******************************************************************************** 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/229/229.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 15424 1.0000 500 20626 1.0000 500 21475 1.0000 500 22170 1.0000 500 22221 1.0000 500 22240 1.0000 500 23175 1.0000 500 23356 1.0000 500 23385 1.0000 500 23472 1.0000 500 23887 1.0000 500 24834 1.0000 500 25869 1.0000 500 261047 1.0000 500 26403 1.0000 500 26686 1.0000 500 268068 1.0000 500 268238 1.0000 500 268350 1.0000 500 268714 1.0000 500 269616 1.0000 500 28570 1.0000 500 2920 1.0000 500 31809 1.0000 500 31929 1.0000 500 35164 1.0000 500 39255 1.0000 500 40774 1.0000 500 41122 1.0000 500 42213 1.0000 500 42226 1.0000 500 6780 1.0000 500 7322 1.0000 500 9318 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/229/229.seqs.fa -oc motifs/229 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.230 G 0.254 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.230 G 0.254 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 30 llr = 338 E-value = 9.9e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 14412422514955:65277: pos.-specific C 82573186266141a328115 probability G :11:31:2:2:::3:12:::4 matrix T 12:213::31::11::1:22: bits 2.1 * 1.9 * 1.7 * 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 * * * * * (16.3 bits) 0.8 * * * * ** *** 0.6 * * ** **** ** **** 0.4 * ** ******* ******* 0.2 ********************* 0.0 --------------------- Multilevel CACCCACCACCAAACAACAAC consensus CA GTAGTGA CG CC TTG sequence T A AC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 15424 433 1.04e-11 CCACTCAACA CACCAACCACCACACAACAAG CTACACAAAG 261047 276 5.69e-09 CACACACTGA CACCGACCACCAAGCCACCAG TGGCAGTGGC 28570 443 1.80e-08 CCCAGACACC CTCCCTCCAGCAACCACCAAC CTCGGTAGAT 6780 79 1.49e-07 CCGGACTTCT CACCAACCCCAACGCCGCATG AACAATCTCC 31809 383 2.45e-07 CATTGTACAT CCACAAACATCACGCAACAAC ATTCGATACT 41122 460 3.94e-07 TTGCAGCTCA CCCCCTCCACTACACCAAAAC GTCTTGTGCA 35164 286 4.96e-07 TTGTTTACTG ATACGACAACCACACAAAAAG AGAGCTGAGC 26403 474 4.96e-07 ATCCAAACGA CGACGACCAACAAACAACACC ATGTCG 23175 361 4.96e-07 TTGTTTACTG ATACGACAACCACACAAAAAG AGAGCTGAGC 25869 423 6.93e-07 TCATCGCAGG CCACTGCAACAAAGCACCAAG TCTCCCCCAC 20626 471 6.93e-07 ACCTCTAGGA CAGTGGCGACAAAACCACAAC TCGTACGAG 21475 242 7.73e-07 TTTTGGGGCG CAAAGTCGTGAAAACAGCAAG CGACAGCAAG 23887 367 9.57e-07 TTCAAATGAA CAACCGCCTCCATTCATCAAC CTGTGAAGAT 24834 1 1.06e-06 . AACACACCTGCAAGCAACTAG ACGACTTTCT 2920 81 2.15e-06 ATCAATGTAC CACCATACCTCATACAACATC CATGATTTGC 7322 473 2.61e-06 CACGGACACG CAGCAAACAAAACACAACTAC CGACAGT 42226 268 2.61e-06 AAGCAAACTA CAACCGCGTCCATCCCACCAC TTCGCACCAA 22240 463 2.61e-06 ACAAAGCCGA CGGCAACACCAACACCACTAG ACAACTACAC 26686 477 3.15e-06 CTCCCGTACT CCACCACCAGCAACCAGCTAT CCC 22221 480 4.95e-06 ACAACAGCAG CCTCCACCTGCAAACCGCCAG 42213 354 5.40e-06 CACTAGCATC CACTCTCGTCCCCCCACCATC CTTTGATCCC 23385 344 5.89e-06 CTACGAGAGA CGCCGTAGACAACTCACAAAC GTTCGTCTTC 31929 138 6.98e-06 GCGAGCCAAT TTCTTTCGCCCAAACAGCAAC GGACCAGAAT 22170 332 1.14e-05 CTCGTGCCAC CAACGTCCTGGAAACGCCATG GTGGGGAAGA 40774 465 1.33e-05 CCGTCCCCTC TCCTCTCCTCCACACAAATTC ACAACCACCT 268714 119 1.33e-05 CCATTCCTTC CCATGCCACCACCGCAGCAAC TCAATTCACC 268350 354 1.94e-05 GATTTTTCAG CTCATAACCCAATGCGACAAG AGCACAGAGC 268068 311 2.77e-05 CGTCGTCGAG CTCACTAATCAAATCGCCAAC CTTGGCACCT 23472 428 3.40e-05 GTCTCGTCTT CACCGCCCAGCCAGCCACACA AACGTCGGTG 268238 27 8.14e-05 GGGCAGTCCA AGCCACCGCCAAAGCATCTTG TCCAATCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15424 1e-11 432_[+1]_47 261047 5.7e-09 275_[+1]_204 28570 1.8e-08 442_[+1]_37 6780 1.5e-07 78_[+1]_401 31809 2.5e-07 382_[+1]_97 41122 3.9e-07 459_[+1]_20 35164 5e-07 285_[+1]_194 26403 5e-07 473_[+1]_6 23175 5e-07 360_[+1]_119 25869 6.9e-07 422_[+1]_57 20626 6.9e-07 470_[+1]_9 21475 7.7e-07 241_[+1]_238 23887 9.6e-07 366_[+1]_113 24834 1.1e-06 [+1]_479 2920 2.2e-06 80_[+1]_399 7322 2.6e-06 472_[+1]_7 42226 2.6e-06 267_[+1]_212 22240 2.6e-06 462_[+1]_17 26686 3.1e-06 476_[+1]_3 22221 4.9e-06 479_[+1] 42213 5.4e-06 353_[+1]_126 23385 5.9e-06 343_[+1]_136 31929 7e-06 137_[+1]_342 22170 1.1e-05 331_[+1]_148 40774 1.3e-05 464_[+1]_15 268714 1.3e-05 118_[+1]_361 268350 1.9e-05 353_[+1]_126 268068 2.8e-05 310_[+1]_169 23472 3.4e-05 427_[+1]_52 268238 8.1e-05 26_[+1]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=30 15424 ( 433) CACCAACCACCACACAACAAG 1 261047 ( 276) CACCGACCACCAAGCCACCAG 1 28570 ( 443) CTCCCTCCAGCAACCACCAAC 1 6780 ( 79) CACCAACCCCAACGCCGCATG 1 31809 ( 383) CCACAAACATCACGCAACAAC 1 41122 ( 460) CCCCCTCCACTACACCAAAAC 1 35164 ( 286) ATACGACAACCACACAAAAAG 1 26403 ( 474) CGACGACCAACAAACAACACC 1 23175 ( 361) ATACGACAACCACACAAAAAG 1 25869 ( 423) CCACTGCAACAAAGCACCAAG 1 20626 ( 471) CAGTGGCGACAAAACCACAAC 1 21475 ( 242) CAAAGTCGTGAAAACAGCAAG 1 23887 ( 367) CAACCGCCTCCATTCATCAAC 1 24834 ( 1) AACACACCTGCAAGCAACTAG 1 2920 ( 81) CACCATACCTCATACAACATC 1 7322 ( 473) CAGCAAACAAAACACAACTAC 1 42226 ( 268) CAACCGCGTCCATCCCACCAC 1 22240 ( 463) CGGCAACACCAACACCACTAG 1 26686 ( 477) CCACCACCAGCAACCAGCTAT 1 22221 ( 480) CCTCCACCTGCAAACCGCCAG 1 42213 ( 354) CACTCTCGTCCCCCCACCATC 1 23385 ( 344) CGCCGTAGACAACTCACAAAC 1 31929 ( 138) TTCTTTCGCCCAAACAGCAAC 1 22170 ( 332) CAACGTCCTGGAAACGCCATG 1 40774 ( 465) TCCTCTCCTCCACACAAATTC 1 268714 ( 119) CCATGCCACCACCGCAGCAAC 1 268350 ( 354) CTCATAACCCAATGCGACAAG 1 268068 ( 311) CTCACTAATCAAATCGCCAAC 1 23472 ( 428) CACCGCCCAGCCAGCCACACA 1 268238 ( 27) AGCCACCGCCAAAGCATCTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 9.76003 E= 9.9e-018 -95 180 -1155 -195 75 2 -93 -37 51 112 -134 -295 -95 161 -1155 -63 -15 54 39 -137 75 -120 -93 37 -37 180 -1155 -1155 -37 130 -12 -1155 85 2 -1155 22 -195 146 -12 -195 51 130 -292 -295 180 -120 -1155 -1155 85 80 -1155 -95 85 -79 24 -137 -1155 212 -1155 -1155 129 21 -134 -1155 105 -20 -34 -195 -63 186 -1155 -1155 144 -120 -1155 -37 151 -178 -1155 -37 -295 112 77 -295 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 30 E= 9.9e-018 0.133333 0.800000 0.000000 0.066667 0.433333 0.233333 0.133333 0.200000 0.366667 0.500000 0.100000 0.033333 0.133333 0.700000 0.000000 0.166667 0.233333 0.333333 0.333333 0.100000 0.433333 0.100000 0.133333 0.333333 0.200000 0.800000 0.000000 0.000000 0.200000 0.566667 0.233333 0.000000 0.466667 0.233333 0.000000 0.300000 0.066667 0.633333 0.233333 0.066667 0.366667 0.566667 0.033333 0.033333 0.900000 0.100000 0.000000 0.000000 0.466667 0.400000 0.000000 0.133333 0.466667 0.133333 0.300000 0.100000 0.000000 1.000000 0.000000 0.000000 0.633333 0.266667 0.100000 0.000000 0.533333 0.200000 0.200000 0.066667 0.166667 0.833333 0.000000 0.000000 0.700000 0.100000 0.000000 0.200000 0.733333 0.066667 0.000000 0.200000 0.033333 0.500000 0.433333 0.033333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ACT][CA]C[CGA][AT][CA][CGA][ATC][CG][CA]A[AC][AG]C[AC][ACG]C[AT][AT][CG] -------------------------------------------------------------------------------- Time 11.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 24 llr = 293 E-value = 3.4e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2::32:5213::76:35:42: pos.-specific C 21:32113::1:1:::1:36: probability G 1:82:953633a1:a5:a3:a matrix T 59136::3355:14:13::2: bits 2.1 1.9 * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * * * * * Entropy 1.1 ** * * ** * * (17.6 bits) 0.8 ** * * ** * * 0.6 ** *** * ***** * * 0.4 ** *** ********** ** 0.2 *** *** ************* 0.0 --------------------- Multilevel TTGATGACGTTGAAGGAGACG consensus C CA GTTAG T AT GT sequence T G G C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9318 426 1.71e-09 GTCGTCGTTG TTGCTGGCGTTGGAGGAGCCG TCATAAAGTC 268350 395 1.01e-08 GCTCGATGTG TTGGAGATGAGGAAGGAGCCG TTTTCTACGT 23356 420 1.18e-08 TTGGTATCTG CTGGTGGCTTTGAAGGAGAAG GAAGGGTAAG 261047 84 7.09e-08 GAATTGATGT TTGAAGAGGAGGAAGACGACG ATGACGTGTA 23472 70 2.79e-07 CCGAGTGACG TCGTTGACAGTGATGGAGACG GTGACACTGT 23385 14 2.79e-07 CGTGTCGATG TTGATGGCGTTGTTGTCGGCG GTGGAGGAGG 20626 129 2.79e-07 TGACCAGCGG CTGCTGATGTTGTTGTTGACG ACGACGACTT 15424 97 2.79e-07 GTTGCCGTCG TTGTTGCTTTGGATGACGACG ACGACGATGA 26686 65 6.21e-07 TCAAGTGGCT CTGGTGGTGGTGGTGGTGGTG GTGGTGGTGG 268714 313 7.50e-07 TCAGCTGCAG TTGTAGAGGATGAAGATGACA CAGGTGCTGG 268238 58 8.23e-07 TCCAATCCAC TTTCCGGGGGTGAAGGTGAAG CCGATCATGA 35164 348 9.88e-07 CGTCTTGTGA ATGATGATTACGCAGAAGCCG TCGATACACC 2920 413 9.88e-07 TGCGTCGTGG ATGATGGGATGGATGGTGGTG GCCGCGACAT 23175 423 9.88e-07 CGTCTTGTGA ATGATGATTACGCAGAAGCCG TCGATACACC 31809 15 1.40e-06 CACTTCCGTG ACGCAGACTTTGAAGAAGAAG GGAGAGGATG 28570 256 2.14e-06 GTTGCTGTGT TTGTTGGTGTGGATTGAGAGG TGGTGTGGTT 41122 314 2.32e-06 GAACATTGCT TTGTTGGATTGGAAGTGGCTG GTGGGTTCCC 39255 11 2.72e-06 TAGATCTGGT TTGATCAGTGAGAAGGAGGTG TTGATTGCTC 25869 232 2.72e-06 CACAGGGGGG CTGGTCGGTATGAAGGTGTCG ATATTCAAAT 22240 125 2.94e-06 CCAGTCGAGG GTGGCGACGGGGGTGATGACG GGGCCTTCAG 40774 230 3.43e-06 ATATTTGACT CTCCAGCAGATGAAGGAGGCG AGTTGAAATG 6780 260 4.00e-06 AATGGAAGAC GTGACGGAGGCGATGAAGGTG GGAATGCCGA 31929 65 4.31e-06 AAATTAGATA TTTCTGGAGTTTTAGGAGGCG AGGAGTAATC 269616 111 8.72e-06 TGATGAAGGG TGATCGACGTTGAAGGAGCAG AGAATTACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9318 1.7e-09 425_[+2]_54 268350 1e-08 394_[+2]_85 23356 1.2e-08 419_[+2]_60 261047 7.1e-08 83_[+2]_396 23472 2.8e-07 69_[+2]_410 23385 2.8e-07 13_[+2]_466 20626 2.8e-07 128_[+2]_351 15424 2.8e-07 96_[+2]_383 26686 6.2e-07 64_[+2]_415 268714 7.5e-07 312_[+2]_167 268238 8.2e-07 57_[+2]_422 35164 9.9e-07 347_[+2]_132 2920 9.9e-07 412_[+2]_67 23175 9.9e-07 422_[+2]_57 31809 1.4e-06 14_[+2]_465 28570 2.1e-06 255_[+2]_224 41122 2.3e-06 313_[+2]_166 39255 2.7e-06 10_[+2]_469 25869 2.7e-06 231_[+2]_248 22240 2.9e-06 124_[+2]_355 40774 3.4e-06 229_[+2]_250 6780 4e-06 259_[+2]_220 31929 4.3e-06 64_[+2]_415 269616 8.7e-06 110_[+2]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=24 9318 ( 426) TTGCTGGCGTTGGAGGAGCCG 1 268350 ( 395) TTGGAGATGAGGAAGGAGCCG 1 23356 ( 420) CTGGTGGCTTTGAAGGAGAAG 1 261047 ( 84) TTGAAGAGGAGGAAGACGACG 1 23472 ( 70) TCGTTGACAGTGATGGAGACG 1 23385 ( 14) TTGATGGCGTTGTTGTCGGCG 1 20626 ( 129) CTGCTGATGTTGTTGTTGACG 1 15424 ( 97) TTGTTGCTTTGGATGACGACG 1 26686 ( 65) CTGGTGGTGGTGGTGGTGGTG 1 268714 ( 313) TTGTAGAGGATGAAGATGACA 1 268238 ( 58) TTTCCGGGGGTGAAGGTGAAG 1 35164 ( 348) ATGATGATTACGCAGAAGCCG 1 2920 ( 413) ATGATGGGATGGATGGTGGTG 1 23175 ( 423) ATGATGATTACGCAGAAGCCG 1 31809 ( 15) ACGCAGACTTTGAAGAAGAAG 1 28570 ( 256) TTGTTGGTGTGGATTGAGAGG 1 41122 ( 314) TTGTTGGATTGGAAGTGGCTG 1 39255 ( 11) TTGATCAGTGAGAAGGAGGTG 1 25869 ( 232) CTGGTCGGTATGAAGGTGTCG 1 22240 ( 125) GTGGCGACGGGGGTGATGACG 1 40774 ( 230) CTCCAGCAGATGAAGGAGGCG 1 6780 ( 260) GTGACGGAGGCGATGAAGGTG 1 31929 ( 65) TTTCTGGAGTTTTAGGAGGCG 1 269616 ( 111) TGATCGACGTTGAAGGAGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 9.85529 E= 3.4e-014 -63 -14 -160 107 -1123 -146 -260 176 -263 -246 172 -163 18 12 -28 -5 -31 -46 -1123 127 -1123 -146 185 -1123 83 -146 85 -1123 -63 34 -2 18 -163 -1123 120 37 18 -1123 -2 83 -263 -88 20 107 -1123 -1123 192 -263 137 -146 -102 -105 127 -1123 -1123 54 -1123 -1123 192 -263 37 -1123 109 -105 107 -88 -260 18 -1123 -1123 198 -1123 69 12 20 -263 -63 134 -260 -31 -263 -1123 192 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 3.4e-014 0.166667 0.208333 0.083333 0.541667 0.000000 0.083333 0.041667 0.875000 0.041667 0.041667 0.833333 0.083333 0.291667 0.250000 0.208333 0.250000 0.208333 0.166667 0.000000 0.625000 0.000000 0.083333 0.916667 0.000000 0.458333 0.083333 0.458333 0.000000 0.166667 0.291667 0.250000 0.291667 0.083333 0.000000 0.583333 0.333333 0.291667 0.000000 0.250000 0.458333 0.041667 0.125000 0.291667 0.541667 0.000000 0.000000 0.958333 0.041667 0.666667 0.083333 0.125000 0.125000 0.625000 0.000000 0.000000 0.375000 0.000000 0.000000 0.958333 0.041667 0.333333 0.000000 0.541667 0.125000 0.541667 0.125000 0.041667 0.291667 0.000000 0.000000 1.000000 0.000000 0.416667 0.250000 0.291667 0.041667 0.166667 0.583333 0.041667 0.208333 0.041667 0.000000 0.958333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]TG[ACTG][TA]G[AG][CTG][GT][TAG][TG]GA[AT]G[GA][AT]G[AGC][CT]G -------------------------------------------------------------------------------- Time 23.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 26 llr = 265 E-value = 2.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::2::23:11::: pos.-specific C 3:1::3::1::22:15 probability G 3921a23951a41953 matrix T 3179:37137:36132 bits 2.1 1.9 * * 1.7 * * 1.5 * * * * * Relative 1.3 * ** * * * Entropy 1.1 * ** ** * * (14.7 bits) 0.8 * ** ** ** * 0.6 **** ** ** ** 0.4 **** ** ** **** 0.2 ***** ********** 0.0 ---------------- Multilevel GGTTGCTGGTGGTGGC consensus T TG TA TC TG sequence C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 15424 174 1.24e-08 CATTCGTCCA CGTTGCTGGTGGTGGG TGGAGGTGAA 26686 90 1.69e-07 GTGGTGGTGG TGGTGGTGGTGGTGGC AGTTGTGGCT 7322 2 1.07e-06 G GGTTGTTGTTGGGGGG TCGCAGAACA 6780 405 1.22e-06 ATGGTGACAA GGTTGTGGGAGCTGGG TTCACGTTGT 35164 18 1.38e-06 CACTGACGAT CGTTGTTGGTGATGCC TATGCTGATT 23175 93 1.38e-06 CACTGACGAT CGTTGTTGGTGATGCC TATGCTGATT 20626 20 1.38e-06 ATTGCCATTT CGTTGCTGTTGTCGTT TGCGAGAGGT 269616 40 2.79e-06 ACTGATACGA CGTTGATGTTGTGGGG ATAACTCATG 31929 317 3.11e-06 GGTACTCTTT GGTTGTGGAAGTTGGT TAATCGGATT 9318 215 3.46e-06 ATACGTGACG GGGTGATGATGGTGGT GCGGCGGAGG 39255 405 3.46e-06 TAGAGGTTGA GGTGGCGGGTGGTGGT AGGTGGGATG 28570 300 3.85e-06 TCTCTTGTTT GGTTGGTTGTGTCGGC AACGAGCGGG 268714 95 3.85e-06 CTCGAGCACG TGTTGTGGGAGGCGCC ATTCCTTCCC 22240 84 4.73e-06 CCTGCGCATT GGATGGTGGAGGTGGC GAGTGGGGTG 2920 217 5.78e-06 TCAGAAACAA TGGTGCTGTTGATGTG ATGGGAGCTG 261047 42 7.70e-06 TTGGATAATA TGTTGAGGATGTAGGC ATTGTCTGGG 23356 97 7.70e-06 CAGTTGAGGT GGTTGCTGTGGCTGTG GCAATACCAA 23385 192 1.11e-05 TGAAAGTTTT GGTTGCTGTTGCTTTG TTGTTATTTG 41122 80 1.21e-05 GTTGTGTCAT CGTTGGTGCAGTCGTT GTGTGATGGT 42226 221 1.43e-05 CTCCATCCGC TGCTGCTGCTGCCGGC GACAAAAAGG 268238 152 2.49e-05 ATGAAGGCTG CGGCGATGGAGGTGGC GAGGCCTGGT 23887 279 4.38e-05 TGTGGTGGTC ATTTGGTGGTGTCGTC CCTAGTTTGA 31809 258 5.68e-05 GTTGGTATCC TGGTGGGGGGGGTTGC ATCGTCTGAT 42213 219 6.43e-05 CTCCCTTGAC TGCTGCGGATGTAGTG CTTACCATTA 26403 338 8.64e-05 TTTGGATGGG TGTTGTGTTAGGGGTT TGTTACACCA 21475 103 1.14e-04 TTCATTTGAA TTTGGAGGCTGTTGTC TCATTCGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15424 1.2e-08 173_[+3]_311 26686 1.7e-07 89_[+3]_395 7322 1.1e-06 1_[+3]_483 6780 1.2e-06 404_[+3]_80 35164 1.4e-06 17_[+3]_467 23175 1.4e-06 92_[+3]_392 20626 1.4e-06 19_[+3]_465 269616 2.8e-06 39_[+3]_445 31929 3.1e-06 316_[+3]_168 9318 3.5e-06 214_[+3]_270 39255 3.5e-06 404_[+3]_80 28570 3.8e-06 299_[+3]_185 268714 3.8e-06 94_[+3]_390 22240 4.7e-06 83_[+3]_401 2920 5.8e-06 216_[+3]_268 261047 7.7e-06 41_[+3]_443 23356 7.7e-06 96_[+3]_388 23385 1.1e-05 191_[+3]_293 41122 1.2e-05 79_[+3]_405 42226 1.4e-05 220_[+3]_264 268238 2.5e-05 151_[+3]_333 23887 4.4e-05 278_[+3]_206 31809 5.7e-05 257_[+3]_227 42213 6.4e-05 218_[+3]_266 26403 8.6e-05 337_[+3]_147 21475 0.00011 102_[+3]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=26 15424 ( 174) CGTTGCTGGTGGTGGG 1 26686 ( 90) TGGTGGTGGTGGTGGC 1 7322 ( 2) GGTTGTTGTTGGGGGG 1 6780 ( 405) GGTTGTGGGAGCTGGG 1 35164 ( 18) CGTTGTTGGTGATGCC 1 23175 ( 93) CGTTGTTGGTGATGCC 1 20626 ( 20) CGTTGCTGTTGTCGTT 1 269616 ( 40) CGTTGATGTTGTGGGG 1 31929 ( 317) GGTTGTGGAAGTTGGT 1 9318 ( 215) GGGTGATGATGGTGGT 1 39255 ( 405) GGTGGCGGGTGGTGGT 1 28570 ( 300) GGTTGGTTGTGTCGGC 1 268714 ( 95) TGTTGTGGGAGGCGCC 1 22240 ( 84) GGATGGTGGAGGTGGC 1 2920 ( 217) TGGTGCTGTTGATGTG 1 261047 ( 42) TGTTGAGGATGTAGGC 1 23356 ( 97) GGTTGCTGTGGCTGTG 1 23385 ( 192) GGTTGCTGTTGCTTTG 1 41122 ( 80) CGTTGGTGCAGTCGTT 1 42226 ( 221) TGCTGCTGCTGCCGGC 1 268238 ( 152) CGGCGATGGAGGTGGC 1 23887 ( 279) ATTTGGTGGTGTCGTC 1 31809 ( 258) TGGTGGGGGGGGTTGC 1 42213 ( 219) TGCTGCGGATGTAGTG 1 26403 ( 338) TGTTGTGTTAGGGGTT 1 21475 ( 103) TTTGGAGGCTGTTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16490 bayes= 9.8378 E= 2.0e-007 -274 23 45 42 -1134 -1134 186 -175 -274 -158 -40 142 -1134 -258 -172 178 -1134 -1134 198 -1134 -43 42 -14 6 -1134 -1134 45 134 -1134 -1134 186 -175 -75 -99 86 6 6 -1134 -172 134 -1134 -1134 198 -1134 -116 -58 60 42 -175 1 -114 116 -1134 -1134 186 -175 -1134 -99 109 42 -1134 101 28 -16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 26 E= 2.0e-007 0.038462 0.269231 0.346154 0.346154 0.000000 0.000000 0.923077 0.076923 0.038462 0.076923 0.192308 0.692308 0.000000 0.038462 0.076923 0.884615 0.000000 0.000000 1.000000 0.000000 0.192308 0.307692 0.230769 0.269231 0.000000 0.000000 0.346154 0.653846 0.000000 0.000000 0.923077 0.076923 0.153846 0.115385 0.461538 0.269231 0.269231 0.000000 0.076923 0.653846 0.000000 0.000000 1.000000 0.000000 0.115385 0.153846 0.384615 0.346154 0.076923 0.230769 0.115385 0.576923 0.000000 0.000000 0.923077 0.076923 0.000000 0.115385 0.538462 0.346154 0.000000 0.461538 0.307692 0.230769 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GTC]GTTG[CTG][TG]G[GT][TA]G[GT][TC]G[GT][CGT] -------------------------------------------------------------------------------- Time 34.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15424 3.37e-15 96_[+2(2.79e-07)]_11_[+2(2.35e-05)]_\ 24_[+3(1.24e-08)]_96_[+3(5.33e-05)]_131_[+1(1.04e-11)]_10_[+1(7.59e-06)]_\ 16 20626 9.51e-09 19_[+3(1.38e-06)]_93_[+2(2.79e-07)]_\ 321_[+1(6.93e-07)]_9 21475 7.36e-04 241_[+1(7.73e-07)]_198_\ [+1(6.43e-05)]_19 22170 3.61e-02 331_[+1(1.14e-05)]_148 22221 5.94e-02 479_[+1(4.95e-06)] 22240 8.39e-07 83_[+3(4.73e-06)]_25_[+2(2.94e-06)]_\ 317_[+1(2.61e-06)]_17 23175 2.24e-08 31_[+3(6.43e-05)]_45_[+3(1.38e-06)]_\ 252_[+1(4.96e-07)]_41_[+2(9.88e-07)]_57 23356 8.93e-07 96_[+3(7.70e-06)]_307_\ [+2(1.18e-08)]_60 23385 4.47e-07 13_[+2(2.79e-07)]_157_\ [+3(1.11e-05)]_136_[+1(5.89e-06)]_136 23472 1.18e-04 69_[+2(2.79e-07)]_337_\ [+1(3.40e-05)]_52 23887 6.41e-04 278_[+3(4.38e-05)]_72_\ [+1(9.57e-07)]_113 24834 7.23e-03 [+1(1.06e-06)]_155_[+1(6.05e-05)]_\ 303 25869 3.48e-05 231_[+2(2.72e-06)]_13_\ [+1(5.03e-05)]_136_[+1(6.93e-07)]_57 261047 1.53e-10 41_[+3(7.70e-06)]_26_[+2(7.09e-08)]_\ 171_[+1(5.69e-09)]_170_[+1(6.98e-06)]_13 26403 5.40e-04 337_[+3(8.64e-05)]_120_\ [+1(4.96e-07)]_6 26686 1.16e-08 64_[+2(6.21e-07)]_4_[+3(1.69e-07)]_\ 371_[+1(3.15e-06)]_3 268068 1.62e-01 310_[+1(2.77e-05)]_169 268238 2.49e-05 26_[+1(8.14e-05)]_10_[+2(8.23e-07)]_\ 73_[+3(2.49e-05)]_333 268350 1.89e-06 353_[+1(1.94e-05)]_20_\ [+2(1.01e-08)]_85 268714 8.81e-07 94_[+3(3.85e-06)]_8_[+1(1.33e-05)]_\ 173_[+2(7.50e-07)]_167 269616 3.24e-04 39_[+3(2.79e-06)]_55_[+2(8.72e-06)]_\ 369 28570 5.51e-09 255_[+2(2.14e-06)]_23_\ [+3(3.85e-06)]_127_[+1(1.80e-08)]_10_[+1(4.72e-05)]_6 2920 3.15e-07 80_[+1(2.15e-06)]_115_\ [+3(5.78e-06)]_180_[+2(9.88e-07)]_67 31809 4.74e-07 14_[+2(1.40e-06)]_222_\ [+3(5.68e-05)]_109_[+1(2.45e-07)]_97 31929 1.96e-06 64_[+2(4.31e-06)]_52_[+1(6.98e-06)]_\ 158_[+3(3.11e-06)]_168 35164 2.24e-08 17_[+3(1.38e-06)]_252_\ [+1(4.96e-07)]_41_[+2(9.88e-07)]_132 39255 1.16e-04 10_[+2(2.72e-06)]_373_\ [+3(3.46e-06)]_80 40774 7.03e-04 229_[+2(3.43e-06)]_214_\ [+1(1.33e-05)]_15 41122 2.85e-07 79_[+3(1.21e-05)]_218_\ [+2(2.32e-06)]_125_[+1(3.94e-07)]_20 42213 2.86e-03 218_[+3(6.43e-05)]_119_\ [+1(5.40e-06)]_18_[+1(2.41e-05)]_87 42226 3.44e-04 220_[+3(1.43e-05)]_31_\ [+1(2.61e-06)]_212 6780 2.38e-08 78_[+1(1.49e-07)]_160_\ [+2(4.00e-06)]_124_[+3(1.22e-06)]_80 7322 6.33e-05 1_[+3(1.07e-06)]_455_[+1(2.61e-06)]_\ 7 9318 2.60e-07 83_[+2(8.73e-05)]_110_\ [+3(3.46e-06)]_195_[+2(1.71e-09)]_54 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************