******************************************************************************** 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/384/384.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10836 1.0000 500 11394 1.0000 500 11932 1.0000 500 1764 1.0000 500 1976 1.0000 500 21557 1.0000 500 21636 1.0000 500 22220 1.0000 500 22701 1.0000 500 24561 1.0000 500 24699 1.0000 500 24894 1.0000 500 25075 1.0000 500 25407 1.0000 500 2574 1.0000 500 262248 1.0000 500 262249 1.0000 500 262378 1.0000 500 263215 1.0000 500 2635 1.0000 500 263936 1.0000 500 264656 1.0000 500 3629 1.0000 500 37710 1.0000 500 4229 1.0000 500 4348 1.0000 500 4668 1.0000 500 4781 1.0000 500 5120 1.0000 500 5357 1.0000 500 5479 1.0000 500 6944 1.0000 500 7895 1.0000 500 8219 1.0000 500 8704 1.0000 500 8705 1.0000 500 9014 1.0000 500 9440 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/384/384.seqs.fa -oc motifs/384 -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= 38 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= 19000 N= 38 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.278 C 0.236 G 0.216 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.278 C 0.236 G 0.216 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 26 llr = 277 E-value = 7.4e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::5::13:31::21 pos.-specific C ::5:11:21::1:::: probability G 47:63:55283:5a:9 matrix T 5354294242485:8: bits 2.2 2.0 * 1.8 * * 1.5 * * Relative 1.3 * * *** Entropy 1.1 * * * * *** (15.4 bits) 0.9 **** ** * ***** 0.7 **** ** * ***** 0.4 **** *** ******* 0.2 **************** 0.0 ---------------- Multilevel TGCGATGGTGTTGGTG consensus GTTTG T A A T sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 262249 155 2.18e-07 TGTGTAGCAA TGCGATGTAGATTGTG TGGATTGTAG 262248 155 2.18e-07 TGTGTAGCAA TGCGATGTAGATTGTG TGGATTGTAG 21557 150 5.21e-07 GACCAGCGTT GTTGATGTTGGTGGTG TTCTGATGAT 21636 81 5.92e-07 CTGCGGTTGG TGTGCTGCAGGTGGTG ATGGCAAGAC 4348 419 7.55e-07 TATTGGAGCA TGCTTTGCAGTTGGTG GAGTGGTCAT 2574 233 7.55e-07 TAGTGTGATG CGCGGTGGAGTTGGTG AATTAAGTTG 2635 97 1.33e-06 TTTGTGTTCT GGTTATTGTTATTGTG CGAGAGATAG 9014 42 1.51e-06 GAACAGACGT GGCTCTGGTGGCGGTG GCACCAACCC 22701 315 1.67e-06 AATGATCGGG GGCTATGGTGATGGTA GGAGGAGCAC 8219 91 1.87e-06 CTCGCACGCT TGCTTTTCGGTTTGTG CAGGGAGACA 8704 39 2.57e-06 GTTGGTTTCT TGTGCTTGTGGATGTG CTCACACCTG 264656 425 3.13e-06 CTTCCTCTAC GGCTATTGCGTTGGAG GTATGCTCAT 263936 294 3.13e-06 TGCCATGAAA TTTGATGCTTTTGGTG ATGAAATTTG 263215 349 4.58e-06 TTTTACTATG TGGGATGGAGTAGGTG ACGGGTAAGT 24561 232 4.58e-06 TGTTCGTTCT TGCTATTTGGTTTGAG AACGTGGGTG 4229 102 5.51e-06 CCCTGTCGTC GTCGTTTGTGGCTGTG AGTGAGAGGA 6944 294 6.55e-06 GTTTCGTCAT GGTGTCGGTGTCGGTG TTTGGGTGAA 8705 39 7.77e-06 TCACCATGGA TGCTATCTAGGTTGTG AGGCTCTCGT 1764 150 9.23e-06 AGTTGTCATG GTCGGTTCGTGTTGTG GAGGTTCGTA 22220 2 1.00e-05 G TGTTGTTGATGTTGAG TGTTGCATCT 11394 201 1.48e-05 CCGTTGCTCT TTTGACGATGATGGTG TCAACTGAAG 7895 290 1.85e-05 TGGTGGTAAG TGTTGTTGTGTAGGTA GGATAAAACT 5357 21 2.00e-05 AGCAAGTACT GTTGGTTGGAATTGTG ACCACACTAT 5120 104 2.30e-05 TCTTCACCAT TGTGATGGCGATAGAG TGTACTTCTT 24699 44 2.30e-05 CATCCTGATG GGTGGTGAGGTTGATG AGATCAATGT 9440 154 3.46e-05 TACTTGAAAG GTCTGCTGGTATTGTG AAACAACATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262249 2.2e-07 154_[+1]_330 262248 2.2e-07 154_[+1]_330 21557 5.2e-07 149_[+1]_335 21636 5.9e-07 80_[+1]_404 4348 7.6e-07 418_[+1]_66 2574 7.6e-07 232_[+1]_252 2635 1.3e-06 96_[+1]_388 9014 1.5e-06 41_[+1]_443 22701 1.7e-06 314_[+1]_170 8219 1.9e-06 90_[+1]_394 8704 2.6e-06 38_[+1]_446 264656 3.1e-06 424_[+1]_60 263936 3.1e-06 293_[+1]_191 263215 4.6e-06 348_[+1]_136 24561 4.6e-06 231_[+1]_253 4229 5.5e-06 101_[+1]_383 6944 6.6e-06 293_[+1]_191 8705 7.8e-06 38_[+1]_446 1764 9.2e-06 149_[+1]_335 22220 1e-05 1_[+1]_483 11394 1.5e-05 200_[+1]_284 7895 1.9e-05 289_[+1]_195 5357 2e-05 20_[+1]_464 5120 2.3e-05 103_[+1]_381 24699 2.3e-05 43_[+1]_441 9440 3.5e-05 153_[+1]_331 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=26 262249 ( 155) TGCGATGTAGATTGTG 1 262248 ( 155) TGCGATGTAGATTGTG 1 21557 ( 150) GTTGATGTTGGTGGTG 1 21636 ( 81) TGTGCTGCAGGTGGTG 1 4348 ( 419) TGCTTTGCAGTTGGTG 1 2574 ( 233) CGCGGTGGAGTTGGTG 1 2635 ( 97) GGTTATTGTTATTGTG 1 9014 ( 42) GGCTCTGGTGGCGGTG 1 22701 ( 315) GGCTATGGTGATGGTA 1 8219 ( 91) TGCTTTTCGGTTTGTG 1 8704 ( 39) TGTGCTTGTGGATGTG 1 264656 ( 425) GGCTATTGCGTTGGAG 1 263936 ( 294) TTTGATGCTTTTGGTG 1 263215 ( 349) TGGGATGGAGTAGGTG 1 24561 ( 232) TGCTATTTGGTTTGAG 1 4229 ( 102) GTCGTTTGTGGCTGTG 1 6944 ( 294) GGTGTCGGTGTCGGTG 1 8705 ( 39) TGCTATCTAGGTTGTG 1 1764 ( 150) GTCGGTTCGTGTTGTG 1 22220 ( 2) TGTTGTTGATGTTGAG 1 11394 ( 201) TTTGACGATGATGGTG 1 7895 ( 290) TGTTGTTGTGTAGGTA 1 5357 ( 21) GTTGGTTGGAATTGTG 1 5120 ( 104) TGTGATGGCGATAGAG 1 24699 ( 44) GGTGGTGAGGTTGATG 1 9440 ( 154) GTCTGCTGGTATTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 18430 bayes= 9.99843 E= 7.4e-009 -1134 -261 97 99 -1134 -1134 176 -1 -1134 108 -248 77 -1134 -1134 142 64 73 -103 32 -82 -1134 -103 -1134 171 -1134 -261 132 64 -185 -29 132 -50 15 -161 10 50 -285 -1134 183 -50 15 -1134 51 50 -127 -103 -1134 150 -285 -1134 121 77 -285 -1134 216 -1134 -85 -1134 -1134 164 -185 -1134 210 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 26 E= 7.4e-009 0.000000 0.038462 0.423077 0.538462 0.000000 0.000000 0.730769 0.269231 0.000000 0.500000 0.038462 0.461538 0.000000 0.000000 0.576923 0.423077 0.461538 0.115385 0.269231 0.153846 0.000000 0.115385 0.000000 0.884615 0.000000 0.038462 0.538462 0.423077 0.076923 0.192308 0.538462 0.192308 0.307692 0.076923 0.230769 0.384615 0.038462 0.000000 0.769231 0.192308 0.307692 0.000000 0.307692 0.384615 0.115385 0.115385 0.000000 0.769231 0.038462 0.000000 0.500000 0.461538 0.038462 0.000000 0.961538 0.000000 0.153846 0.000000 0.000000 0.846154 0.076923 0.000000 0.923077 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][GT][CT][GT][AG]T[GT]G[TAG]G[TAG]T[GT]GTG -------------------------------------------------------------------------------- Time 13.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 28 llr = 315 E-value = 3.1e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :146:61:65513664426:: pos.-specific C 66329:2931:653465631a probability G :1:::11:11:31:::11:1: matrix T 42221371:34::1::1119: bits 2.2 2.0 1.8 * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * * * ** (16.2 bits) 0.9 * * * ** ** 0.7 * * *** ** ** *** 0.4 ** ****** *********** 0.2 ********************* 0.0 --------------------- Multilevel CCAACATCAAACCAACCCATC consensus T CC T CTTGACCAAAC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8219 431 7.76e-09 ATCGAGACAC CCACCATCAATCAACAACATC ACCAAACAAT 7895 424 5.62e-08 AGAGGATCAT CCAACATTCAACGCACCCATC ACTCTCACAC 24699 461 6.45e-08 CTGTCGTGTT TCAACAACAATGCACACCATC ATCGTCTGTT 262249 310 8.45e-08 ATACTCTCTT CCTACTTCGTACCACCACCTC TCACATGACA 262248 310 8.45e-08 ATACTCTCTT CCTACTTCGTACCACCACCTC TCACATGACA 22220 477 1.82e-07 CAATCTATCC TGTACATCAAACATACACATC ACA 3629 446 2.95e-07 CGCACATACA TCACCACCCTTCCAACGCATC ACCTTTCTCA 5357 274 5.22e-07 GCTCCTCCTA CCATCACCATAGCCCCCGATC ATTGGGGTGG 11932 443 5.22e-07 CTCACACAAA TCAACATCAATCCACCCATCC ATCCATCCAT 4781 470 8.93e-07 TTGGATTGAG GCCCCATCAAAGCAACATCTC ATAACCCAAC 263936 181 9.91e-07 AATGAGACCA CTCACATCAATGCAACCTCGC CATACATTCG 24894 480 1.22e-06 CACTCCACTA CCAACATCAACCTAACCGATC 262378 353 1.49e-06 TACACCGATA CCAACATCACATCACATCATC ATCACATCGA 25075 189 1.49e-06 TCTCCCGATC CACACATCAAACACCCCGTTC CCTCTTGGAA 4348 366 2.41e-06 GCAAATACAA TCCATATCAATGATACAAATC CAGACAGTCG 6944 348 2.90e-06 GGGGGGGGAT TTCCCGCCAATCCAACCACTC ACATAATCTT 8705 431 3.80e-06 GGCTCACAAA TCCTCATCGGTCGCAAACATC GTTCAGCACA 1976 230 4.15e-06 AACATAGTTG CTATCTCCATTGCCAACAATC AATCGATACA 24561 115 4.53e-06 ATCTAGATTA TGCTCTTCCGTCAAACACCTC TCCACGTCGT 8704 109 5.38e-06 GCGAAATTGG CTCACTTCCTTGACCAGCATC AACTGTAGGC 21557 450 5.38e-06 AAAAATGTGA CCTCCTTCCAACGTCATCATC GAATGATCGG 264656 314 1.31e-05 TTTGTGAACT TGTACGTTCAACACACCCCTC GTCCAACGAT 4668 57 1.41e-05 AGCAGAAACT CTGACAACACAACAACACATC AGATACTGTC 2574 278 1.52e-05 GCCAGGGTGA CAAACTGCAAAGCTACCAAGC ACGGGTTGTT 21636 467 1.76e-05 CAGTACAAAC CAAACATCACACAAACACACA ATATCAACGC 25407 146 1.90e-05 AATCTCCCGT TCCCCTCCCAAAGAAAACTTC CCCATTGAAA 10836 476 2.70e-05 TCCGTCGTCG TCTACCTTCCTCCAAACTATC AACC 2635 420 3.31e-05 AGGGTAAACA CCATTTGCATAGCCAACACTC TCAACAATAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8219 7.8e-09 430_[+2]_49 7895 5.6e-08 423_[+2]_56 24699 6.5e-08 460_[+2]_19 262249 8.4e-08 309_[+2]_170 262248 8.4e-08 309_[+2]_170 22220 1.8e-07 476_[+2]_3 3629 2.9e-07 445_[+2]_34 5357 5.2e-07 273_[+2]_206 11932 5.2e-07 442_[+2]_37 4781 8.9e-07 469_[+2]_10 263936 9.9e-07 180_[+2]_299 24894 1.2e-06 479_[+2] 262378 1.5e-06 352_[+2]_127 25075 1.5e-06 188_[+2]_291 4348 2.4e-06 365_[+2]_114 6944 2.9e-06 347_[+2]_132 8705 3.8e-06 430_[+2]_49 1976 4.1e-06 229_[+2]_250 24561 4.5e-06 114_[+2]_365 8704 5.4e-06 108_[+2]_371 21557 5.4e-06 449_[+2]_30 264656 1.3e-05 313_[+2]_166 4668 1.4e-05 56_[+2]_423 2574 1.5e-05 277_[+2]_202 21636 1.8e-05 466_[+2]_13 25407 1.9e-05 145_[+2]_334 10836 2.7e-05 475_[+2]_4 2635 3.3e-05 419_[+2]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=28 8219 ( 431) CCACCATCAATCAACAACATC 1 7895 ( 424) CCAACATTCAACGCACCCATC 1 24699 ( 461) TCAACAACAATGCACACCATC 1 262249 ( 310) CCTACTTCGTACCACCACCTC 1 262248 ( 310) CCTACTTCGTACCACCACCTC 1 22220 ( 477) TGTACATCAAACATACACATC 1 3629 ( 446) TCACCACCCTTCCAACGCATC 1 5357 ( 274) CCATCACCATAGCCCCCGATC 1 11932 ( 443) TCAACATCAATCCACCCATCC 1 4781 ( 470) GCCCCATCAAAGCAACATCTC 1 263936 ( 181) CTCACATCAATGCAACCTCGC 1 24894 ( 480) CCAACATCAACCTAACCGATC 1 262378 ( 353) CCAACATCACATCACATCATC 1 25075 ( 189) CACACATCAAACACCCCGTTC 1 4348 ( 366) TCCATATCAATGATACAAATC 1 6944 ( 348) TTCCCGCCAATCCAACCACTC 1 8705 ( 431) TCCTCATCGGTCGCAAACATC 1 1976 ( 230) CTATCTCCATTGCCAACAATC 1 24561 ( 115) TGCTCTTCCGTCAAACACCTC 1 8704 ( 109) CTCACTTCCTTGACCAGCATC 1 21557 ( 450) CCTCCTTCCAACGTCATCATC 1 264656 ( 314) TGTACGTTCAACACACCCCTC 1 4668 ( 57) CTGACAACACAACAACACATC 1 2574 ( 278) CAAACTGCAAAGCTACCAAGC 1 21636 ( 467) CAAACATCACACAAACACACA 1 25407 ( 146) TCCCCTCCCAAAGAAAACTTC 1 10836 ( 476) TCTACCTTCCTCCAAACTATC 1 2635 ( 420) CCATTTGCATAGCCAACACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 9.95173 E= 3.1e-008 -1145 128 -259 54 -137 136 -101 -60 63 45 -259 -34 113 -14 -1145 -60 -1145 198 -1145 -192 104 -272 -159 25 -196 -40 -159 132 -1145 192 -1145 -134 113 28 -101 -1145 95 -72 -159 -12 95 -272 -1145 66 -196 128 58 -292 4 118 -59 -292 104 28 -1145 -92 121 60 -1145 -1145 36 145 -1145 -1145 50 98 -159 -192 -37 128 -101 -134 113 28 -1145 -134 -1145 -172 -159 166 -295 203 -1145 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 28 E= 3.1e-008 0.000000 0.571429 0.035714 0.392857 0.107143 0.607143 0.107143 0.178571 0.428571 0.321429 0.035714 0.214286 0.607143 0.214286 0.000000 0.178571 0.000000 0.928571 0.000000 0.071429 0.571429 0.035714 0.071429 0.321429 0.071429 0.178571 0.071429 0.678571 0.000000 0.892857 0.000000 0.107143 0.607143 0.285714 0.107143 0.000000 0.535714 0.142857 0.071429 0.250000 0.535714 0.035714 0.000000 0.428571 0.071429 0.571429 0.321429 0.035714 0.285714 0.535714 0.142857 0.035714 0.571429 0.285714 0.000000 0.142857 0.642857 0.357143 0.000000 0.000000 0.357143 0.642857 0.000000 0.000000 0.392857 0.464286 0.071429 0.071429 0.214286 0.571429 0.107143 0.107143 0.607143 0.285714 0.000000 0.107143 0.000000 0.071429 0.071429 0.857143 0.035714 0.964286 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]C[ACT][AC]C[AT]TC[AC][AT][AT][CG][CA][AC][AC][CA][CA][CA][AC]TC -------------------------------------------------------------------------------- Time 25.61 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 151 E-value = 1.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:2:1:1323:2::4211::a pos.-specific C :a:1712::1:12:47:::7: probability G ::64:9277:a3:a1:9:33: matrix T 9:242:4:16:38::1:97:: bits 2.2 * * 2.0 * * * 1.8 * * * * * * 1.5 * * * * * * Relative 1.3 ** * * * ** * Entropy 1.1 ** * * * ** ***** (24.3 bits) 0.9 ** ** ** * ** ****** 0.7 ****** ** * ********* 0.4 ****** **** ********* 0.2 ********************* 0.0 --------------------- Multilevel TCGGCGTGGTGGTGACGTTCA consensus ATT CAAA TC CA GG sequence T G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262249 185 2.30e-11 TTGTAGAGTT TCGGCGTAGTGATGCCGTTCA ACGGCTCTTC 262248 185 2.30e-11 TTGTAGAGTT TCGGCGTAGTGATGCCGTTCA ACGGCTCTTC 1764 180 2.45e-09 TTCGTAGGCG TCGGTGCGGTGTCGACGTGGA ACTTGAAACT 5357 219 7.29e-09 TACCGCTCAA ACGTCCCGGTGTTGCCGTTCA CCCTCCTACT 8705 115 8.74e-09 GAAACGGAGG TCGGAGGGGAGGTGGAGTTCA TGGGTACTTG 24561 302 2.93e-08 TCTCATTGTT TCACCGGGAAGCTGCCGTTGA ATGAACAAAG 22701 193 5.45e-08 GGACTTCACT TCTTCGAAACGTTGACGTTGA CCACGTAATA 263215 156 6.59e-08 ACAATTCAAG TCTTTGTGGAGGTGATGAGCA ACAAATTCGT 22220 144 1.24e-07 GTTTGCTTCA TCATCGTGTTGGCGAAATGCA GGAGTGTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262249 2.3e-11 184_[+3]_295 262248 2.3e-11 184_[+3]_295 1764 2.5e-09 179_[+3]_300 5357 7.3e-09 218_[+3]_261 8705 8.7e-09 114_[+3]_365 24561 2.9e-08 301_[+3]_178 22701 5.4e-08 192_[+3]_287 263215 6.6e-08 155_[+3]_324 22220 1.2e-07 143_[+3]_336 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 262249 ( 185) TCGGCGTAGTGATGCCGTTCA 1 262248 ( 185) TCGGCGTAGTGATGCCGTTCA 1 1764 ( 180) TCGGTGCGGTGTCGACGTGGA 1 5357 ( 219) ACGTCCCGGTGTTGCCGTTCA 1 8705 ( 115) TCGGAGGGGAGGTGGAGTTCA 1 24561 ( 302) TCACCGGGAAGCTGCCGTTGA 1 22701 ( 193) TCTTCGAAACGTTGACGTTGA 1 263215 ( 156) TCTTTGTGGAGGTGATGAGCA 1 22220 ( 144) TCATCGTGTTGGCGAAATGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 11.8325 E= 1.2e-001 -132 -982 -982 171 -982 208 -982 -982 -32 -982 136 -29 -982 -108 104 71 -132 150 -982 -29 -982 -108 204 -982 -132 -9 4 71 26 -982 163 -982 -32 -982 163 -128 26 -108 -982 103 -982 -982 221 -982 -32 -108 63 30 -982 -9 -982 152 -982 -982 221 -982 68 91 -95 -982 -32 150 -982 -128 -132 -982 204 -982 -132 -982 -982 171 -982 -982 63 130 -982 150 63 -982 185 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.2e-001 0.111111 0.000000 0.000000 0.888889 0.000000 1.000000 0.000000 0.000000 0.222222 0.000000 0.555556 0.222222 0.000000 0.111111 0.444444 0.444444 0.111111 0.666667 0.000000 0.222222 0.000000 0.111111 0.888889 0.000000 0.111111 0.222222 0.222222 0.444444 0.333333 0.000000 0.666667 0.000000 0.222222 0.000000 0.666667 0.111111 0.333333 0.111111 0.000000 0.555556 0.000000 0.000000 1.000000 0.000000 0.222222 0.111111 0.333333 0.333333 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 1.000000 0.000000 0.444444 0.444444 0.111111 0.000000 0.222222 0.666667 0.000000 0.111111 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TC[GAT][GT][CT]G[TCG][GA][GA][TA]G[GTA][TC]G[AC][CA]GT[TG][CG]A -------------------------------------------------------------------------------- Time 37.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10836 1.94e-02 475_[+2(2.70e-05)]_4 11394 4.34e-02 29_[+1(7.96e-05)]_155_\ [+1(1.48e-05)]_284 11932 2.09e-03 442_[+2(5.22e-07)]_37 1764 1.31e-07 149_[+1(9.23e-06)]_14_\ [+3(2.45e-09)]_300 1976 6.48e-03 229_[+2(4.15e-06)]_174_\ [+2(9.41e-05)]_55 21557 4.20e-05 149_[+1(5.21e-07)]_128_\ [+1(4.74e-05)]_140_[+2(5.38e-06)]_30 21636 4.84e-05 42_[+1(3.03e-05)]_22_[+1(5.92e-07)]_\ 370_[+2(1.76e-05)]_13 22220 8.16e-09 1_[+1(1.00e-05)]_126_[+3(1.24e-07)]_\ 7_[+1(5.67e-05)]_289_[+2(1.82e-07)]_3 22701 7.04e-07 192_[+3(5.45e-08)]_101_\ [+1(1.67e-06)]_170 24561 2.03e-08 114_[+2(4.53e-06)]_96_\ [+1(4.58e-06)]_54_[+3(2.93e-08)]_178 24699 6.61e-06 43_[+1(2.30e-05)]_401_\ [+2(6.45e-08)]_19 24894 1.39e-02 453_[+2(4.88e-05)]_5_[+2(1.22e-06)] 25075 1.23e-02 188_[+2(1.49e-06)]_291 25407 1.45e-01 145_[+2(1.90e-05)]_334 2574 3.41e-05 232_[+1(7.55e-07)]_29_\ [+2(1.52e-05)]_202 262248 3.53e-14 132_[+1(5.03e-05)]_6_[+1(2.18e-07)]_\ 14_[+3(2.30e-11)]_104_[+2(8.45e-08)]_170 262249 3.53e-14 132_[+1(5.03e-05)]_6_[+1(2.18e-07)]_\ 14_[+3(2.30e-11)]_104_[+2(8.45e-08)]_170 262378 4.95e-03 352_[+2(1.49e-06)]_127 263215 8.65e-06 155_[+3(6.59e-08)]_172_\ [+1(4.58e-06)]_136 2635 2.11e-04 96_[+1(1.33e-06)]_307_\ [+2(3.31e-05)]_60 263936 8.80e-06 180_[+2(9.91e-07)]_92_\ [+1(3.13e-06)]_191 264656 5.32e-04 313_[+2(1.31e-05)]_90_\ [+1(3.13e-06)]_60 3629 2.33e-03 445_[+2(2.95e-07)]_34 37710 6.00e-01 500 4229 7.09e-03 101_[+1(5.51e-06)]_383 4348 9.44e-06 365_[+2(2.41e-06)]_32_\ [+1(7.55e-07)]_66 4668 6.51e-02 56_[+2(1.41e-05)]_423 4781 3.22e-03 469_[+2(8.93e-07)]_10 5120 2.22e-02 103_[+1(2.30e-05)]_381 5357 2.97e-09 20_[+1(2.00e-05)]_182_\ [+3(7.29e-09)]_34_[+2(5.22e-07)]_206 5479 6.82e-01 500 6944 7.40e-05 293_[+1(6.55e-06)]_38_\ [+2(2.90e-06)]_132 7895 2.93e-05 58_[+2(7.93e-05)]_210_\ [+1(1.85e-05)]_118_[+2(5.62e-08)]_56 8219 3.55e-07 90_[+1(1.87e-06)]_324_\ [+2(7.76e-09)]_49 8704 2.55e-04 38_[+1(2.57e-06)]_54_[+2(5.38e-06)]_\ 371 8705 9.19e-09 38_[+1(7.77e-06)]_60_[+3(8.74e-09)]_\ 295_[+2(3.80e-06)]_49 9014 2.73e-03 41_[+1(1.51e-06)]_443 9440 1.09e-01 153_[+1(3.46e-05)]_331 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************