******************************************************************************** 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/228/228.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11660 1.0000 500 12061 1.0000 500 20873 1.0000 500 21398 1.0000 500 21706 1.0000 500 22261 1.0000 500 22854 1.0000 500 24390 1.0000 500 25475 1.0000 500 261250 1.0000 500 263463 1.0000 500 268451 1.0000 500 26926 1.0000 500 270004 1.0000 500 28185 1.0000 500 31438 1.0000 500 3314 1.0000 500 35224 1.0000 500 36321 1.0000 500 36501 1.0000 500 37156 1.0000 500 39698 1.0000 500 5053 1.0000 500 bd96 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/228/228.seqs.fa -oc motifs/228 -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= 24 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= 12000 N= 24 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.247 G 0.241 T 0.254 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.247 G 0.241 T 0.254 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 24 llr = 271 E-value = 2.8e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:8:163:25334233237:4 pos.-specific C 3a:a81894173472375295 probability G ::::1::13::11:33:2:1: matrix T 5:2::3::14:312221:1:: bits 2.1 * * 1.8 * * 1.6 * * 1.4 * * * * Relative 1.2 * * ** * Entropy 1.0 **** ** * * (16.3 bits) 0.8 **** ** * * ** 0.6 ******* ** * * *** 0.4 ******** ** * ***** 0.2 *********** ** ***** 0.0 --------------------- Multilevel TCACCACCCACCACAACCACC consensus C T TA GTAAC GC AC A sequence A A T CG G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24390 395 4.00e-10 CGCTCTACAC TCACCTCCGACCACAACCACC CATCATCCAC 11660 395 4.00e-10 CGCTCTACAC TCACCTCCGACCACAACCACC CATCATCCAC 26926 16 5.25e-09 ACAAGATGTG TCACCACCGTAAACAGCCACA TTCACTGAAA 261250 18 1.78e-08 ATCACCATCA CCACCACCATCACCGTCAACA TCACTCATGT 20873 439 2.46e-08 ACTCAAAGCA CCACCACCCAAGCCTGCCACA ACGCCAGCCA 21398 82 3.89e-08 CCCCTTGCCA TCACCACCATCACCACCATCC GTTGTCGTCT 36321 357 6.97e-08 CGTCACTCCA CCACCACCCACCCACCCACCC ACCAAACTAA 270004 441 2.93e-07 ACAGGGGAGG ACACCCCCCCCCACCGCCACC ACACCACGCC 35224 402 4.68e-07 ACACAACCAC ACACCAAGCACCTCAACCACC CATTCATTTC 3314 259 4.68e-07 TCCTCACCAC TCACCACCCTCTTTCCCCTCC TCGCGTGTAG 28185 79 1.37e-06 GATTGGTCTT CCTCCTCCGACGACGAAGACA ACGACAGCGA 5053 82 1.52e-06 ACAACATGGT ACACCACCGACAACGCTGACG TACAACACTG bd96 97 4.22e-06 TGCGCCGACT TCACCACCCAATCCTTCGCAC GCACCGGCGA 21706 458 4.22e-06 GTAGAAAAAT CCTCCAACCTCCCCTCCTCCA GGTCCTTCAC 263463 175 5.46e-06 GTTGTTGATA CCACCACCGTCTGAGGAGCCA TTCACACCAT 22854 156 5.46e-06 TGCATCTTCT TCTCATACCAATCCAACGACA GTTTCGACAC 25475 298 8.21e-06 CAGGCGAAAG TCACGTCCAAATCTGGACACA TACGACCGAT 37156 431 1.12e-05 CTGTCTGGCG ACACCACCTTAAGCCACAAGC CACTCAGTGC 268451 476 1.12e-05 ATGCTTTCGC TCACAACCAACCAAGAAAAGC AGGG 36501 147 4.04e-05 GTAGAGGAGT CCACGCAGCACACAGCCCTCC CTCTTCGTTG 22261 468 4.04e-05 AGACGTCGAG TCTCCTCCCCTCTCTCTCACA ACACAGGCAA 12061 57 5.10e-05 CAGAGTCATC TCGCGAAGGACGATAGCCACC TACTTTGTTG 39698 27 7.49e-05 GAGGCGCCTG TCACCAACTTCAGCCTTACCT TCCCTCCGAG 31438 133 1.74e-04 TCTGCAATTC ACTCACCCATCTATTTGAACA GTAAACTCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24390 4e-10 394_[+1]_85 11660 4e-10 394_[+1]_85 26926 5.3e-09 15_[+1]_464 261250 1.8e-08 17_[+1]_462 20873 2.5e-08 438_[+1]_41 21398 3.9e-08 81_[+1]_398 36321 7e-08 356_[+1]_123 270004 2.9e-07 440_[+1]_39 35224 4.7e-07 401_[+1]_78 3314 4.7e-07 258_[+1]_221 28185 1.4e-06 78_[+1]_401 5053 1.5e-06 81_[+1]_398 bd96 4.2e-06 96_[+1]_383 21706 4.2e-06 457_[+1]_22 263463 5.5e-06 174_[+1]_305 22854 5.5e-06 155_[+1]_324 25475 8.2e-06 297_[+1]_182 37156 1.1e-05 430_[+1]_49 268451 1.1e-05 475_[+1]_4 36501 4e-05 146_[+1]_333 22261 4e-05 467_[+1]_12 12061 5.1e-05 56_[+1]_423 39698 7.5e-05 26_[+1]_453 31438 0.00017 132_[+1]_347 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=24 24390 ( 395) TCACCTCCGACCACAACCACC 1 11660 ( 395) TCACCTCCGACCACAACCACC 1 26926 ( 16) TCACCACCGTAAACAGCCACA 1 261250 ( 18) CCACCACCATCACCGTCAACA 1 20873 ( 439) CCACCACCCAAGCCTGCCACA 1 21398 ( 82) TCACCACCATCACCACCATCC 1 36321 ( 357) CCACCACCCACCCACCCACCC 1 270004 ( 441) ACACCCCCCCCCACCGCCACC 1 35224 ( 402) ACACCAAGCACCTCAACCACC 1 3314 ( 259) TCACCACCCTCTTTCCCCTCC 1 28185 ( 79) CCTCCTCCGACGACGAAGACA 1 5053 ( 82) ACACCACCGACAACGCTGACG 1 bd96 ( 97) TCACCACCCAATCCTTCGCAC 1 21706 ( 458) CCTCCAACCTCCCCTCCTCCA 1 263463 ( 175) CCACCACCGTCTGAGGAGCCA 1 22854 ( 156) TCTCATACCAATCCAACGACA 1 25475 ( 298) TCACGTCCAAATCTGGACACA 1 37156 ( 431) ACACCACCTTAAGCCACAAGC 1 268451 ( 476) TCACAACCAACCAAGAAAAGC 1 36501 ( 147) CCACGCAGCACACAGCCCTCC 1 22261 ( 468) TCTCCTCCCCTCTCTCTCACA 1 12061 ( 57) TCGCGAAGGACGATAGCCACC 1 39698 ( 27) TCACCAACTTCAGCCTTACCT 1 31438 ( 133) ACTCACCCATCTATTTGAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11520 bayes= 9.35214 E= 2.8e-013 -31 24 -1123 98 -1123 202 -1123 -1123 154 -1123 -253 -29 -1123 202 -1123 -1123 -104 160 -95 -1123 128 -98 -1123 -2 -4 160 -1123 -1123 -1123 182 -95 -1123 -31 75 27 -161 107 -157 -1123 56 -4 152 -1123 -261 18 43 -95 -2 54 60 -95 -102 -63 143 -1123 -61 18 -25 27 -29 18 24 5 -61 -63 143 -253 -102 18 89 -21 -261 137 -25 -1123 -102 -262 182 -153 -1123 69 102 -253 -261 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 2.8e-013 0.208333 0.291667 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.041667 0.208333 0.000000 1.000000 0.000000 0.000000 0.125000 0.750000 0.125000 0.000000 0.625000 0.125000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.208333 0.416667 0.291667 0.083333 0.541667 0.083333 0.000000 0.375000 0.250000 0.708333 0.000000 0.041667 0.291667 0.333333 0.125000 0.250000 0.375000 0.375000 0.125000 0.125000 0.166667 0.666667 0.000000 0.166667 0.291667 0.208333 0.291667 0.208333 0.291667 0.291667 0.250000 0.166667 0.166667 0.666667 0.041667 0.125000 0.291667 0.458333 0.208333 0.041667 0.666667 0.208333 0.000000 0.125000 0.041667 0.875000 0.083333 0.000000 0.416667 0.500000 0.041667 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TCA]C[AT]CC[AT][CA]C[CGA][AT][CA][CAT][AC]C[AGCT][ACG]C[CAG][AC]C[CA] -------------------------------------------------------------------------------- Time 5.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 9 llr = 149 E-value = 2.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1:32::47:7::1111:::1 pos.-specific C ::12::21:::1::::3::2: probability G a24218142a::a14911a:9 matrix T :742727:1:39:84:49:8: bits 2.1 * * * * 1.8 * * * * 1.6 * * * * 1.4 * * ** * ** * Relative 1.2 * * * ** * **** Entropy 1.0 * * ***** * **** (23.9 bits) 0.8 ** *** ****** * **** 0.6 *** ************ **** 0.4 *** ************ **** 0.2 *** ***************** 0.0 --------------------- Multilevel GTGATGTAAGATGTGGTTGTG consensus GTCATCGG T T C C sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24390 263 3.30e-12 CTCAAACGAT GTGATGTGAGATGTGGCTGTG GCACCGTTCA 11660 263 3.30e-12 CTCAAACGAT GTGATGTGAGATGTGGCTGTG GCACCGTTCA 28185 450 5.32e-09 CTTCAAACCA GTGTTGGAAGATGATGCTGTG TTGATGTGCA 36501 102 1.43e-08 GGGTGCTTAT GGGGAGTAGGATGGTGTTGTG GATCGGAAGT 263463 50 2.91e-08 TTGACAGATG GGTATGTAGGTTGTGATTGCG AACTCGTATT 26926 284 4.47e-08 GGTCTTCTTC GTCCATTGTGTTGTTGTTGTG GAAGGGGAGA 261250 196 5.14e-08 GCTTGTTGTT GTTCTTCGAGTTGTTGTGGCG TTGCCGGTGT 25475 28 5.14e-08 TGTAGGATGT GTTTGGCAAGACGTGGGTGTG ATCAACGATT 22261 94 1.69e-07 GACGATAGGT GATGTGTCAGATGTAGATGTA CAACAATTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24390 3.3e-12 262_[+2]_217 11660 3.3e-12 262_[+2]_217 28185 5.3e-09 449_[+2]_30 36501 1.4e-08 101_[+2]_378 263463 2.9e-08 49_[+2]_430 26926 4.5e-08 283_[+2]_196 261250 5.1e-08 195_[+2]_284 25475 5.1e-08 27_[+2]_452 22261 1.7e-07 93_[+2]_386 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=9 24390 ( 263) GTGATGTGAGATGTGGCTGTG 1 11660 ( 263) GTGATGTGAGATGTGGCTGTG 1 28185 ( 450) GTGTTGGAAGATGATGCTGTG 1 36501 ( 102) GGGGAGTAGGATGGTGTTGTG 1 263463 ( 50) GGTATGTAGGTTGTGATTGCG 1 26926 ( 284) GTCCATTGTGTTGTTGTTGTG 1 261250 ( 196) GTTCTTCGAGTTGTTGTGGCG 1 25475 ( 28) GTTTGGCAAGACGTGGGTGTG 1 22261 ( 94) GATGTGTCAGATGTAGATGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11520 bayes= 11.1693 E= 2.7e-003 -982 -982 205 -982 -121 -982 -12 139 -982 -115 88 81 37 -15 -12 -19 -21 -982 -112 139 -982 -982 169 -19 -982 -15 -112 139 79 -115 88 -982 137 -982 -12 -119 -982 -982 205 -982 137 -982 -982 39 -982 -115 -982 180 -982 -982 205 -982 -121 -982 -112 161 -121 -982 88 81 -121 -982 188 -982 -121 43 -112 81 -982 -982 -112 180 -982 -982 205 -982 -982 -15 -982 161 -121 -982 188 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 2.7e-003 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.222222 0.666667 0.000000 0.111111 0.444444 0.444444 0.333333 0.222222 0.222222 0.222222 0.222222 0.000000 0.111111 0.666667 0.000000 0.000000 0.777778 0.222222 0.000000 0.222222 0.111111 0.666667 0.444444 0.111111 0.444444 0.000000 0.666667 0.000000 0.222222 0.111111 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.111111 0.777778 0.111111 0.000000 0.444444 0.444444 0.111111 0.000000 0.888889 0.000000 0.111111 0.333333 0.111111 0.444444 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 1.000000 0.000000 0.000000 0.222222 0.000000 0.777778 0.111111 0.000000 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TG][GT][ACGT][TA][GT][TC][AG][AG]G[AT]TGT[GT]G[TC]TG[TC]G -------------------------------------------------------------------------------- Time 11.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 24 llr = 247 E-value = 1.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:6::5251::21:6:13 pos.-specific C :6:11:225:16:1:2121: probability G 2:98:47122248:75:773 matrix T 84:13612126:27233114 bits 2.1 1.8 1.6 * 1.4 * Relative 1.2 * * Entropy 1.0 * * * ** (14.8 bits) 0.8 **** * *** * 0.6 ******* **** *** 0.4 ******* ************ 0.2 ******************** 0.0 -------------------- Multilevel TCGGATGACATCGTGGAGGT consensus T TGCCAG GT TTTC G sequence T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 12061 130 3.06e-11 GTTGTCGTGG TCGGATGACATCGTGTTGGT TGCGTTCTGT 270004 218 2.44e-07 TACTGTGCAG TCGGAGGAGATGGAAGAGGT ATTGGGTTGA 36321 89 2.76e-07 GAAGTCTTCT TCGGAGCTCATCTTGCTGGA TGGCGGGTGT 21398 271 7.78e-07 CTTCATTGTT TCGGATCCCATGGTTCAGAT TTGTGAGGAG 24390 355 8.68e-07 CTTGCTCGTT TCAGTTGACAGCGTGGCGGG AGGAGTCTGG 21706 324 8.68e-07 CGGTTGTAGG TTGCATGTCTTCGTGTAGTG GTTGAGCTCG 11660 355 8.68e-07 CTTGCTCGTT TCAGTTGACAGCGTGGCGGG AGGAGTCTGG 20873 349 1.08e-06 CGTCGGGGGG TTGGTTCCGTTGGTGTTGGT GATGGTCCCG 26926 252 1.20e-06 TTCGTCTTCG TCGGAGGAGTTGTTGTAGCG GCGGTCTTCT 22261 54 1.48e-06 CAGTTTGCAT TAGGAGGTCATCGATTAGGT ACACGTAATG bd96 454 1.64e-06 ATGGGTGGCC GTGGAGGACGCGGTGGACGA GGCCCGTGGA 31438 12 4.83e-06 TTGCTTTGCA TCGGATGTGATCTTTCTGTA GATGGCAGCT 39698 217 5.81e-06 ATTGTCATCT TTGCATGAAAACGTGGACTT GTCTAAAGAC 261250 393 5.81e-06 ATTTCCTTTG GCGGATGACGACGTAGATGT CATTTCTGCT 268451 108 6.36e-06 AGAGGATAGT TTGATGTAAATGGTGGAGGG TAATGGAGTG 36501 74 2.10e-05 TTCACCTGGC TTGGATAGCATGGTCGTCGG GTGCTTATGG 35224 212 2.27e-05 TGCAGCTCGA TCGTATGACATGGCTCTCAT CACTTGTCCC 5053 416 2.66e-05 AGACCTTCAA GTGGTTCACTTCGCGTTGCG TGGAAACCCA 263463 74 2.66e-05 GATTGCGAAC TCGTATTGAATGTCGGAGGA TAAGAGGCTG 3314 60 2.87e-05 GACAGAGGCG GTGGCGGCAGGCGAGGAGGA GTAAAAGGAC 25475 214 3.34e-05 GACAAAGAGA TCGGTGGCTGGCTTGAAGGA GTGGTCGTTC 28185 345 6.88e-05 CGATGGATCG TTGGGTGGTGACGAGTTGGG TAAGCTGCTT 22854 305 1.17e-04 CCTCTCTTCG CCGGAGGCATCGGTGTACAT GAGGCCTCGG 37156 165 1.33e-04 AAGATACTTC TCGTCTCTCCTCGTTGATGA TGCAACTTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12061 3.1e-11 129_[+3]_351 270004 2.4e-07 217_[+3]_263 36321 2.8e-07 88_[+3]_392 21398 7.8e-07 270_[+3]_210 24390 8.7e-07 354_[+3]_126 21706 8.7e-07 323_[+3]_157 11660 8.7e-07 354_[+3]_126 20873 1.1e-06 348_[+3]_132 26926 1.2e-06 251_[+3]_229 22261 1.5e-06 53_[+3]_427 bd96 1.6e-06 453_[+3]_27 31438 4.8e-06 11_[+3]_469 39698 5.8e-06 216_[+3]_264 261250 5.8e-06 392_[+3]_88 268451 6.4e-06 107_[+3]_373 36501 2.1e-05 73_[+3]_407 35224 2.3e-05 211_[+3]_269 5053 2.7e-05 415_[+3]_65 263463 2.7e-05 73_[+3]_407 3314 2.9e-05 59_[+3]_421 25475 3.3e-05 213_[+3]_267 28185 6.9e-05 344_[+3]_136 22854 0.00012 304_[+3]_176 37156 0.00013 164_[+3]_316 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=24 12061 ( 130) TCGGATGACATCGTGTTGGT 1 270004 ( 218) TCGGAGGAGATGGAAGAGGT 1 36321 ( 89) TCGGAGCTCATCTTGCTGGA 1 21398 ( 271) TCGGATCCCATGGTTCAGAT 1 24390 ( 355) TCAGTTGACAGCGTGGCGGG 1 21706 ( 324) TTGCATGTCTTCGTGTAGTG 1 11660 ( 355) TCAGTTGACAGCGTGGCGGG 1 20873 ( 349) TTGGTTCCGTTGGTGTTGGT 1 26926 ( 252) TCGGAGGAGTTGTTGTAGCG 1 22261 ( 54) TAGGAGGTCATCGATTAGGT 1 bd96 ( 454) GTGGAGGACGCGGTGGACGA 1 31438 ( 12) TCGGATGTGATCTTTCTGTA 1 39698 ( 217) TTGCATGAAAACGTGGACTT 1 261250 ( 393) GCGGATGACGACGTAGATGT 1 268451 ( 108) TTGATGTAAATGGTGGAGGG 1 36501 ( 74) TTGGATAGCATGGTCGTCGG 1 35224 ( 212) TCGTATGACATGGCTCTCAT 1 5053 ( 416) GTGGTTCACTTCGCGTTGCG 1 263463 ( 74) TCGTATTGAATGTCGGAGGA 1 3314 ( 60) GTGGCGGCAGGCGAGGAGGA 1 25475 ( 214) TCGGTGGCTGGCTTGAAGGA 1 28185 ( 345) TTGGGTGGTGACGAGTTGGG 1 22854 ( 305) CCGGAGGCATCGGTGTACAT 1 37156 ( 165) TCGTCTCTCCTCGTTGATGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 11544 bayes= 8.90689 E= 1.6e-002 -1123 -256 -53 164 -262 124 -1123 56 -163 -1123 193 -1123 -262 -157 164 -102 128 -157 -253 -2 -1123 -1123 64 130 -262 -25 147 -161 83 -25 -95 -29 -31 113 -53 -161 107 -256 -21 -29 -104 -157 -53 130 -1123 124 79 -1123 -1123 -1123 171 -29 -63 -98 -1123 148 -163 -256 147 -29 -262 -57 93 39 118 -157 -1123 39 -1123 -25 155 -161 -104 -157 147 -102 18 -1123 47 56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 24 E= 1.6e-002 0.000000 0.041667 0.166667 0.791667 0.041667 0.583333 0.000000 0.375000 0.083333 0.000000 0.916667 0.000000 0.041667 0.083333 0.750000 0.125000 0.625000 0.083333 0.041667 0.250000 0.000000 0.000000 0.375000 0.625000 0.041667 0.208333 0.666667 0.083333 0.458333 0.208333 0.125000 0.208333 0.208333 0.541667 0.166667 0.083333 0.541667 0.041667 0.208333 0.208333 0.125000 0.083333 0.166667 0.625000 0.000000 0.583333 0.416667 0.000000 0.000000 0.000000 0.791667 0.208333 0.166667 0.125000 0.000000 0.708333 0.083333 0.041667 0.666667 0.208333 0.041667 0.166667 0.458333 0.333333 0.583333 0.083333 0.000000 0.333333 0.000000 0.208333 0.708333 0.083333 0.125000 0.083333 0.666667 0.125000 0.291667 0.000000 0.333333 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT]GG[AT][TG][GC][ACT][CA][AGT]T[CG][GT]T[GT][GT][AT][GC]G[TGA] -------------------------------------------------------------------------------- Time 16.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11660 1.26e-16 262_[+2(3.30e-12)]_71_\ [+3(8.68e-07)]_20_[+1(4.00e-10)]_85 12061 1.26e-08 56_[+1(5.10e-05)]_31_[+3(5.58e-05)]_\ 1_[+3(3.06e-11)]_351 20873 3.94e-07 348_[+3(1.08e-06)]_70_\ [+1(2.46e-08)]_41 21398 3.98e-07 81_[+1(3.89e-08)]_168_\ [+3(7.78e-07)]_210 21706 1.47e-05 323_[+3(8.68e-07)]_114_\ [+1(4.22e-06)]_22 22261 2.59e-07 53_[+3(1.48e-06)]_20_[+2(1.69e-07)]_\ 353_[+1(4.04e-05)]_12 22854 3.49e-03 155_[+1(5.46e-06)]_324 24390 1.26e-16 262_[+2(3.30e-12)]_71_\ [+3(8.68e-07)]_20_[+1(4.00e-10)]_85 25475 3.51e-07 27_[+2(5.14e-08)]_165_\ [+3(3.34e-05)]_64_[+1(8.21e-06)]_182 261250 2.51e-10 17_[+1(1.78e-08)]_157_\ [+2(5.14e-08)]_176_[+3(5.81e-06)]_88 263463 1.18e-07 49_[+2(2.91e-08)]_3_[+3(2.66e-05)]_\ 81_[+1(5.46e-06)]_305 268451 3.42e-04 107_[+3(6.36e-06)]_348_\ [+1(1.12e-05)]_4 26926 1.61e-11 15_[+1(5.25e-09)]_68_[+1(5.40e-05)]_\ 126_[+3(1.20e-06)]_12_[+2(4.47e-08)]_161_[+1(1.12e-05)]_14 270004 5.25e-07 217_[+3(2.44e-07)]_203_\ [+1(2.93e-07)]_[+1(7.58e-06)]_18 28185 1.66e-08 78_[+1(1.37e-06)]_245_\ [+3(6.88e-05)]_85_[+2(5.32e-09)]_30 31438 6.98e-03 11_[+3(4.83e-06)]_469 3314 1.70e-04 59_[+3(2.87e-05)]_127_\ [+1(9.19e-05)]_1_[+1(2.44e-05)]_9_[+1(4.68e-07)]_221 35224 2.09e-04 211_[+3(2.27e-05)]_170_\ [+1(4.68e-07)]_8_[+1(4.28e-05)]_49 36321 1.22e-07 88_[+3(2.76e-07)]_248_\ [+1(6.97e-08)]_84_[+1(8.31e-05)]_18 36501 3.05e-07 73_[+3(2.10e-05)]_8_[+2(1.43e-08)]_\ 24_[+1(4.04e-05)]_333 37156 4.58e-03 430_[+1(1.12e-05)]_49 39698 2.20e-03 26_[+1(7.49e-05)]_169_\ [+3(5.81e-06)]_264 5053 1.66e-04 81_[+1(1.52e-06)]_313_\ [+3(2.66e-05)]_65 bd96 9.90e-06 96_[+1(4.22e-06)]_306_\ [+2(8.51e-05)]_9_[+3(1.64e-06)]_27 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************