** ** * ** (15.5 bits) 0.9 *** **** ** ** 0.7 *** **** ** ** * 0.4 ******** ** ** * 0.2 **************** 0.0 ---------------- Multilevel GGAAGAGACGGCGAAG consensus AGC T AT sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11169 150 4.90e-08 AACGATACAA GGAGGAGATGGAGAAG TTTCTCTTGA 38656 463 4.71e-07 TAGTCACAAG GGAAGAAACGGGGAAG GATTGCGGGT 31771 269 6.61e-07 AAGTCAGGAG GGGAGAGAGGGAGATG TCGAAGTGGC 6486 172 7.43e-07 TTTTGCGATT GGGAGAGATGATGAGG GAGGGCTTGT 10898 349 9.28e-07 TACTTTGAGT AGACGAAACGATGAAG CGAGTGTTGG 7723 4 1.41e-06 GAA GGAGGAGCCGACGATG ATTCGGTTGA 6787 117 2.30e-06 TGTATGTTGC GGAAGAGAGAATGATG TCCAAATCAA 22148 239 3.33e-06 GGCTCATACT GAGCGATACGGCGAAG GCAAGCAGCA 4064 297 4.76e-06 CACCTACGAG AGAAAAGAAGGCGAAG ACTGACAAAG 36764 403 5.65e-06 GTGGAGGCAG GAAGGAGACGACGACA GCAGTAGTCC 30701 139 5.65e-06 AGGACGTTAT GGAAGAGGAGGAGAAT TCAGGACTAT 261470 466 6.14e-06 GGCAGTGGCG AGACGTGATGGCGAAC ACTGCAGTTC 11271 5 6.14e-06 CGAA CAACGAGACGAAGACG GCTACTGGCA 268314 327 7.24e-06 GAGCACGACG GAACGCGAGGGTGACG TAAGTAGGTG 4068 236 1.35e-05 GCAGGAGCAG GGAAGTGGCGATGTAG AACACAGCAA 11163 231 2.55e-05 GATTCCTTTA GGGAGAAATGGTGGAC GAAGGATTTC 261878 77 3.53e-05 GAGTGAGGAA GGAGGAGGAAGCGAGC CGGAACAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11169 4.9e-08 149_[+2]_335 38656 4.7e-07 462_[+2]_22 31771 6.6e-07 268_[+2]_216 6486 7.4e-07 171_[+2]_313 10898 9.3e-07 348_[+2]_136 7723 1.4e-06 3_[+2]_481 6787 2.3e-06 116_[+2]_368 22148 3.3e-06 238_[+2]_246 4064 4.8e-06 296_[+2]_188 36764 5.6e-06 402_[+2]_82 30701 5.6e-06 138_[+2]_346 261470 6.1e-06 465_[+2]_19 11271 6.1e-06 4_[+2]_480 268314 7.2e-06 326_[+2]_158 4068 1.3e-05 235_[+2]_249 11163 2.5e-05 230_[+2]_254 261878 3.5e-05 76_[+2]_408 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=17 11169 ( 150) GGAGGAGATGGAGAAG 1 38656 ( 463) GGAAGAAACGGGGAAG 1 31771 ( 269) GGGAGAGAGGGAGATG 1 6486 ( 172) GGGAGAGATGATGAGG 1 10898 ( 349) AGACGAAACGATGAAG 1 7723 ( 4) GGAGGAGCCGACGATG 1 6787 ( 117) GGAAGAGAGAATGATG 1 22148 ( 239) GAGCGATACGGCGAAG 1 4064 ( 297) AGAAAAGAAGGCGAAG 1 36764 ( 403) GAAGGAGACGACGACA 1 30701 ( 139) GGAAGAGGAGGAGAAT 1 261470 ( 466) AGACGTGATGGCGAAC 1 11271 ( 5) CAACGAGACGAAGACG 1 268314 ( 327) GAACGCGAGGGTGACG 1 4068 ( 236) GGAAGTGGCGATGTAG 1 11163 ( 231) GGGAGAAATGGTGGAC 1 261878 ( 77) GGAGGAGGAAGCGAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10185 bayes= 9.29394 E= 4.6e-001 -62 -187 161 -1073 -21 -1073 161 -1073 149 -1073 -9 -1073 79 45 -9 -1073 -220 -1073 191 -1073 160 -187 -1073 -116 -62 -1073 161 -216 149 -187 -51 -1073 -62 94 -51 -16 -120 -1073 181 -1073 60 -1073 123 -1073 -21 71 -209 43 -1073 -1073 199 -1073 170 -1073 -209 -216 96 -28 -109 -57 -220 -28 149 -216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 4.6e-001 0.176471 0.058824 0.764706 0.000000 0.235294 0.000000 0.764706 0.000000 0.764706 0.000000 0.235294 0.000000 0.470588 0.294118 0.235294 0.000000 0.058824 0.000000 0.941176 0.000000 0.823529 0.058824 0.000000 0.117647 0.176471 0.000000 0.764706 0.058824 0.764706 0.058824 0.176471 0.000000 0.176471 0.411765 0.176471 0.235294 0.117647 0.000000 0.882353 0.000000 0.411765 0.000000 0.588235 0.000000 0.235294 0.352941 0.058824 0.352941 0.000000 0.000000 1.000000 0.000000 0.882353 0.000000 0.058824 0.058824 0.529412 0.176471 0.117647 0.176471 0.058824 0.176471 0.705882 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GA][AG][ACG]GAGA[CT]G[GA][CTA]GAAG -------------------------------------------------------------------------------- Time 9.79 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 5 llr = 100 E-value = 3.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2::2::2:::22:6:6:: pos.-specific C a:8a:62486:a2:a:::2: probability G :2:::::6:::::::4::84 matrix T :8::a28::4a:68::a4:6 bits 2.2 * * * * 2.0 * ** ** * * 1.8 * ** ** * * 1.6 * ** ** * * Relative 1.3 * *** * * ** * * * Entropy 1.1 ***** ****** ** * * (29.0 bits) 0.9 ***** ****** ******* 0.7 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CTCCTCTGCCTCTTCATAGT consensus GA ACCAT AA G TCG sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 4064 366 1.25e-10 GACAAAGTCC CTCCTTTCCTTCTTCATAGG AAATATTAAA 4068 362 2.06e-10 GACAAAGTCC CTCCTATCCTTCTTCATTGG AAATATTAAA 11271 387 3.11e-10 CGCTCACGTG CTCCTCTGACTCATCATTGT TTCACTCTTC 7955 453 3.80e-10 GCAGCTTCAT CGACTCTGCCTCTTCGTAGT ATCAACTCTG 11719 112 2.00e-09 CCGTATCCTC CTCCTCCGCCTCCACGTACT CCATTCGTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4064 1.2e-10 365_[+3]_115 4068 2.1e-10 361_[+3]_119 11271 3.1e-10 386_[+3]_94 7955 3.8e-10 452_[+3]_28 11719 2e-09 111_[+3]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=5 4064 ( 366) CTCCTTTCCTTCTTCATAGG 1 4068 ( 362) CTCCTATCCTTCTTCATTGG 1 11271 ( 387) CTCCTCTGACTCATCATTGT 1 7955 ( 453) CGACTCTGCCTCTTCGTAGT 1 11719 ( 112) CTCCTCCGCCTCCACGTACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 10101 bayes= 10.4136 E= 3.0e+000 -897 222 -897 -897 -897 -897 -33 160 -44 189 -897 -897 -897 222 -897 -897 -897 -897 -897 193 -44 148 -897 -39 -897 -10 -897 160 -897 89 126 -897 -44 189 -897 -897 -897 148 -897 61 -897 -897 -897 193 -897 222 -897 -897 -44 -10 -897 119 -44 -897 -897 160 -897 222 -897 -897 114 -897 67 -897 -897 -897 -897 193 114 -897 -897 61 -897 -10 167 -897 -897 -897 67 119 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 3.0e+000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.600000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.600000 0.200000 0.000000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.400000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TG][CA]CT[CAT][TC][GC][CA][CT]TC[TAC][TA]C[AG]T[AT][GC][TG] -------------------------------------------------------------------------------- Time 14.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10898 1.70e-03 348_[+2(9.28e-07)]_136 11163 1.86e-05 230_[+2(2.55e-05)]_215_\ [+1(9.82e-08)]_18 11169 9.50e-10 149_[+2(4.90e-08)]_294_\ [+1(2.75e-10)]_20 11271 4.97e-08 4_[+2(6.14e-06)]_366_[+3(3.11e-10)]_\ 94 11719 5.43e-10 111_[+3(2.00e-09)]_329_\ [+1(3.37e-09)]_19 22148 7.85e-03 238_[+2(3.33e-06)]_246 24348 1.82e-06 347_[+3(6.35e-05)]_48_\ [+1(7.41e-10)]_64 261470 4.65e-02 465_[+2(6.14e-06)]_19 261878 4.28e-06 76_[+2(3.53e-05)]_315_\ [+1(6.35e-08)]_72 268314 4.32e-06 326_[+2(7.24e-06)]_133_\ [+1(1.88e-08)]_4 30701 2.54e-02 138_[+2(5.65e-06)]_346 31771 1.91e-03 268_[+2(6.61e-07)]_216 36764 3.73e-02 402_[+2(5.65e-06)]_82 37867 3.45e-01 500 38656 6.15e-03 462_[+2(4.71e-07)]_22 4064 8.78e-17 296_[+2(4.76e-06)]_53_\ [+3(1.25e-10)]_73_[+1(1.31e-12)]_21 4068 3.82e-16 235_[+2(1.35e-05)]_110_\ [+3(2.06e-10)]_77_[+1(1.31e-12)]_21 6486 1.51e-07 171_[+2(7.43e-07)]_267_\ [+1(1.35e-08)]_25 6787 8.80e-03 116_[+2(2.30e-06)]_368 7723 1.88e-02 3_[+2(1.41e-06)]_481 7955 7.07e-06 452_[+3(3.80e-10)]_2_[+3(6.61e-06)]_\ 6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************