******************************************************************************** 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/369/369.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11640 1.0000 500 20670 1.0000 500 20835 1.0000 500 21058 1.0000 500 21292 1.0000 500 21488 1.0000 500 21582 1.0000 500 22639 1.0000 500 23225 1.0000 500 2418 1.0000 500 25049 1.0000 500 267958 1.0000 500 268958 1.0000 500 4659 1.0000 500 7536 1.0000 500 8386 1.0000 500 9092 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/369/369.seqs.fa -oc motifs/369 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.239 G 0.226 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.239 G 0.226 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 17 llr = 174 E-value = 3.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :2::1::75122:::1 pos.-specific C 2:95:9a:15314416 probability G :61:91:2112:138: matrix T 8215:1:133375422 bits 2.1 * 1.9 * 1.7 * 1.5 * *** Relative 1.3 * * *** Entropy 1.1 * ***** * (14.7 bits) 0.9 * ****** ** ** 0.6 ******** ** ** 0.4 ******** * ***** 0.2 ********** ***** 0.0 ---------------- Multilevel TGCCGCCAACCTTCGC consensus CT T GTTT CT T sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2418 338 1.62e-10 TTTCCCGATT TGCCGCCAACCTTCGC CGGAGAGCTT 23225 121 1.67e-08 ACTTGCCTCA TGCCGCCGACTTTCGC GGCTGATGCT 268958 337 3.12e-07 TCTCGCAAAG TGCTGCCAAAATTCGC CATTTTGGCG 7536 112 1.92e-06 CATTGACAAT CGCCGCCGTCTTCGGT CTACTTCAAC 267958 190 4.34e-06 CTCGTGATTA CACTGCCATCTTCGGT GGAGTTCTAG 20670 426 4.78e-06 CCCCCCCCTC TGCCGCCAGTCTTTTT GATGGCCGCC 21058 354 5.25e-06 CACATCAAAC TGCTGCCAACGACGTT CACAAGATAC 11640 91 5.76e-06 GTGGGTGATG TGCTGTCGTCGTCGGC AGCAGCAGCA 8386 400 6.31e-06 CCTTACAAAC TGCCACCAATCCCTGC CTCCTCTCGC 21488 129 6.91e-06 TTGACACCAC TGCTGGCACTTTTTGC AACGACGACA 22639 327 7.57e-06 CCAAACTATC TACTGCCACCTTGGGC ACACAAAGTG 4659 251 1.48e-05 AAATCAAACG TTTCGCCAGTCTTCGC TAACAGCATT 21292 133 1.73e-05 TCTGGGTGGG TACTGCCGTTGTCTGA AACGTCTACA 25049 333 1.87e-05 CAACTGTTCT TTCCGCCAAAGATTTC TCCATCCAAC 21582 202 5.03e-05 GAGAAAATCC CTGTGCCAACACTCGC CAGTCTTTCG 20835 170 6.47e-05 GTCACCGAAC TGCCGCCTTGCTTCCC CAACGCATCA 9092 382 1.15e-04 CCCAATCAAC CTCCACCAACAACTGA GGGTTCTACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2418 1.6e-10 337_[+1]_147 23225 1.7e-08 120_[+1]_364 268958 3.1e-07 336_[+1]_148 7536 1.9e-06 111_[+1]_373 267958 4.3e-06 189_[+1]_295 20670 4.8e-06 425_[+1]_59 21058 5.2e-06 353_[+1]_131 11640 5.8e-06 90_[+1]_394 8386 6.3e-06 399_[+1]_85 21488 6.9e-06 128_[+1]_356 22639 7.6e-06 326_[+1]_158 4659 1.5e-05 250_[+1]_234 21292 1.7e-05 132_[+1]_352 25049 1.9e-05 332_[+1]_152 21582 5e-05 201_[+1]_283 20835 6.5e-05 169_[+1]_315 9092 0.00012 381_[+1]_103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=17 2418 ( 338) TGCCGCCAACCTTCGC 1 23225 ( 121) TGCCGCCGACTTTCGC 1 268958 ( 337) TGCTGCCAAAATTCGC 1 7536 ( 112) CGCCGCCGTCTTCGGT 1 267958 ( 190) CACTGCCATCTTCGGT 1 20670 ( 426) TGCCGCCAGTCTTTTT 1 21058 ( 354) TGCTGCCAACGACGTT 1 11640 ( 91) TGCTGTCGTCGTCGGC 1 8386 ( 400) TGCCACCAATCCCTGC 1 21488 ( 129) TGCTGGCACTTTTTGC 1 22639 ( 327) TACTGCCACCTTGGGC 1 4659 ( 251) TTTCGCCAGTCTTCGC 1 21292 ( 133) TACTGCCGTTGTCTGA 1 25049 ( 333) TTCCGCCAAAGATTTC 1 21582 ( 202) CTGTGCCAACACTCGC 1 20835 ( 170) TGCCGCCTTGCTTCCC 1 9092 ( 382) CTCCACCAACAACTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 8.98854 E= 3.4e-001 -1073 -2 -1073 157 -65 -1073 138 -13 -1073 188 -194 -213 -1073 115 -1073 87 -124 -1073 197 -1073 -1073 188 -194 -213 -1073 206 -1073 -1073 135 -1073 6 -213 76 -102 -94 19 -124 115 -194 19 -65 30 6 19 -65 -102 -1073 145 -1073 78 -194 104 -1073 56 38 45 -1073 -202 176 -55 -124 144 -1073 -13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 3.4e-001 0.000000 0.235294 0.000000 0.764706 0.176471 0.000000 0.588235 0.235294 0.000000 0.882353 0.058824 0.058824 0.000000 0.529412 0.000000 0.470588 0.117647 0.000000 0.882353 0.000000 0.000000 0.882353 0.058824 0.058824 0.000000 1.000000 0.000000 0.000000 0.705882 0.000000 0.235294 0.058824 0.470588 0.117647 0.117647 0.294118 0.117647 0.529412 0.058824 0.294118 0.176471 0.294118 0.235294 0.294118 0.176471 0.117647 0.000000 0.705882 0.000000 0.411765 0.058824 0.529412 0.000000 0.352941 0.294118 0.352941 0.000000 0.058824 0.764706 0.176471 0.117647 0.647059 0.000000 0.235294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC][GT]C[CT]GCC[AG][AT][CT][CTG]T[TC][CTG]G[CT] -------------------------------------------------------------------------------- Time 2.80 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 11 llr = 137 E-value = 2.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::2:2::221129:: pos.-specific C 2:2:11:51:::::2: probability G 837551a228:181:8 matrix T :71456:35:98::82 bits 2.1 * 1.9 * 1.7 * 1.5 * * ** ** * Relative 1.3 * * ** **** Entropy 1.1 *** * ******* (18.0 bits) 0.9 *** * ******* 0.6 *** * ** ******* 0.4 ******** ******* 0.2 **************** 0.0 ---------------- Multilevel GTGGGTGCTGTTGATG consensus G TT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23225 168 1.85e-08 TGTATCACCA GTGGTTGGAGTTGATG ATTTGTGGTC 2418 230 2.70e-08 GGTGCGGTTA GTGGTTGTTGTTGATT GTGTTGTTCA 21058 106 1.75e-07 AGTATTTTTT GTGAGAGCTGTTGACG ACGGGCTTTG 9092 86 2.89e-07 TAAAACTGTA GGGTTTGCAATTGATG GAAGGAGACT 11640 54 3.17e-07 TACGTTGCTG GTGGTGGTTGTTAATG GACGGGCTGT 21488 96 6.06e-07 TTGGTGGGGC GGCGGCGCGGTTGATG GACACGGTTG 8386 214 6.64e-07 GAAGTAGGAG GTCGCTGCTGTTGGTG TAAGTATTTA 4659 181 1.52e-06 CGGTTTGTTG CTGTTTGCTGTGAATG TTGAAATTAA 21582 99 1.52e-06 AAGACCGCGC CTTAGTGGTGTTGATG ACATTTTGCT 21292 186 6.05e-06 ATAGAGATGT GTGTGTGCCAATGACG GTCCCTTGGA 7536 341 9.12e-06 AGGAAAGGCC GGGTGAGTGGTAGATT TCCGTGTGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23225 1.8e-08 167_[+2]_317 2418 2.7e-08 229_[+2]_255 21058 1.8e-07 105_[+2]_379 9092 2.9e-07 85_[+2]_399 11640 3.2e-07 53_[+2]_431 21488 6.1e-07 95_[+2]_389 8386 6.6e-07 213_[+2]_271 4659 1.5e-06 180_[+2]_304 21582 1.5e-06 98_[+2]_386 21292 6e-06 185_[+2]_299 7536 9.1e-06 340_[+2]_144 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=11 23225 ( 168) GTGGTTGGAGTTGATG 1 2418 ( 230) GTGGTTGTTGTTGATT 1 21058 ( 106) GTGAGAGCTGTTGACG 1 9092 ( 86) GGGTTTGCAATTGATG 1 11640 ( 54) GTGGTGGTTGTTAATG 1 21488 ( 96) GGCGGCGCGGTTGATG 1 8386 ( 214) GTCGCTGCTGTTGGTG 1 4659 ( 181) CTGTTTGCTGTGAATG 1 21582 ( 99) CTTAGTGGTGTTGATG 1 21292 ( 186) GTGTGTGCCAATGACG 1 7536 ( 341) GGGTGAGTGGTAGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.90346 E= 2.4e+000 -1010 -39 186 -1010 -1010 -1010 27 149 -1010 -39 169 -150 -61 -1010 101 49 -1010 -139 101 82 -61 -139 -131 130 -1010 -1010 215 -1010 -1010 119 -31 8 -61 -139 -31 108 -61 -1010 186 -1010 -161 -1010 -1010 182 -161 -1010 -131 166 -61 -1010 186 -1010 171 -1010 -131 -1010 -1010 -39 -1010 166 -1010 -1010 186 -50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 2.4e+000 0.000000 0.181818 0.818182 0.000000 0.000000 0.000000 0.272727 0.727273 0.000000 0.181818 0.727273 0.090909 0.181818 0.000000 0.454545 0.363636 0.000000 0.090909 0.454545 0.454545 0.181818 0.090909 0.090909 0.636364 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.181818 0.272727 0.181818 0.090909 0.181818 0.545455 0.181818 0.000000 0.818182 0.000000 0.090909 0.000000 0.000000 0.909091 0.090909 0.000000 0.090909 0.818182 0.181818 0.000000 0.818182 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.181818 0.000000 0.818182 0.000000 0.000000 0.818182 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TG]G[GT][GT]TG[CT]TGTTGATG -------------------------------------------------------------------------------- Time 5.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 138 E-value = 5.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :19a323:7941a91312:2a pos.-specific C 49::78292138::7:6147: probability G 1:::::11::1::114::61: matrix T 4:1:::3:1:11::1237::: bits 2.1 1.9 * * * 1.7 * * * 1.5 * * * * * Relative 1.3 *** * * * ** * Entropy 1.1 ***** * * *** * * (22.1 bits) 0.9 ***** * * *** *** 0.6 ****** *** **** ***** 0.4 ****** *** ********** 0.2 ****** ************** 0.0 --------------------- Multilevel CCAACCACAAACAACGCTGCA consensus T AAT C C ATACA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 267958 416 2.69e-09 AAAACAAATG GCAAACTCCAACAACACTGCA ACATTACTAC 21058 391 2.69e-09 ACCCCCATCA TCAACCACCACCAACGTCGCA CCGCTCTCGC 25049 304 4.26e-09 TCCTACTCGC CCAACCCCACTCAACGCTCCA ACTGTTCTTT 8386 475 1.21e-08 CAACATCACA CCAACACCAAACAGCTCTCCA ACACA 4659 410 4.71e-08 ATTTGCCGGG CAAACCGCAACAAACGTTGCA CACTTCAACA 11640 442 8.88e-08 GAAGAACATA TCTAACACAACCAAAACTGAA GTGGTTTCTG 20670 470 1.48e-07 TCCGCCAACA CCAACAACAAATAACGATCGA CGAAGAAGAT 23225 202 1.59e-07 TCGCGACGAC TCAACCTCTAGCAAGTTAGCA TCCACTGTCT 9092 478 2.70e-07 TTCTTTGAAT TCAAACTGAAACAATACACAA CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 267958 2.7e-09 415_[+3]_64 21058 2.7e-09 390_[+3]_89 25049 4.3e-09 303_[+3]_176 8386 1.2e-08 474_[+3]_5 4659 4.7e-08 409_[+3]_70 11640 8.9e-08 441_[+3]_38 20670 1.5e-07 469_[+3]_10 23225 1.6e-07 201_[+3]_278 9092 2.7e-07 477_[+3]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 267958 ( 416) GCAAACTCCAACAACACTGCA 1 21058 ( 391) TCAACCACCACCAACGTCGCA 1 25049 ( 304) CCAACCCCACTCAACGCTCCA 1 8386 ( 475) CCAACACCAAACAGCTCTCCA 1 4659 ( 410) CAAACCGCAACAAACGTTGCA 1 11640 ( 442) TCTAACACAACCAAAACTGAA 1 20670 ( 470) CCAACAACAAATAACGATCGA 1 23225 ( 202) TCAACCTCTAGCAAGTTAGCA 1 9092 ( 478) TCAAACTGAAACAATACACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8160 bayes= 9.12387 E= 5.0e+000 -982 89 -102 78 -132 189 -982 -982 168 -982 -982 -121 185 -982 -982 -982 27 148 -982 -982 -32 170 -982 -982 27 -10 -102 37 -982 189 -102 -982 126 -10 -982 -121 168 -110 -982 -982 68 48 -102 -121 -132 170 -982 -121 185 -982 -982 -982 168 -982 -102 -982 -132 148 -102 -121 27 -982 98 -22 -132 122 -982 37 -32 -110 -982 137 -982 89 130 -982 -32 148 -102 -982 185 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 5.0e+000 0.000000 0.444444 0.111111 0.444444 0.111111 0.888889 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 0.333333 0.222222 0.111111 0.333333 0.000000 0.888889 0.111111 0.000000 0.666667 0.222222 0.000000 0.111111 0.888889 0.111111 0.000000 0.000000 0.444444 0.333333 0.111111 0.111111 0.111111 0.777778 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.111111 0.666667 0.111111 0.111111 0.333333 0.000000 0.444444 0.222222 0.111111 0.555556 0.000000 0.333333 0.222222 0.111111 0.000000 0.666667 0.000000 0.444444 0.555556 0.000000 0.222222 0.666667 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]CAA[CA][CA][ATC]C[AC]A[AC]CAAC[GAT][CT][TA][GC][CA]A -------------------------------------------------------------------------------- Time 8.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11640 6.07e-09 53_[+2(3.17e-07)]_2_[+2(1.40e-05)]_\ 3_[+1(5.76e-06)]_335_[+3(8.88e-08)]_38 20670 9.59e-06 239_[+1(9.77e-05)]_170_\ [+1(4.78e-06)]_28_[+3(1.48e-07)]_10 20835 4.85e-02 169_[+1(6.47e-05)]_315 21058 1.25e-10 105_[+2(1.75e-07)]_232_\ [+1(5.25e-06)]_21_[+3(2.69e-09)]_89 21292 1.23e-03 132_[+1(1.73e-05)]_37_\ [+2(6.05e-06)]_299 21488 4.50e-05 95_[+2(6.06e-07)]_17_[+1(6.91e-06)]_\ 356 21582 1.18e-03 98_[+2(1.52e-06)]_87_[+1(5.03e-05)]_\ 283 22639 1.16e-02 326_[+1(7.57e-06)]_158 23225 3.16e-12 120_[+1(1.67e-08)]_31_\ [+2(1.85e-08)]_18_[+3(1.59e-07)]_278 2418 2.31e-10 229_[+2(2.70e-08)]_92_\ [+1(1.62e-10)]_147 25049 8.09e-07 303_[+3(4.26e-09)]_8_[+1(1.87e-05)]_\ 152 267958 4.45e-07 189_[+1(4.34e-06)]_210_\ [+3(2.69e-09)]_64 268958 1.81e-03 336_[+1(3.12e-07)]_148 4659 3.39e-08 180_[+2(1.52e-06)]_54_\ [+1(1.48e-05)]_143_[+3(4.71e-08)]_70 7536 3.94e-05 111_[+1(1.92e-06)]_213_\ [+2(9.12e-06)]_144 8386 2.08e-09 213_[+2(6.64e-07)]_170_\ [+1(6.31e-06)]_59_[+3(1.21e-08)]_5 9092 2.34e-07 85_[+2(2.89e-07)]_275_\ [+3(8.87e-06)]_80_[+3(2.70e-07)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************