******************************************************************************** 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/318/318.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10556 1.0000 500 10738 1.0000 500 11018 1.0000 500 11111 1.0000 500 1132 1.0000 500 11984 1.0000 500 1505 1.0000 500 15246 1.0000 500 1693 1.0000 500 1841 1.0000 500 20625 1.0000 500 2070 1.0000 500 21280 1.0000 500 21460 1.0000 500 2237 1.0000 500 22385 1.0000 500 22690 1.0000 500 22757 1.0000 500 22929 1.0000 500 23095 1.0000 500 23096 1.0000 500 24109 1.0000 500 2443 1.0000 500 25202 1.0000 500 262258 1.0000 500 262616 1.0000 500 264322 1.0000 500 268661 1.0000 500 30550 1.0000 500 32561 1.0000 500 35230 1.0000 500 35274 1.0000 500 36183 1.0000 500 38231 1.0000 500 3840 1.0000 500 4062 1.0000 500 42543 1.0000 500 5797 1.0000 500 5907 1.0000 500 649 1.0000 500 7356 1.0000 500 8934 1.0000 500 bd1939 1.0000 500 bd1940 1.0000 96 bd521 1.0000 500 bd655 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/318/318.seqs.fa -oc motifs/318 -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= 46 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= 22596 N= 46 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.253 C 0.236 G 0.241 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.236 G 0.241 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 27 llr = 336 E-value = 1.1e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :434:33:141:341531733 pos.-specific C a344a71a6227658359174 probability G ::::::1:::2::1:1::1:: matrix T :342::5:24421:112:1:3 bits 2.1 * * 1.9 * * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * * * * Entropy 1.0 * ** * * * * (18.0 bits) 0.8 * ** * * ** * * 0.6 * ** ** **** **** 0.4 ********* **** ***** 0.2 ********************* 0.0 --------------------- Multilevel CACCCCTCCATCCCCACCACC consensus TTA AA TTCTAA CA AA sequence CA C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7356 457 3.30e-08 CAGCACAACC CTCACCTCCTTCCAAGCCACC ACCGATCAAC 1132 459 8.47e-08 CCCACTCCCT CCTCCCTCCCTCCCCACCGAT CGCCTCTGCC bd521 30 9.61e-08 ACCTCGGCTC CTTTCCACCATTTCCACCACC GACATCCTCC 22385 475 1.09e-07 TCCTCTTCCT CTCACATCCACCAACTCCACA ACAAC 23096 480 1.23e-07 CGCCAACAAC CCTCCCACCTCCCCCCAAACA 2070 440 1.23e-07 ACGTCCTGAA CCTCCCTCTCTCAACAACAAC ACTCACGGTC 5797 450 1.39e-07 GGATAGGCAT CACACCACTTCTCACATCACC CATCACGTTC 25202 275 1.39e-07 CTCATCTGAA CCAACCTCCATCTGCAACACC TATCTATGCA 22690 412 1.76e-07 TACAATATCG CAAACAGCCAGCACCACCACT TCTTCTCTCC 2443 461 2.47e-07 CTCCAAAGAG CACTCCTCTCTCCGCAACACA CCCACTCACC 3840 447 3.82e-07 TTCTCCCCTC AACCCCTCCACCACCGCCACC AGCAAATAAA 35230 35 4.24e-07 AGCAAGAAAG CAACCACCAAACCCCACCACA GGCCGTCTCT 32561 403 5.76e-07 AAATGTTATC CCCTCCTCTTCCTCCGCCACT AGTCGTCAGC 24109 382 7.01e-07 GACACATCTG CCAACCTCCTGCCACCTCCAC CTCCTGTCCA 23095 477 9.33e-07 TTGCGGGTAA CCTCCCTCCTGTCACAACCAA TCA 262258 468 1.12e-06 TCATTTTTGC CTCTCCTCCTTTCACCACCAC CGAGCTCTAG 22929 271 1.12e-06 ACCGAGTGAC CTTCCAACCGTCCCCAAAACT TCATACTAGT 20625 374 1.12e-06 GCCCATCCAT CAACCCTCTCTCCCTCCCTCC CAGAGCCCCC 649 165 1.23e-06 ACTCATAACC CATTCCGCCCGCCCACCCACT ATTTTCCTCC 10738 391 1.23e-06 GCTCCTTACT CTTCCCTCCAATCAACTCACT TCGTCGCTTG 11111 159 1.34e-06 CATCAACAAC CACACCACCTACACCGTCTCT ACTCGCGTGG 268661 414 1.47e-06 CAGCAAGCCC CAACCAACCAACCACTCAAAC TCAAAACACG 30550 457 1.60e-06 GTCTGTCTTC CACACAACAACCACCAACTCA CACCGATACA 2237 384 2.63e-06 GCTACACTTA CTCCCAACCTGACACACAACA CGCACCCCTC 1841 155 5.53e-06 CAAAGTTGGT CAAACCACAATGACCACCGCT ACAACCATTA bd1940 63 5.93e-06 AAGTAGTGTG CTTACATCTTTCTATTCCACA AACACTCTTA 21280 432 5.93e-06 AAAGGCAAAG CATCCACCACTTCACCTCAAC GTCTGTCCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7356 3.3e-08 456_[+1]_23 1132 8.5e-08 458_[+1]_21 bd521 9.6e-08 29_[+1]_450 22385 1.1e-07 474_[+1]_5 23096 1.2e-07 479_[+1] 2070 1.2e-07 439_[+1]_40 5797 1.4e-07 449_[+1]_30 25202 1.4e-07 274_[+1]_205 22690 1.8e-07 411_[+1]_68 2443 2.5e-07 460_[+1]_19 3840 3.8e-07 446_[+1]_33 35230 4.2e-07 34_[+1]_445 32561 5.8e-07 402_[+1]_77 24109 7e-07 381_[+1]_98 23095 9.3e-07 476_[+1]_3 262258 1.1e-06 467_[+1]_12 22929 1.1e-06 270_[+1]_209 20625 1.1e-06 373_[+1]_106 649 1.2e-06 164_[+1]_315 10738 1.2e-06 390_[+1]_89 11111 1.3e-06 158_[+1]_321 268661 1.5e-06 413_[+1]_66 30550 1.6e-06 456_[+1]_23 2237 2.6e-06 383_[+1]_96 1841 5.5e-06 154_[+1]_325 bd1940 5.9e-06 62_[+1]_13 21280 5.9e-06 431_[+1]_48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=27 7356 ( 457) CTCACCTCCTTCCAAGCCACC 1 1132 ( 459) CCTCCCTCCCTCCCCACCGAT 1 bd521 ( 30) CTTTCCACCATTTCCACCACC 1 22385 ( 475) CTCACATCCACCAACTCCACA 1 23096 ( 480) CCTCCCACCTCCCCCCAAACA 1 2070 ( 440) CCTCCCTCTCTCAACAACAAC 1 5797 ( 450) CACACCACTTCTCACATCACC 1 25202 ( 275) CCAACCTCCATCTGCAACACC 1 22690 ( 412) CAAACAGCCAGCACCACCACT 1 2443 ( 461) CACTCCTCTCTCCGCAACACA 1 3840 ( 447) AACCCCTCCACCACCGCCACC 1 35230 ( 35) CAACCACCAAACCCCACCACA 1 32561 ( 403) CCCTCCTCTTCCTCCGCCACT 1 24109 ( 382) CCAACCTCCTGCCACCTCCAC 1 23095 ( 477) CCTCCCTCCTGTCACAACCAA 1 262258 ( 468) CTCTCCTCCTTTCACCACCAC 1 22929 ( 271) CTTCCAACCGTCCCCAAAACT 1 20625 ( 374) CAACCCTCTCTCCCTCCCTCC 1 649 ( 165) CATTCCGCCCGCCCACCCACT 1 10738 ( 391) CTTCCCTCCAATCAACTCACT 1 11111 ( 159) CACACCACCTACACCGTCTCT 1 268661 ( 414) CAACCAACCAACCACTCAAAC 1 30550 ( 457) CACACAACAACCACCAACTCA 1 2237 ( 384) CTCCCAACCTGACACACAACA 1 1841 ( 155) CAAACCACAATGACCACCGCT 1 bd1940 ( 63) CTTACATCTTTCTATTCCACA 1 21280 ( 432) CATCCACCACTTCACCTCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21676 bayes= 11.596 E= 1.1e-017 -277 203 -1140 -1140 81 14 -1140 13 3 65 -1140 46 55 91 -1140 -54 -1140 208 -1140 -1140 39 150 -1140 -1140 39 -167 -170 94 -1140 208 -1140 -1140 -77 142 -1140 -28 55 -9 -270 46 -77 -9 -38 72 -277 158 -270 -28 3 133 -1140 -87 81 103 -170 -1140 -119 179 -1140 -186 93 14 -70 -128 23 114 -1140 -54 -77 185 -1140 -1140 147 -109 -170 -128 3 165 -1140 -1140 23 79 -1140 13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 1.1e-017 0.037037 0.962963 0.000000 0.000000 0.444444 0.259259 0.000000 0.296296 0.259259 0.370370 0.000000 0.370370 0.370370 0.444444 0.000000 0.185185 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.074074 0.074074 0.518519 0.000000 1.000000 0.000000 0.000000 0.148148 0.629630 0.000000 0.222222 0.370370 0.222222 0.037037 0.370370 0.148148 0.222222 0.185185 0.444444 0.037037 0.703704 0.037037 0.222222 0.259259 0.592593 0.000000 0.148148 0.444444 0.481481 0.074074 0.000000 0.111111 0.814815 0.000000 0.074074 0.481481 0.259259 0.148148 0.111111 0.296296 0.518519 0.000000 0.185185 0.148148 0.851852 0.000000 0.000000 0.703704 0.111111 0.074074 0.111111 0.259259 0.740741 0.000000 0.000000 0.296296 0.407407 0.000000 0.296296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ATC][CTA][CA]C[CA][TA]C[CT][ATC][TC][CT][CA][CA]C[AC][CA]CA[CA][CAT] -------------------------------------------------------------------------------- Time 17.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 46 llr = 388 E-value = 1.5e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::1:3::331:63:6: pos.-specific C ::11:1::21:11:2: probability G 36463:65169:2a15 matrix T 7453494342:34:14 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * Entropy 1.0 * ** * * (12.2 bits) 0.8 ** ** * * 0.6 ** * ** ** * * 0.4 **** *** *** *** 0.2 ******** ******* 0.0 ---------------- Multilevel TGTGTTGGTGGATGAG consensus GTGTG TTA TA T sequence A AC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 24109 50 1.15e-08 GCGGATGGCG TGTGGTGGAGGAAGAG CGGTTTGATG 35274 9 4.33e-07 GTTGACTT GTTGATGGTGGATGAT AGCGTGGAAG 262258 90 4.33e-07 TCAGGGTCAC TGTGTTTTTGGAGGAT GCGTGGATCA 11984 60 7.77e-07 ATCTGGGGTT TGTGTTTGAGGATGCG ATATGATGAT 649 59 2.58e-06 GCGTATTCGG TTGCTTGGCGGAGGAG AGAGTCGATA 8934 60 3.50e-06 CGAGGAGTTT TGGTTTGTTGGTAGAT ATCTGCTGTT 38231 184 3.50e-06 ATTGTCATTG TTTGTTGTGGGTTGAG TCAAGTTGAG 22385 131 3.50e-06 GCGTCGGGAG GGTGGTGATGGATGTG CGTAAACACG 42543 45 6.19e-06 GTGGAGTGAA TTTTGTTGTGGTTGAT GACTCTCCGT 2070 2 8.10e-06 T TTGCTTTGTGGTTGAG TTGTCGTTGG 1841 296 8.10e-06 CAGTCTCATG TTGTTTGGTGGAGGCT CGGTTCGTCG 7356 41 9.20e-06 CTACACCGAG TGTGATGATTGCAGAG GAGGTCGGAC 268661 69 9.20e-06 GTGCTCGGAT TGGGGTGTCCGAGGAT GAGTGTCAGA 32561 263 1.05e-05 GAACGAGTTT GTTGGTTTTGGTGGAG TAAGTTGTAC bd1939 81 1.34e-05 ACGAGGATGG TGTGTTGTCGGCAGCT GCTGCTGATG 1132 343 1.34e-05 GTTGTGTTGC GTTGTTGTCGGCAGAT CGATGTGATT 23095 186 1.51e-05 GGATGGATGG TGTTGTTGTGGATGAC ATTGTGTGAG 21460 129 1.51e-05 TGCTCCTCAT GGGTGTGTCGGCTGAG TTGGTGTTGT 10556 24 1.51e-05 GATGGGGTGG TGTGATGAGCGATGAT GTTGTGATGA 11111 15 1.70e-05 TGATGTCCAA TGTGCTGTTTGATGAT GTGACATCCG bd655 315 2.13e-05 GACACGTCGT TGTGGTGACGGGAGAG AAGAGGTTGA 1693 197 2.65e-05 TCTGATACTT TTGGCTGATGGATGCG TTGTCTTGGT 20625 50 2.95e-05 TGACGATGTG TGATGTGGAGGAAGCG ATTGAGCGAT 22757 86 3.28e-05 TGATCAGAGG TGTCGTGTTGGTAGCT CGGCGGCTTG 2443 63 4.44e-05 TATATTTGAT GGGTTCGACGGATGAG GGACGGTGAA 11018 196 4.90e-05 CGATTGATAG TGAGGTGGGAGATGAT CGTGACGAAC 5907 353 5.92e-05 GATGAAGGAG TTGTTCGTCGGAGGAG GGACGGCGTT 262616 331 6.49e-05 GAAGCAACTG GTTCATTTTGGATGCG TCGAGTCGGA 2237 86 6.49e-05 GTCCGCCCAT GGTGTTTATAGACGAT GTACTGAAGA 4062 85 7.11e-05 TCAGTGAACG GGAGATTGAGGAAGTG CAAGGGTTGG 1505 313 7.11e-05 TATATCCATC TGGTATGAAGGAAGAA ATTTAGTTTG 30550 196 8.50e-05 TTCCTCACAA GTGGATTTATGACGAG GGATATGACC 264322 451 9.27e-05 TCTTCGTGAC TTGGATTATTGTTGCT GTAGGCCCGA 5797 76 1.01e-04 ATGGAACGAC GGTGAAGAAGGAAGAT TTGGGAAGCA 25202 148 1.10e-04 CTGTACAGTC TGTGTTTACTAATGAT TATACTCACG bd521 350 1.19e-04 ATGTTGACAT TGGTTTTGGTGATGGG GTTGCCCTTG 21280 79 1.19e-04 CTGGCTGTTG TTCTGTGGTGGTGGTG TGGCAAAAAA 23096 190 1.29e-04 ATTGAGAAGA TTGCATTGGGGTCGAG TCTTGAGAGA 35230 208 1.40e-04 GTCAAACAGG GAGGGTTGCGGTGGAG ACATTGTGCT 15246 209 2.38e-04 TTCAAAAGGC TTGGATTGCCGTGGTT GCATCTCTTG 22690 35 2.56e-04 TTTACGTCAA TGCCTTGGAAGAAGTG AGATGGTGTG 3840 118 2.94e-04 CGTGGTGTAC GGCGTCGGACGAGGAG GGAGGTTCTG bd1940 22 3.37e-04 GTATGTTGTT TTGGTTTGATGCCGTT TGAGATCGTT 10738 49 4.37e-04 GCTATCACAA TTTGATGAGTATTGAT GATCTTTGGA 36183 159 6.30e-04 CGTTTCCGTA TGCTTTTGATGCAGGG AAGATATATT 22929 224 2.87e-03 AGGCAGAACA GGTGGTGGAACAAGGC AAAGAGGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24109 1.2e-08 49_[+2]_435 35274 4.3e-07 8_[+2]_476 262258 4.3e-07 89_[+2]_395 11984 7.8e-07 59_[+2]_425 649 2.6e-06 58_[+2]_426 8934 3.5e-06 59_[+2]_425 38231 3.5e-06 183_[+2]_301 22385 3.5e-06 130_[+2]_354 42543 6.2e-06 44_[+2]_440 2070 8.1e-06 1_[+2]_483 1841 8.1e-06 295_[+2]_189 7356 9.2e-06 40_[+2]_444 268661 9.2e-06 68_[+2]_416 32561 1e-05 262_[+2]_222 bd1939 1.3e-05 80_[+2]_404 1132 1.3e-05 342_[+2]_142 23095 1.5e-05 185_[+2]_299 21460 1.5e-05 128_[+2]_356 10556 1.5e-05 23_[+2]_461 11111 1.7e-05 14_[+2]_470 bd655 2.1e-05 314_[+2]_170 1693 2.7e-05 196_[+2]_288 20625 3e-05 49_[+2]_435 22757 3.3e-05 85_[+2]_399 2443 4.4e-05 62_[+2]_422 11018 4.9e-05 195_[+2]_289 5907 5.9e-05 352_[+2]_132 262616 6.5e-05 330_[+2]_154 2237 6.5e-05 85_[+2]_399 4062 7.1e-05 84_[+2]_400 1505 7.1e-05 312_[+2]_172 30550 8.5e-05 195_[+2]_289 264322 9.3e-05 450_[+2]_34 5797 0.0001 75_[+2]_409 25202 0.00011 147_[+2]_337 bd521 0.00012 349_[+2]_135 21280 0.00012 78_[+2]_406 23096 0.00013 189_[+2]_295 35230 0.00014 207_[+2]_277 15246 0.00024 208_[+2]_276 22690 0.00026 34_[+2]_450 3840 0.00029 117_[+2]_367 bd1940 0.00034 21_[+2]_59 10738 0.00044 48_[+2]_436 36183 0.00063 158_[+2]_326 22929 0.0029 223_[+2]_261 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=46 24109 ( 50) TGTGGTGGAGGAAGAG 1 35274 ( 9) GTTGATGGTGGATGAT 1 262258 ( 90) TGTGTTTTTGGAGGAT 1 11984 ( 60) TGTGTTTGAGGATGCG 1 649 ( 59) TTGCTTGGCGGAGGAG 1 8934 ( 60) TGGTTTGTTGGTAGAT 1 38231 ( 184) TTTGTTGTGGGTTGAG 1 22385 ( 131) GGTGGTGATGGATGTG 1 42543 ( 45) TTTTGTTGTGGTTGAT 1 2070 ( 2) TTGCTTTGTGGTTGAG 1 1841 ( 296) TTGTTTGGTGGAGGCT 1 7356 ( 41) TGTGATGATTGCAGAG 1 268661 ( 69) TGGGGTGTCCGAGGAT 1 32561 ( 263) GTTGGTTTTGGTGGAG 1 bd1939 ( 81) TGTGTTGTCGGCAGCT 1 1132 ( 343) GTTGTTGTCGGCAGAT 1 23095 ( 186) TGTTGTTGTGGATGAC 1 21460 ( 129) GGGTGTGTCGGCTGAG 1 10556 ( 24) TGTGATGAGCGATGAT 1 11111 ( 15) TGTGCTGTTTGATGAT 1 bd655 ( 315) TGTGGTGACGGGAGAG 1 1693 ( 197) TTGGCTGATGGATGCG 1 20625 ( 50) TGATGTGGAGGAAGCG 1 22757 ( 86) TGTCGTGTTGGTAGCT 1 2443 ( 63) GGGTTCGACGGATGAG 1 11018 ( 196) TGAGGTGGGAGATGAT 1 5907 ( 353) TTGTTCGTCGGAGGAG 1 262616 ( 331) GTTCATTTTGGATGCG 1 2237 ( 86) GGTGTTTATAGACGAT 1 4062 ( 85) GGAGATTGAGGAAGTG 1 1505 ( 313) TGGTATGAAGGAAGAA 1 30550 ( 196) GTGGATTTATGACGAG 1 264322 ( 451) TTGGATTATTGTTGCT 1 5797 ( 76) GGTGAAGAAGGAAGAT 1 25202 ( 148) TGTGTTTACTAATGAT 1 bd521 ( 350) TGGTTTTGGTGATGGG 1 21280 ( 79) TTCTGTGGTGGTGGTG 1 23096 ( 190) TTGCATTGGGGTCGAG 1 35230 ( 208) GAGGGTTGCGGTGGAG 1 15246 ( 209) TTGGATTGCCGTGGTT 1 22690 ( 35) TGCCTTGGAAGAAGTG 1 3840 ( 118) GGCGTCGGACGAGGAG 1 bd1940 ( 22) TTGGTTTGATGCCGTT 1 10738 ( 49) TTTGATGAGTATTGAT 1 36183 ( 159) TGCTTTTGATGCAGGG 1 22929 ( 224) GGTGGTGGAACAAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 21906 bayes= 8.89244 E= 1.5e-008 -1217 -1217 34 137 -354 -1217 129 54 -196 -144 62 82 -1217 -85 134 -5 4 -244 34 54 -354 -185 -1217 176 -1217 -1217 134 54 4 -1217 92 7 4 2 -88 45 -154 -144 139 -46 -254 -344 196 -1217 121 -85 -347 -5 26 -144 -15 54 -1217 -1217 205 -1217 131 -44 -188 -105 -354 -244 112 61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 46 E= 1.5e-008 0.000000 0.000000 0.304348 0.695652 0.021739 0.000000 0.586957 0.391304 0.065217 0.086957 0.369565 0.478261 0.000000 0.130435 0.608696 0.260870 0.260870 0.043478 0.304348 0.391304 0.021739 0.065217 0.000000 0.913043 0.000000 0.000000 0.608696 0.391304 0.260870 0.000000 0.456522 0.282609 0.260870 0.239130 0.130435 0.369565 0.086957 0.086957 0.630435 0.195652 0.043478 0.021739 0.934783 0.000000 0.586957 0.130435 0.021739 0.260870 0.304348 0.086957 0.217391 0.391304 0.000000 0.000000 1.000000 0.000000 0.630435 0.173913 0.065217 0.130435 0.021739 0.043478 0.521739 0.413043 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GT][TG][GT][TGA]T[GT][GTA][TAC]GG[AT][TAG]GA[GT] -------------------------------------------------------------------------------- Time 35.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 27 llr = 311 E-value = 8.1e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :111:::3::2:314111::3 pos.-specific C 3635:97:49:957:563663 probability G :312:::2::1::22:::1:: matrix T 7:62913451611:4425434 bits 2.1 1.9 1.7 * 1.5 ** * * Relative 1.3 *** * * Entropy 1.0 * *** * * (16.6 bits) 0.8 * *** * * * * 0.6 ** *** ****** * ** 0.4 *** ***************** 0.2 ********************* 0.0 --------------------- Multilevel TCTCTCCTTCTCCCTCCTCCT consensus CGCG TAC A AGATTCTTC sequence G G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1132 438 1.43e-08 TAGCCAGCCC TCACTCCTCCTCCCACTCCCT CCTCCCTCCC 22690 436 6.19e-08 CACCACTTCT TCTCTCCTCCTCCAACCATCC ACAGGAAGAA 2070 289 6.19e-08 ACCGGAAGCC CCTCTCCTTCTCCTTTCTTCT ACAAAGCAAA 32561 433 8.08e-08 TAGTCGTCAG CCTATCCTCCTCCCTCATCTC AAGTCTCCTT 22757 390 8.08e-08 TTCCCCGTAG TGTATCCGCCGCCCTTCTCCT CGCGCCAAGC bd521 82 1.53e-07 CATCCCGGTA CGTCTCCTCCTCCCATCCGTC CATGTGACAC 649 436 1.72e-07 GTGAGTCCCC TGCCTCCTCCTCACTATTCCT AGTGGAATTA 1505 154 1.72e-07 CCCAGCTTTG TATTTCCATCTCACACTTCCA AATCACTCTG 262258 340 2.19e-07 CACAATTTCG CCTCTCTTTCTCTCAACTCCC TCCAGTGCTT 23096 448 2.19e-07 GAAACACCGG TAGCTCCTTCACCCTTCCCTT CCGCCAACAA 20625 466 6.65e-07 CCCTCTAGTT CATCTTCATCACCCGTCTCCT CCTATCCTAC 35274 233 1.10e-06 AAGAGAGCCA CCCCTCTGTCACCGGCCTTCA ACGCCAACGA 36183 286 1.34e-06 TTGGGGTAGT TCTTTCCATCACCCGCAATCA GTATTTCTGC 35230 63 1.78e-06 ACAGGCCGTC TCTCTCTGCCGCACTCCGCTC TATCATGACG 22929 89 3.64e-06 ATGTCTCTGA CGTTTCTATCTCTGTCCTCTA ACCAAATGAA 21280 454 3.96e-06 CACCTCAACG TCTGTCCGCTTCAGTTACTCA ACATCGTTTC 1693 456 3.96e-06 ATCTGCGAGG TACCTCCACCACAAACCACCA GATTGATTGC 24109 405 4.31e-06 ACCTCCACCT CCTGTCCACCTCTCACTCTAC ACTACCCCAA 11111 292 4.31e-06 TATTGAGTCG TCGGTCCATCGTACTTCTTCC ATTATCGGTT 2443 348 6.47e-06 TGACAGAGTG TCCTTTCATTTCCCGTCTTTC AAGGTACTCG 4062 234 7.00e-06 ATTTTCATTT TGACTCTTTCTCAGACTCCTA AACACAGATC 5797 331 8.82e-06 CTCGTCGGCC TCCGCTTTTCTCACTTCTCCT ACTGCCTCTT 3840 233 1.19e-05 GATCAAATCC TCTCACCGCCACCCGGTCCCT CCGCCCAACC 11984 464 1.19e-05 AGCAAGAAAC TCCGTCCTGTTCTGACCTCTT GTAATTGTTT 23095 342 1.28e-05 TTGGATTGTT TGTGTCTGTCGCCCGTCCTGT CGCCTGTCGC 15246 83 1.37e-05 TTGGGCCTGC CCCTTCCAACTTACTTCCTCC ATTGCCAATG 1841 122 2.71e-05 TGTTAGGAGT TGGATCCTCTTCCGACATGCT GGCAAAGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1132 1.4e-08 437_[+3]_42 22690 6.2e-08 435_[+3]_44 2070 6.2e-08 288_[+3]_191 32561 8.1e-08 432_[+3]_47 22757 8.1e-08 389_[+3]_90 bd521 1.5e-07 81_[+3]_398 649 1.7e-07 435_[+3]_44 1505 1.7e-07 153_[+3]_326 262258 2.2e-07 339_[+3]_140 23096 2.2e-07 447_[+3]_32 20625 6.6e-07 465_[+3]_14 35274 1.1e-06 232_[+3]_247 36183 1.3e-06 285_[+3]_194 35230 1.8e-06 62_[+3]_417 22929 3.6e-06 88_[+3]_391 21280 4e-06 453_[+3]_26 1693 4e-06 455_[+3]_24 24109 4.3e-06 404_[+3]_75 11111 4.3e-06 291_[+3]_188 2443 6.5e-06 347_[+3]_132 4062 7e-06 233_[+3]_246 5797 8.8e-06 330_[+3]_149 3840 1.2e-05 232_[+3]_247 11984 1.2e-05 463_[+3]_16 23095 1.3e-05 341_[+3]_138 15246 1.4e-05 82_[+3]_397 1841 2.7e-05 121_[+3]_358 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=27 1132 ( 438) TCACTCCTCCTCCCACTCCCT 1 22690 ( 436) TCTCTCCTCCTCCAACCATCC 1 2070 ( 289) CCTCTCCTTCTCCTTTCTTCT 1 32561 ( 433) CCTATCCTCCTCCCTCATCTC 1 22757 ( 390) TGTATCCGCCGCCCTTCTCCT 1 bd521 ( 82) CGTCTCCTCCTCCCATCCGTC 1 649 ( 436) TGCCTCCTCCTCACTATTCCT 1 1505 ( 154) TATTTCCATCTCACACTTCCA 1 262258 ( 340) CCTCTCTTTCTCTCAACTCCC 1 23096 ( 448) TAGCTCCTTCACCCTTCCCTT 1 20625 ( 466) CATCTTCATCACCCGTCTCCT 1 35274 ( 233) CCCCTCTGTCACCGGCCTTCA 1 36183 ( 286) TCTTTCCATCACCCGCAATCA 1 35230 ( 63) TCTCTCTGCCGCACTCCGCTC 1 22929 ( 89) CGTTTCTATCTCTGTCCTCTA 1 21280 ( 454) TCTGTCCGCTTCAGTTACTCA 1 1693 ( 456) TACCTCCACCACAAACCACCA 1 24109 ( 405) CCTGTCCACCTCTCACTCTAC 1 11111 ( 292) TCGGTCCATCGTACTTCTTCC 1 2443 ( 348) TCCTTTCATTTCCCGTCTTTC 1 4062 ( 234) TGACTCTTTCTCAGACTCCTA 1 5797 ( 331) TCCGCTTTTCTCACTTCTCCT 1 3840 ( 233) TCTCACCGCCACCCGGTCCCT 1 11984 ( 464) TCCGTCCTGTTCTGACCTCTT 1 23095 ( 342) TGTGTCTGTCGCCCGTCCTGT 1 15246 ( 83) CCCTTCCAACTTACTTCCTCC 1 1841 ( 122) TGGATCCTCTTCCGACATGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21676 bayes= 10.2167 E= 8.1e-006 -1140 50 -1140 130 -77 133 11 -1140 -177 14 -111 104 -119 103 -11 -54 -277 -267 -1140 178 -1140 191 -1140 -128 -1140 165 -1140 -6 39 -1140 -11 72 -277 91 -270 83 -1140 185 -1140 -87 -19 -1140 -70 122 -1140 197 -1140 -186 39 114 -1140 -87 -177 150 -11 -286 55 -1140 -11 59 -177 103 -270 59 -77 142 -1140 -28 -119 50 -270 94 -1140 124 -170 46 -277 142 -270 13 3 50 -1140 59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 8.1e-006 0.000000 0.333333 0.000000 0.666667 0.148148 0.592593 0.259259 0.000000 0.074074 0.259259 0.111111 0.555556 0.111111 0.481481 0.222222 0.185185 0.037037 0.037037 0.000000 0.925926 0.000000 0.888889 0.000000 0.111111 0.000000 0.740741 0.000000 0.259259 0.333333 0.000000 0.222222 0.444444 0.037037 0.444444 0.037037 0.481481 0.000000 0.851852 0.000000 0.148148 0.222222 0.000000 0.148148 0.629630 0.000000 0.925926 0.000000 0.074074 0.333333 0.518519 0.000000 0.148148 0.074074 0.666667 0.222222 0.037037 0.370370 0.000000 0.222222 0.407407 0.074074 0.481481 0.037037 0.407407 0.148148 0.629630 0.000000 0.222222 0.111111 0.333333 0.037037 0.518519 0.000000 0.555556 0.074074 0.370370 0.037037 0.629630 0.037037 0.296296 0.259259 0.333333 0.000000 0.407407 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][CG][TC][CG]TC[CT][TAG][TC]C[TA]C[CA][CG][TAG][CT][CT][TC][CT][CT][TCA] -------------------------------------------------------------------------------- Time 52.22 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10556 6.14e-02 23_[+2(1.51e-05)]_461 10738 2.12e-03 390_[+1(1.23e-06)]_89 11018 1.69e-01 195_[+2(4.90e-05)]_289 11111 2.04e-06 14_[+2(1.70e-05)]_128_\ [+1(1.34e-06)]_112_[+3(4.31e-06)]_188 1132 7.11e-10 342_[+2(1.34e-05)]_79_\ [+3(1.43e-08)]_[+1(8.47e-08)]_21 11984 1.62e-04 59_[+2(7.77e-07)]_388_\ [+3(1.19e-05)]_16 1505 7.61e-05 153_[+3(1.72e-07)]_138_\ [+2(7.11e-05)]_172 15246 6.76e-03 82_[+3(1.37e-05)]_397 1693 4.52e-04 196_[+2(2.65e-05)]_243_\ [+3(3.96e-06)]_24 1841 1.90e-05 121_[+3(2.71e-05)]_12_\ [+1(5.53e-06)]_120_[+2(8.10e-06)]_189 20625 5.31e-07 49_[+2(2.95e-05)]_308_\ [+1(1.12e-06)]_71_[+3(6.65e-07)]_14 2070 2.45e-09 1_[+2(8.10e-06)]_271_[+3(6.19e-08)]_\ 130_[+1(1.23e-07)]_40 21280 3.90e-05 431_[+1(5.93e-06)]_1_[+3(3.96e-06)]_\ 26 21460 1.72e-02 67_[+2(9.27e-05)]_45_[+2(1.51e-05)]_\ 356 2237 7.99e-04 85_[+2(6.49e-05)]_282_\ [+1(2.63e-06)]_96 22385 8.15e-06 130_[+2(3.50e-06)]_328_\ [+1(1.09e-07)]_5 22690 7.72e-08 411_[+1(1.76e-07)]_3_[+3(6.19e-08)]_\ 44 22757 1.52e-05 85_[+2(3.28e-05)]_288_\ [+3(8.08e-08)]_90 22929 8.15e-05 88_[+3(3.64e-06)]_161_\ [+1(1.12e-06)]_209 23095 3.51e-06 185_[+2(1.51e-05)]_140_\ [+3(1.28e-05)]_114_[+1(9.33e-07)]_3 23096 9.75e-08 362_[+3(9.51e-06)]_19_\ [+3(2.22e-05)]_24_[+3(2.19e-07)]_11_[+1(1.23e-07)] 24109 1.45e-09 49_[+2(1.15e-08)]_83_[+2(8.50e-05)]_\ 217_[+1(7.01e-07)]_2_[+3(4.31e-06)]_47_[+3(5.93e-05)]_7 2443 1.52e-06 62_[+2(4.44e-05)]_269_\ [+3(6.47e-06)]_92_[+1(2.47e-07)]_19 25202 3.44e-05 274_[+1(1.39e-07)]_205 262258 4.08e-09 89_[+2(4.33e-07)]_82_[+1(1.51e-05)]_\ 53_[+3(2.88e-05)]_57_[+3(2.19e-07)]_51_[+1(7.36e-05)]_34_[+3(1.00e-06)]_13 262616 5.77e-02 330_[+2(6.49e-05)]_154 264322 1.20e-01 450_[+2(9.27e-05)]_34 268661 2.74e-04 68_[+2(9.20e-06)]_329_\ [+1(1.47e-06)]_66 30550 5.35e-04 195_[+2(8.50e-05)]_245_\ [+1(1.60e-06)]_23 32561 1.65e-08 262_[+2(1.05e-05)]_124_\ [+1(5.76e-07)]_9_[+3(8.08e-08)]_47 35230 2.14e-06 34_[+1(4.24e-07)]_7_[+3(1.78e-06)]_\ 417 35274 4.00e-06 8_[+2(4.33e-07)]_208_[+3(1.10e-06)]_\ 247 36183 1.61e-03 285_[+3(1.34e-06)]_194 38231 1.71e-02 183_[+2(3.50e-06)]_301 3840 1.96e-05 232_[+3(1.19e-05)]_60_\ [+1(7.87e-05)]_112_[+1(3.82e-07)]_33 4062 7.74e-04 84_[+2(7.11e-05)]_133_\ [+3(7.00e-06)]_246 42543 1.67e-02 44_[+2(6.19e-06)]_440 5797 2.47e-06 330_[+3(8.82e-06)]_98_\ [+1(1.39e-07)]_30 5907 1.27e-01 352_[+2(5.92e-05)]_132 649 1.84e-08 58_[+2(2.58e-06)]_90_[+1(1.23e-06)]_\ 250_[+3(1.72e-07)]_44 7356 7.18e-06 40_[+2(9.20e-06)]_363_\ [+1(6.63e-05)]_16_[+1(3.30e-08)]_23 8934 1.03e-02 59_[+2(3.50e-06)]_425 bd1939 6.82e-02 80_[+2(1.34e-05)]_404 bd1940 1.62e-04 62_[+1(5.93e-06)]_13 bd521 5.20e-08 29_[+1(9.61e-08)]_31_[+3(1.53e-07)]_\ 398 bd655 2.67e-02 314_[+2(2.13e-05)]_170 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************