******************************************************************************** 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/231/231.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10053 1.0000 500 10273 1.0000 500 15976 1.0000 500 17511 1.0000 500 20580 1.0000 500 20613 1.0000 500 20643 1.0000 500 20930 1.0000 500 21654 1.0000 500 21769 1.0000 500 22427 1.0000 500 22465 1.0000 500 22808 1.0000 500 22826 1.0000 500 23331 1.0000 500 23599 1.0000 500 24226 1.0000 500 24552 1.0000 500 24642 1.0000 500 24893 1.0000 500 25247 1.0000 500 25539 1.0000 500 25824 1.0000 500 260923 1.0000 500 261777 1.0000 500 262091 1.0000 500 262699 1.0000 500 263363 1.0000 500 263630 1.0000 500 26492 1.0000 500 267957 1.0000 500 269018 1.0000 500 269966 1.0000 500 270286 1.0000 500 27083 1.0000 500 3007 1.0000 500 30301 1.0000 500 3135 1.0000 500 31404 1.0000 500 33670 1.0000 500 34059 1.0000 500 34303 1.0000 500 36007 1.0000 500 38225 1.0000 500 39924 1.0000 500 42621 1.0000 500 42821 1.0000 500 7450 1.0000 500 bd1828 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/231/231.seqs.fa -oc motifs/231 -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= 49 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= 24500 N= 49 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.238 G 0.241 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.238 G 0.241 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 40 llr = 435 E-value = 9.5e-023 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :13314:2735:573634634 pos.-specific C 763491881718326376275 probability G :31::41:2:21:1:1::::: matrix T 3143122:1:312:11:12:1 bits 2.1 1.9 1.7 1.4 Relative 1.2 * * * * Entropy 1.0 * * ** * * * * (15.7 bits) 0.8 * * ** * * * ** ** 0.6 * * **** * ******** 0.4 ** * **** ********** 0.2 ********************* 0.0 --------------------- Multilevel CCTCCGCCACACAACACCACC consensus TGAA A AGAT CCACAACAA sequence CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10053 386 4.98e-11 ACCTCCCTCT CCTCCGCCACACAACACCAAA GCCGACTGAC 38225 477 1.68e-08 TCGTCTCTCT CCTACGCCACGGTACACCACC GAA 34303 396 2.30e-08 CCCTCCGTCC TCTCCACCACACAACCACAAA CACAACCTCC 27083 444 4.20e-08 AGTCAGAGTC CGTCCACCACACACCACACAC CCGTTCTCTG 39924 345 6.45e-08 TGCGTCTTTC TCCTCACCAAATCACACCACC AGAAGAGATA 30301 479 8.53e-08 CACGTACGTC CCAACGCCGCTGAACACAACA C 42821 177 2.14e-07 CGACAACAAC TCCTCGCCACTCCAACCAAAC CGGGTGACAT 33670 390 2.43e-07 CCAACTCAAC CGAACTCAACGCAAAACCACA AGAACCCGAC 267957 466 2.43e-07 TCAGCCACCG CCGACGCCGAGCCACACCACA TAGGTCGAGG 263630 447 3.95e-07 CACAGCCTCA CGTTCACCACCGACAACCACC CAACAATCGC 22808 446 3.95e-07 ACGTTTGTCA TCCCCTCCCCACCACACACCC CGTAACATAC 263363 219 4.45e-07 CTACCACTGC CGTTCATCAATCAATACCACC AAAGTCATTG 21654 463 1.09e-06 TGCACCGCTG CGCTCGCCACTTCACCACTCC AATTATCACC 24893 176 1.67e-06 CCACCAATCG CCTTGGCCACACACAACATCC CCACTCCCTC 26492 250 1.85e-06 TCCTCCCAAC TCAACACCGCATCACCCACCC ACAAAGCAGA 24552 154 1.85e-06 AACATTGAAG CTCTCACCACACCCACACTCC CCCTTACTAT 10273 457 1.85e-06 CCTCTACACA CTCTCGTCAACCCACACAACA ACTCAGCAAC 24226 78 2.05e-06 CGTAGCAGCA CAAACAACACACAACAACACA AGGAACACAA 31404 120 2.50e-06 CAAACCTTAA CGCCCATCACACGACACATCA ACTATCACAT 15976 431 2.50e-06 CTTAAGCAGC TGCTCGTCACTCACCAACCCA TTCCTCTCCC 36007 341 3.04e-06 GGTACCGTAA CCTACACATAGCTACAACACA CCACGCTTAA 270286 342 3.04e-06 GGTACCGTAA CCTACACATAGCTACAACACA CCACGCTTAA 20930 207 4.88e-06 ACGGTGACTG CCTACACCAATCAAATCTCCC CATCAGATGA 262091 472 5.35e-06 TCTCTCTCTC TCTTTGCCGCAGCACCCAACA GCAGCACC 260923 468 5.86e-06 AGAGAATACA CCTCCGTCACTCTACAACCAT GGCTTCGAAA 21769 408 5.86e-06 ATAGCCGATG CCTCCTCCAGCCAATACCAAC GCTCACACTC 261777 64 6.41e-06 ACCGACGGCT TGAACACAAAACTACTACACC GCAACCGTTG 3007 453 7.01e-06 AAACGTTGTC TCACAGCCGCACAATCCAACA GCCTACCGAT 25247 425 7.66e-06 CCTCCTTCCC CTCCCGCCCCTCCCCAACCAC CGAACGAGCC 23331 102 9.93e-06 GTCAGTGCAC CTGCCTCCAATCAATACCAAC CACCCTTCTT 269018 392 1.39e-05 AGCATCTTGA CCTCTCCAGCACCAACACACA TCAGCCAAAT 23599 43 1.77e-05 TCTGGTCACA CACCTACCACACTCCACATAC ACCAGACCTC 22427 56 2.07e-05 AGCTTCAGCG CCCTCGCCCAGCCAAGCATCA ACACCGAACA 7450 446 2.42e-05 CTGCAACAGG CGACATCCACACAAATCCACT GGCGGCTGGC 20643 457 2.61e-05 ATTGTGATTG TCATCGGCGACCAGCACCACC TGCTATCTGC 20580 434 3.27e-05 CATCCACTGG TCTCCCCAACAGACAGCAACC GGCCGACGAC 34059 178 4.06e-05 TCTCCGCCTA CGAACGGAGCTCAAAAACCAC CAGCAGCACC 25539 252 5.38e-05 CAGCTCAATG CGAGCTCAACATACCCCCAAA ATGATGAGCC 269966 462 7.53e-05 TAAAAGACTT TCAACATCTCATCACACTTCA GATTGCCGCC 3135 420 9.74e-05 ACACAGCCAG CATCCCCCAAGCTGACAAACC ACGTTTCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10053 5e-11 385_[+1]_94 38225 1.7e-08 476_[+1]_3 34303 2.3e-08 395_[+1]_84 27083 4.2e-08 443_[+1]_36 39924 6.5e-08 344_[+1]_135 30301 8.5e-08 478_[+1]_1 42821 2.1e-07 176_[+1]_303 33670 2.4e-07 389_[+1]_90 267957 2.4e-07 465_[+1]_14 263630 4e-07 446_[+1]_33 22808 4e-07 445_[+1]_34 263363 4.4e-07 218_[+1]_261 21654 1.1e-06 462_[+1]_17 24893 1.7e-06 175_[+1]_304 26492 1.8e-06 249_[+1]_230 24552 1.8e-06 153_[+1]_326 10273 1.8e-06 456_[+1]_23 24226 2e-06 77_[+1]_402 31404 2.5e-06 119_[+1]_360 15976 2.5e-06 430_[+1]_49 36007 3e-06 340_[+1]_139 270286 3e-06 341_[+1]_138 20930 4.9e-06 206_[+1]_273 262091 5.4e-06 471_[+1]_8 260923 5.9e-06 467_[+1]_12 21769 5.9e-06 407_[+1]_72 261777 6.4e-06 63_[+1]_416 3007 7e-06 452_[+1]_27 25247 7.7e-06 424_[+1]_55 23331 9.9e-06 101_[+1]_378 269018 1.4e-05 391_[+1]_88 23599 1.8e-05 42_[+1]_437 22427 2.1e-05 55_[+1]_424 7450 2.4e-05 445_[+1]_34 20643 2.6e-05 456_[+1]_23 20580 3.3e-05 433_[+1]_46 34059 4.1e-05 177_[+1]_302 25539 5.4e-05 251_[+1]_228 269966 7.5e-05 461_[+1]_18 3135 9.7e-05 419_[+1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=40 10053 ( 386) CCTCCGCCACACAACACCAAA 1 38225 ( 477) CCTACGCCACGGTACACCACC 1 34303 ( 396) TCTCCACCACACAACCACAAA 1 27083 ( 444) CGTCCACCACACACCACACAC 1 39924 ( 345) TCCTCACCAAATCACACCACC 1 30301 ( 479) CCAACGCCGCTGAACACAACA 1 42821 ( 177) TCCTCGCCACTCCAACCAAAC 1 33670 ( 390) CGAACTCAACGCAAAACCACA 1 267957 ( 466) CCGACGCCGAGCCACACCACA 1 263630 ( 447) CGTTCACCACCGACAACCACC 1 22808 ( 446) TCCCCTCCCCACCACACACCC 1 263363 ( 219) CGTTCATCAATCAATACCACC 1 21654 ( 463) CGCTCGCCACTTCACCACTCC 1 24893 ( 176) CCTTGGCCACACACAACATCC 1 26492 ( 250) TCAACACCGCATCACCCACCC 1 24552 ( 154) CTCTCACCACACCCACACTCC 1 10273 ( 457) CTCTCGTCAACCCACACAACA 1 24226 ( 78) CAAACAACACACAACAACACA 1 31404 ( 120) CGCCCATCACACGACACATCA 1 15976 ( 431) TGCTCGTCACTCACCAACCCA 1 36007 ( 341) CCTACACATAGCTACAACACA 1 270286 ( 342) CCTACACATAGCTACAACACA 1 20930 ( 207) CCTACACCAATCAAATCTCCC 1 262091 ( 472) TCTTTGCCGCAGCACCCAACA 1 260923 ( 468) CCTCCGTCACTCTACAACCAT 1 21769 ( 408) CCTCCTCCAGCCAATACCAAC 1 261777 ( 64) TGAACACAAAACTACTACACC 1 3007 ( 453) TCACAGCCGCACAATCCAACA 1 25247 ( 425) CTCCCGCCCCTCCCCAACCAC 1 23331 ( 102) CTGCCTCCAATCAATACCAAC 1 269018 ( 392) CCTCTCCAGCACCAACACACA 1 23599 ( 43) CACCTACCACACTCCACATAC 1 22427 ( 56) CCCTCGCCCAGCCAAGCATCA 1 7450 ( 446) CGACATCCACACAAATCCACT 1 20643 ( 457) TCATCGGCGACCAGCACCACC 1 20580 ( 434) TCTCCCCAACAGACAGCAACC 1 34059 ( 178) CGAACGGAGCTCAAAAACCAC 1 25539 ( 252) CGAGCTCAACATACCCCCAAA 1 269966 ( 462) TCAACATCTCATCACACTTCA 1 3135 ( 420) CATCCCCCAAGCTGACAAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 23520 bayes= 9.44915 E= 9.5e-023 -1197 156 -1197 23 -182 121 19 -136 6 21 -227 64 18 66 -327 23 -240 184 -327 -177 51 -167 73 -77 -340 170 -227 -77 -40 175 -1197 -1197 130 -167 -27 -177 18 150 -327 -1197 85 -125 -46 -4 -1197 166 -95 -104 85 45 -327 -55 146 -8 -227 -1197 18 133 -1197 -136 124 7 -227 -177 30 150 -1197 -1197 41 133 -1197 -236 124 -25 -1197 -55 6 161 -1197 -1197 69 114 -1197 -236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 40 E= 9.5e-023 0.000000 0.700000 0.000000 0.300000 0.075000 0.550000 0.275000 0.100000 0.275000 0.275000 0.050000 0.400000 0.300000 0.375000 0.025000 0.300000 0.050000 0.850000 0.025000 0.075000 0.375000 0.075000 0.400000 0.150000 0.025000 0.775000 0.050000 0.150000 0.200000 0.800000 0.000000 0.000000 0.650000 0.075000 0.200000 0.075000 0.300000 0.675000 0.025000 0.000000 0.475000 0.100000 0.175000 0.250000 0.000000 0.750000 0.125000 0.125000 0.475000 0.325000 0.025000 0.175000 0.725000 0.225000 0.050000 0.000000 0.300000 0.600000 0.000000 0.100000 0.625000 0.250000 0.050000 0.075000 0.325000 0.675000 0.000000 0.000000 0.350000 0.600000 0.000000 0.050000 0.625000 0.200000 0.000000 0.175000 0.275000 0.725000 0.000000 0.000000 0.425000 0.525000 0.000000 0.050000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CG][TAC][CAT]C[GA]C[CA][AG][CA][AT]C[AC][AC][CA][AC][CA][CA][AC][CA][CA] -------------------------------------------------------------------------------- Time 18.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 40 llr = 386 E-value = 3.4e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :31:3::431:331:: pos.-specific C ::2:11:2:1311:1: probability G 82:821a173474329 matrix T 257249:4:63:2782 bits 2.1 1.9 * 1.7 * 1.4 ** * Relative 1.2 * * ** * * Entropy 1.0 * * ** * ** (13.9 bits) 0.8 * ** ** * * *** 0.6 * ** ** ** * *** 0.4 **** ** **** *** 0.2 **************** 0.0 ---------------- Multilevel GTTGTTGTGTGGGTTG consensus TAC A AAGTAAGG sequence G C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 261777 149 7.30e-09 GCATTATTGA GTTGTTGAGTTGATTG TTGCATATCA 262699 101 1.06e-07 ATGGTGGTCG GTTGTTGCATGGGTTG GCCTCCCTGT 22826 431 2.50e-07 CTGACGGGTT GATGTTGAGTTGATGG TTGAAGGTTG bd1828 108 3.45e-07 TGGAGATGTA GTCGATGTGGCGGTTG ACTGGAGAAC 21769 373 7.19e-07 GATGCCCATA GTTGTTGTGTGGAATG AATAATGAAA 34303 138 1.08e-06 TAGTTGATGG GTTGATGAGTTGGTCG AGAGTGGAAG 30301 211 1.08e-06 ATGGTGTTGT GTCGCTGTGTCGATTG GTAATGTTGC 21654 209 1.08e-06 AAGAAAGGGA GGTTGTGTGTTGGTTG TCCATTGTCT 24552 468 1.24e-06 TAGTGTCGTT GTTGTTGTGTTGTGTT GAGAGATTAG 36007 195 1.41e-06 TCCGGAGGAG TTTGATGAGTGGCTTG GCTATTAGAT 270286 196 1.41e-06 TCCGGAGGAG TTTGATGAGTGGCTTG GCTATTAGAT 17511 153 2.05e-06 ATATTCACTG GTTTGTGCGTTGATTG GTACAGGGTA 10273 40 2.05e-06 TTGAGCCGCT GATGGTGTGTTAGTTT GGTGTAGGAA 42621 34 2.92e-06 CGACTAAGAG TGCGTTGTGTGGGGTG GATACTCTGT 25247 113 5.72e-06 GGTGTCAATG GTTGTTGAAGTATGTG TCAGAGAAGC 10053 189 5.72e-06 ATGTTGAAGA GGTGTTTAGTGGGTTG AAGGGAGGGA 26492 476 6.35e-06 CTATTGTGGC GTTGGTGAAACGTTTG GGAGTGGAT 34059 79 7.04e-06 CTCAAAAACT GATGTTGCACTGGTTG GTCGATCTCT 23599 249 7.04e-06 GGCTGTGGTG GGTGTGGTGTCGGGTG CGTCGTTGGT 269966 391 7.79e-06 TCCTACGTGC GTCGTCGCGTCGGTTG ATCTCCATCG 25539 95 9.52e-06 CATCACGATG GTTGATGTGTCAATGT GCTGGATGTG 20643 55 1.05e-05 TATTTATTGC GTTGTTGAAGGAATTT ATGGATTAGA 20930 329 1.40e-05 TAGTGTCGTC GTCGTTGTGGAAGTTG TCGAAAAGTG 20613 26 1.40e-05 TGTAGTAGGG GATGGTGCGTGATGGG GGTGACACCT 269018 2 1.54e-05 G GACGGTGAATGCGTTG GCCGTGGCGA 3135 268 1.85e-05 TGGTGGATTT GATGGTGGGTTGGGTT GCAGAGCGGC 42821 338 2.21e-05 GAAGAAGGGA GGAGATGAGGTGGTGG TGTATCAGAA 22808 78 3.67e-05 CACCCATGAG TATGATGTATGATTTT CTTCACGAGA 38225 72 4.67e-05 TGAGACTATT GATGAGGAGGGAGTGG AACACGATGA 33670 268 5.05e-05 TGTCATCATT GTATTTGAGTTGTGGG AACGAGTCAT 262091 311 5.05e-05 AGCAGAGTTG TATGTTGTGTCATGCG CCGTTGCCCG 263630 42 5.46e-05 CAACGACGAC GGTGGTGGATGATGTG GAGAAGAGAA 22465 154 5.89e-05 TTGTAGCGTC TTCGTTGTGGCTATTG TCTGCAGTTG 23331 420 6.85e-05 TGTACATGAA GATGTTGCACTGCGTG ATTCTTCGTT 15976 84 8.51e-05 ACCACGTTGA GGTAATGAGAGGATTG TAATTTGAAC 3007 292 9.80e-05 GGGAACAAGC TTTGATGTGAGCTGTG AGTGATCCCT 24642 64 9.80e-05 AGAAGAGAGA GATGCCGTAGCAGTTG TTGTTCGCGT 267957 42 1.13e-04 GAAAGGAGCG TTATATGTGGCGGTGG TAATATTGAC 24226 223 1.13e-04 CATTTATCAG TACTCTGTGTCGATGG ATGTCATTGA 7450 225 2.01e-04 GAACGAAGCT GACTGTGAAGGGAATG ATGAACGCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261777 7.3e-09 148_[+2]_336 262699 1.1e-07 100_[+2]_384 22826 2.5e-07 430_[+2]_54 bd1828 3.5e-07 107_[+2]_377 21769 7.2e-07 372_[+2]_112 34303 1.1e-06 137_[+2]_347 30301 1.1e-06 210_[+2]_274 21654 1.1e-06 208_[+2]_276 24552 1.2e-06 467_[+2]_17 36007 1.4e-06 194_[+2]_290 270286 1.4e-06 195_[+2]_289 17511 2e-06 152_[+2]_332 10273 2e-06 39_[+2]_445 42621 2.9e-06 33_[+2]_451 25247 5.7e-06 112_[+2]_372 10053 5.7e-06 188_[+2]_296 26492 6.3e-06 475_[+2]_9 34059 7e-06 78_[+2]_406 23599 7e-06 248_[+2]_236 269966 7.8e-06 390_[+2]_94 25539 9.5e-06 94_[+2]_390 20643 1.1e-05 54_[+2]_430 20930 1.4e-05 328_[+2]_156 20613 1.4e-05 25_[+2]_459 269018 1.5e-05 1_[+2]_483 3135 1.8e-05 267_[+2]_217 42821 2.2e-05 337_[+2]_147 22808 3.7e-05 77_[+2]_407 38225 4.7e-05 71_[+2]_413 33670 5.1e-05 267_[+2]_217 262091 5.1e-05 310_[+2]_174 263630 5.5e-05 41_[+2]_443 22465 5.9e-05 153_[+2]_331 23331 6.8e-05 419_[+2]_65 15976 8.5e-05 83_[+2]_401 3007 9.8e-05 291_[+2]_193 24642 9.8e-05 63_[+2]_421 267957 0.00011 41_[+2]_443 24226 0.00011 222_[+2]_262 7450 0.0002 224_[+2]_260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=40 261777 ( 149) GTTGTTGAGTTGATTG 1 262699 ( 101) GTTGTTGCATGGGTTG 1 22826 ( 431) GATGTTGAGTTGATGG 1 bd1828 ( 108) GTCGATGTGGCGGTTG 1 21769 ( 373) GTTGTTGTGTGGAATG 1 34303 ( 138) GTTGATGAGTTGGTCG 1 30301 ( 211) GTCGCTGTGTCGATTG 1 21654 ( 209) GGTTGTGTGTTGGTTG 1 24552 ( 468) GTTGTTGTGTTGTGTT 1 36007 ( 195) TTTGATGAGTGGCTTG 1 270286 ( 196) TTTGATGAGTGGCTTG 1 17511 ( 153) GTTTGTGCGTTGATTG 1 10273 ( 40) GATGGTGTGTTAGTTT 1 42621 ( 34) TGCGTTGTGTGGGGTG 1 25247 ( 113) GTTGTTGAAGTATGTG 1 10053 ( 189) GGTGTTTAGTGGGTTG 1 26492 ( 476) GTTGGTGAAACGTTTG 1 34059 ( 79) GATGTTGCACTGGTTG 1 23599 ( 249) GGTGTGGTGTCGGGTG 1 269966 ( 391) GTCGTCGCGTCGGTTG 1 25539 ( 95) GTTGATGTGTCAATGT 1 20643 ( 55) GTTGTTGAAGGAATTT 1 20930 ( 329) GTCGTTGTGGAAGTTG 1 20613 ( 26) GATGGTGCGTGATGGG 1 269018 ( 2) GACGGTGAATGCGTTG 1 3135 ( 268) GATGGTGGGTTGGGTT 1 42821 ( 338) GGAGATGAGGTGGTGG 1 22808 ( 78) TATGATGTATGATTTT 1 38225 ( 72) GATGAGGAGGGAGTGG 1 33670 ( 268) GTATTTGAGTTGTGGG 1 262091 ( 311) TATGTTGTGTCATGCG 1 263630 ( 42) GGTGGTGGATGATGTG 1 22465 ( 154) TTCGTTGTGGCTATTG 1 23331 ( 420) GATGTTGCACTGCGTG 1 15976 ( 84) GGTAATGAGAGGATTG 1 3007 ( 292) TTTGATGTGAGCTGTG 1 24642 ( 64) GATGCCGTAGCAGTTG 1 267957 ( 42) TTATATGTGGCGGTGG 1 24226 ( 223) TACTCTGTGTCGATGG 1 7450 ( 225) GACTGTGAAGGGAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 23765 bayes= 9.46412 E= 3.4e-014 -1197 -1197 168 -19 30 -1197 -46 96 -182 -8 -1197 145 -340 -1197 177 -77 6 -167 -10 73 -1197 -225 -227 181 -1197 -1197 201 -335 51 -67 -227 73 6 -1197 159 -1197 -182 -225 5 129 -340 21 63 34 6 -225 143 -335 6 -167 82 -19 -240 -1197 19 140 -1197 -225 -27 155 -1197 -1197 182 -77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 40 E= 3.4e-014 0.000000 0.000000 0.775000 0.225000 0.325000 0.000000 0.175000 0.500000 0.075000 0.225000 0.000000 0.700000 0.025000 0.000000 0.825000 0.150000 0.275000 0.075000 0.225000 0.425000 0.000000 0.050000 0.050000 0.900000 0.000000 0.000000 0.975000 0.025000 0.375000 0.150000 0.050000 0.425000 0.275000 0.000000 0.725000 0.000000 0.075000 0.050000 0.250000 0.625000 0.025000 0.275000 0.375000 0.325000 0.275000 0.050000 0.650000 0.025000 0.275000 0.075000 0.425000 0.225000 0.050000 0.000000 0.275000 0.675000 0.000000 0.050000 0.200000 0.750000 0.000000 0.000000 0.850000 0.150000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][TA][TC]G[TAG]TG[TA][GA][TG][GTC][GA][GAT][TG][TG]G -------------------------------------------------------------------------------- Time 36.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 15 llr = 221 E-value = 3.9e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:217::6:27::84:3:89 pos.-specific C 635119::3325:14:29:1 probability G 3318:1a:1513a1:a::2: matrix T :33:2::46::1::2:51:1 bits 2.1 * * * 1.9 * * * 1.7 ** * * 1.4 ** * * * Relative 1.2 ** * * *** Entropy 1.0 * *** ** * *** (21.3 bits) 0.8 * ****** * ** * *** 0.6 * *********** * *** 0.4 ** ***************** 0.2 ******************** 0.0 -------------------- Multilevel CCCGACGATGACGAAGTCAA consensus GGT T TCCCG C A G sequence TA A T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 20580 456 6.89e-11 ACAGCAACCG GCCGACGACGACGACGTCAA GCCATACTTT 31404 303 5.78e-10 CAGGGCGTTC GCTGACGATGAGGAAGTCAA CGTACAAGCG 25247 91 3.55e-09 CAGGACCTCC CCCGACGATGAGGGTGTCAA TGGTTGTTGA 7450 166 5.29e-09 ATTTGCAAAT CTGGACGTTGACGAAGACAA TGATGCAACG bd1828 438 2.65e-08 CGGGTAGTTC GGAGACGACGACGGTGTCAA CAAAGATACG 36007 48 4.38e-08 CAAAAACAAT CTCGACGTTCCGGAAGTTAA GGCTGAATTC 270286 49 4.38e-08 CAAAAACAAT CTCGACGTTCCGGAAGTTAA GGCTGAATTC 24226 132 6.99e-08 CAACATTAAC AGCAACGACGACGACGACAA CAACAATAAC 24642 438 1.28e-07 AGGCCGACAA CCACACGTCCCCGACGTCAA GTGCTCATGG 3007 34 1.64e-07 GGAGGAGGAA CGAAACGACCACGAAGCCGA ACGCCACCCC 20613 56 2.42e-07 ACACCTCGGC GTTGTCGTTGACGACGTCGT GGTGGTCCAT 10053 31 2.60e-07 GAGGTTGTTG CCCGTCGATGATGCTGCCAA TGATGCGAGC 42621 390 5.59e-07 ACTCAAAAAG CGTGCCGAGAAGGAAGCCAA GGCTGCTGCT 42821 458 7.66e-07 CGGTGGAGCA CTCGTGGATAACGACGACAC GAACAACAAG 22427 206 9.17e-07 AGGAGGTTCG GGTGACGTTAGTGACGACGA CGAGCATCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20580 6.9e-11 455_[+3]_25 31404 5.8e-10 302_[+3]_178 25247 3.5e-09 90_[+3]_390 7450 5.3e-09 165_[+3]_315 bd1828 2.7e-08 437_[+3]_43 36007 4.4e-08 47_[+3]_433 270286 4.4e-08 48_[+3]_432 24226 7e-08 131_[+3]_349 24642 1.3e-07 437_[+3]_43 3007 1.6e-07 33_[+3]_447 20613 2.4e-07 55_[+3]_425 10053 2.6e-07 30_[+3]_450 42621 5.6e-07 389_[+3]_91 42821 7.7e-07 457_[+3]_23 22427 9.2e-07 205_[+3]_275 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=15 20580 ( 456) GCCGACGACGACGACGTCAA 1 31404 ( 303) GCTGACGATGAGGAAGTCAA 1 25247 ( 91) CCCGACGATGAGGGTGTCAA 1 7450 ( 166) CTGGACGTTGACGAAGACAA 1 bd1828 ( 438) GGAGACGACGACGGTGTCAA 1 36007 ( 48) CTCGACGTTCCGGAAGTTAA 1 270286 ( 49) CTCGACGTTCCGGAAGTTAA 1 24226 ( 132) AGCAACGACGACGACGACAA 1 24642 ( 438) CCACACGTCCCCGACGTCAA 1 3007 ( 34) CGAAACGACCACGAAGCCGA 1 20613 ( 56) GTTGTCGTTGACGACGTCGT 1 10053 ( 31) CCCGTCGATGATGCTGCCAA 1 42621 ( 390) CGTGCCGAGAAGGAAGCCAA 1 42821 ( 458) CTCGTGGATAACGACGACAC 1 22427 ( 206) GGTGACGTTAGTGACGACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 23569 bayes= 11.2914 E= 3.9e-007 -198 133 46 -1055 -1055 49 46 38 -40 97 -185 6 -99 -183 173 -1055 147 -183 -1055 -36 -1055 197 -185 -1055 -1055 -1055 205 -1055 118 -1055 -1055 64 -1055 49 -185 123 -40 16 114 -1055 147 -25 -185 -1055 -1055 116 46 -94 -1055 -1055 205 -1055 160 -183 -86 -1055 60 75 -1055 -36 -1055 -1055 205 -1055 1 -25 -1055 106 -1055 186 -1055 -94 160 -1055 -27 -1055 171 -183 -1055 -194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 15 E= 3.9e-007 0.066667 0.600000 0.333333 0.000000 0.000000 0.333333 0.333333 0.333333 0.200000 0.466667 0.066667 0.266667 0.133333 0.066667 0.800000 0.000000 0.733333 0.066667 0.000000 0.200000 0.000000 0.933333 0.066667 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.333333 0.066667 0.600000 0.200000 0.266667 0.533333 0.000000 0.733333 0.200000 0.066667 0.000000 0.000000 0.533333 0.333333 0.133333 0.000000 0.000000 1.000000 0.000000 0.800000 0.066667 0.133333 0.000000 0.400000 0.400000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.266667 0.200000 0.000000 0.533333 0.000000 0.866667 0.000000 0.133333 0.800000 0.000000 0.200000 0.000000 0.866667 0.066667 0.000000 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][CGT][CTA]G[AT]CG[AT][TC][GCA][AC][CG]GA[ACT]G[TAC]C[AG]A -------------------------------------------------------------------------------- Time 53.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10053 4.64e-12 30_[+3(2.60e-07)]_138_\ [+2(5.72e-06)]_181_[+1(4.98e-11)]_94 10273 3.27e-05 39_[+2(2.05e-06)]_401_\ [+1(1.85e-06)]_23 15976 2.36e-03 83_[+2(8.51e-05)]_331_\ [+1(2.50e-06)]_23_[+1(5.02e-05)]_5 17511 2.68e-03 46_[+2(7.37e-05)]_90_[+2(2.05e-06)]_\ 165_[+2(2.86e-05)]_151 20580 9.73e-08 455_[+3(6.89e-11)]_25 20613 4.49e-05 25_[+2(1.40e-05)]_14_[+3(2.42e-07)]_\ 362_[+3(5.34e-05)]_43 20643 2.40e-03 54_[+2(1.05e-05)]_386_\ [+1(2.61e-05)]_23 20930 3.96e-05 206_[+1(4.88e-06)]_101_\ [+2(1.40e-05)]_156 21654 2.43e-05 208_[+2(1.08e-06)]_34_\ [+1(3.03e-05)]_183_[+1(1.09e-06)]_17 21769 9.87e-05 326_[+2(2.63e-05)]_30_\ [+2(7.19e-07)]_19_[+1(5.86e-06)]_72 22427 3.78e-04 55_[+1(2.07e-05)]_129_\ [+3(9.17e-07)]_275 22465 5.05e-02 153_[+2(5.89e-05)]_331 22808 1.79e-04 77_[+2(3.67e-05)]_352_\ [+1(3.95e-07)]_34 22826 1.55e-03 430_[+2(2.50e-07)]_54 23331 6.64e-03 101_[+1(9.93e-06)]_297_\ [+2(6.85e-05)]_65 23599 1.82e-03 42_[+1(1.77e-05)]_185_\ [+2(7.04e-06)]_236 24226 3.93e-07 77_[+1(2.05e-06)]_33_[+3(6.99e-08)]_\ 349 24552 4.23e-05 79_[+1(1.77e-05)]_53_[+1(1.85e-06)]_\ 169_[+2(1.05e-05)]_108_[+2(1.24e-06)]_17 24642 8.00e-05 63_[+2(9.80e-05)]_358_\ [+3(1.28e-07)]_43 24893 1.55e-02 175_[+1(1.67e-06)]_155_\ [+1(1.63e-05)]_128 25247 5.77e-09 90_[+3(3.55e-09)]_2_[+2(5.72e-06)]_\ 296_[+1(7.66e-06)]_21_[+1(3.51e-05)]_13 25539 5.68e-03 52_[+2(9.80e-05)]_26_[+2(9.52e-06)]_\ 141_[+1(5.38e-05)]_228 25824 4.21e-01 500 260923 5.81e-03 467_[+1(5.86e-06)]_12 261777 5.93e-07 63_[+1(6.41e-06)]_64_[+2(7.30e-09)]_\ 336 262091 2.68e-03 310_[+2(5.05e-05)]_145_\ [+1(5.35e-06)]_8 262699 2.14e-03 100_[+2(1.06e-07)]_384 263363 2.32e-03 218_[+1(4.45e-07)]_261 263630 4.05e-05 41_[+2(5.46e-05)]_389_\ [+1(3.95e-07)]_33 26492 4.39e-05 189_[+1(1.51e-05)]_39_\ [+1(1.85e-06)]_205_[+2(6.35e-06)]_9 267957 1.66e-04 465_[+1(2.43e-07)]_14 269018 1.55e-03 1_[+2(1.54e-05)]_374_[+1(1.39e-05)]_\ 88 269966 2.76e-03 390_[+2(7.79e-06)]_55_\ [+1(7.53e-05)]_18 270286 6.88e-09 48_[+3(4.38e-08)]_127_\ [+2(1.41e-06)]_15_[+2(1.05e-05)]_99_[+1(3.04e-06)]_138 27083 3.63e-04 45_[+1(9.14e-05)]_377_\ [+1(4.20e-08)]_36 3007 2.28e-06 33_[+3(1.64e-07)]_238_\ [+2(9.80e-05)]_145_[+1(7.01e-06)]_27 30301 5.78e-07 210_[+2(1.08e-06)]_80_\ [+2(6.35e-05)]_156_[+1(8.53e-08)]_1 3135 5.05e-03 267_[+2(1.85e-05)]_136_\ [+1(9.74e-05)]_60 31404 6.25e-08 119_[+1(2.50e-06)]_162_\ [+3(5.78e-10)]_178 33670 7.66e-05 267_[+2(5.05e-05)]_106_\ [+1(2.43e-07)]_90 34059 8.02e-04 78_[+2(7.04e-06)]_83_[+1(4.06e-05)]_\ 302 34303 6.91e-07 137_[+2(1.08e-06)]_242_\ [+1(2.30e-08)]_84 36007 6.88e-09 47_[+3(4.38e-08)]_127_\ [+2(1.41e-06)]_15_[+2(1.05e-05)]_99_[+1(3.04e-06)]_139 38225 2.91e-06 71_[+2(4.67e-05)]_389_\ [+1(1.68e-08)]_3 39924 2.90e-04 344_[+1(6.45e-08)]_135 42621 4.76e-05 33_[+2(2.92e-06)]_274_\ [+3(5.53e-05)]_46_[+3(5.59e-07)]_91 42821 1.04e-07 55_[+3(8.46e-05)]_101_\ [+1(2.14e-07)]_140_[+2(2.21e-05)]_104_[+3(7.66e-07)]_23 7450 5.87e-07 165_[+3(5.29e-09)]_260_\ [+1(2.42e-05)]_34 bd1828 1.53e-07 58_[+2(3.68e-06)]_33_[+2(3.45e-07)]_\ 314_[+3(2.65e-08)]_43 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************