******************************************************************************** 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/147/147.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17198 1.0000 500 42566 1.0000 500 8720 1.0000 500 42757 1.0000 500 24820 1.0000 500 9411 1.0000 500 8363 1.0000 500 36420 1.0000 500 46612 1.0000 500 20948 1.0000 500 36711 1.0000 500 51005 1.0000 500 21116 1.0000 500 47099 1.0000 500 28551 1.0000 500 28737 1.0000 500 54754 1.0000 500 37835 1.0000 500 38015 1.0000 500 14827 1.0000 500 48371 1.0000 500 48822 1.0000 500 43658 1.0000 500 43732 1.0000 500 43774 1.0000 500 54971 1.0000 500 55122 1.0000 500 18475 1.0000 500 50520 1.0000 500 55215 1.0000 500 19341 1.0000 500 7614 1.0000 500 44959 1.0000 500 19690 1.0000 500 27039 1.0000 500 20167 1.0000 500 20508 1.0000 500 27838 1.0000 500 43838 1.0000 500 32272 1.0000 500 49086 1.0000 500 49132 1.0000 500 49647 1.0000 500 34564 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/147/147.seqs.fa -oc motifs/147 -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= 44 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= 22000 N= 44 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.249 C 0.264 G 0.229 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.249 C 0.264 G 0.229 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 28 llr = 289 E-value = 1.9e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4534:1:9:5:1:a33 pos.-specific C 315:3:5:a1::5:11 probability G 33323:21::a:4:6: matrix T :2:4493::4:91::6 bits 2.1 1.9 * * 1.7 * * * 1.5 ** ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** * (14.9 bits) 0.9 * ** ** * 0.6 * ** **** * 0.4 * ************** 0.2 **************** 0.0 ---------------- Multilevel AACTTTCACAGTCAGT consensus CGAAC T T G AA sequence G G G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 28737 120 1.46e-08 GTCACGGTCG GACTCTCACTGTCAGT CAGCTCCTTA 36711 361 2.15e-08 AAACGTATTA CACTCTCACTGTCAGT TTGGTTCGTC 17198 312 6.85e-07 GTCGATGTGC CGAGGTCACAGTCAGT CAGTCAGTCA 43732 145 7.93e-07 TCACGAATAC GAAATTTACAGTCAGA ATGATGACGA 19690 139 9.22e-07 TGAACTCAAT CACTGTCACAGTCAGC TTATCGCATG 38015 400 9.22e-07 TCCAAACACA AACACTTACAGTTAGT CCAAACACAA 43774 163 1.05e-06 CAGTCGTAGT CAAAGTCACTGTTAGT CGTTCGTGTC 20948 87 1.38e-06 CTACGTTTGC GTCAGTCACCGTCAGT CAGTCAGTCA 18475 154 1.57e-06 ACGTTGTTTT CTATTTTACAGTGAGT CTTCGATACC 48822 110 2.52e-06 TGTTTGTGCT GACTGTGACTGTGACT GTGATTGTAT 24820 158 2.52e-06 ACATGGATTT CGGTTTGACTGTGAGA AAAGCGTTTC 20167 84 3.42e-06 AGTATCTTCT AGAGTTCACAGTCAAA TAAGCTTTCG 55122 358 3.42e-06 CTCTCCACAT ATAATTTACTGTCAAT CACGACAACA 55215 467 5.09e-06 CAATTTTCTT CCATCTCACAGTCAAT CATACCACCG 19341 374 7.25e-06 AACGACGATG AAGAGTCGCAGTCAAT CGTTCTGTCC 43838 255 1.21e-05 TGCACCAGGT CCGACTCACAGTCAGC GTCAGCCGCA 14827 148 1.21e-05 GAAAACTCCA AGCGTTGACTGTGACA GAGCGTTTGG 44959 37 1.41e-05 AACATTTCAA AGCGTACACAGTGAAT CTCTCCAGGA 21116 276 1.65e-05 CTCCCCCCCC AACACACACCGTGAGA CGTTCTCACA 47099 199 1.78e-05 GTGAAATTTT GTGTTTTACTGACAGT GAAGATCAAA 28551 164 2.08e-05 TGGTTAGGCC GGCGTTTACTGTTAGC GCGACGCACC 49132 349 2.24e-05 CATCAAAATT GACACGGACTGTGAGA AATCCATAGA 46612 292 2.24e-05 CTATAGGCAA AAGACTCTCCGTGAGT AGCTATAGGT 34564 376 2.41e-05 ATCAATTCAT AGAATTGACAGTGATA ACTCCTCGCA 8363 282 2.41e-05 ATTCAGATCC GGGTTTCACATTGAAT ACGTTTTTCG 36420 455 4.44e-05 GATAGGAACC AACTCTGAGCGTCAAT CCAGACTCCT 8720 392 5.02e-05 TGGCGTTCTC GTGTGTTGCAGTCACT GGAGGTAGCT 51005 116 5.66e-05 TTCCGTTGGA CACTGTCACTGATACA TCCAATACGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28737 1.5e-08 119_[+1]_365 36711 2.2e-08 360_[+1]_124 17198 6.9e-07 311_[+1]_173 43732 7.9e-07 144_[+1]_340 19690 9.2e-07 138_[+1]_346 38015 9.2e-07 399_[+1]_85 43774 1.1e-06 162_[+1]_322 20948 1.4e-06 86_[+1]_398 18475 1.6e-06 153_[+1]_331 48822 2.5e-06 109_[+1]_375 24820 2.5e-06 157_[+1]_327 20167 3.4e-06 83_[+1]_401 55122 3.4e-06 357_[+1]_127 55215 5.1e-06 466_[+1]_18 19341 7.2e-06 373_[+1]_111 43838 1.2e-05 254_[+1]_230 14827 1.2e-05 147_[+1]_337 44959 1.4e-05 36_[+1]_448 21116 1.7e-05 275_[+1]_209 47099 1.8e-05 198_[+1]_286 28551 2.1e-05 163_[+1]_321 49132 2.2e-05 348_[+1]_136 46612 2.2e-05 291_[+1]_193 34564 2.4e-05 375_[+1]_109 8363 2.4e-05 281_[+1]_203 36420 4.4e-05 454_[+1]_30 8720 5e-05 391_[+1]_93 51005 5.7e-05 115_[+1]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=28 28737 ( 120) GACTCTCACTGTCAGT 1 36711 ( 361) CACTCTCACTGTCAGT 1 17198 ( 312) CGAGGTCACAGTCAGT 1 43732 ( 145) GAAATTTACAGTCAGA 1 19690 ( 139) CACTGTCACAGTCAGC 1 38015 ( 400) AACACTTACAGTTAGT 1 43774 ( 163) CAAAGTCACTGTTAGT 1 20948 ( 87) GTCAGTCACCGTCAGT 1 18475 ( 154) CTATTTTACAGTGAGT 1 48822 ( 110) GACTGTGACTGTGACT 1 24820 ( 158) CGGTTTGACTGTGAGA 1 20167 ( 84) AGAGTTCACAGTCAAA 1 55122 ( 358) ATAATTTACTGTCAAT 1 55215 ( 467) CCATCTCACAGTCAAT 1 19341 ( 374) AAGAGTCGCAGTCAAT 1 43838 ( 255) CCGACTCACAGTCAGC 1 14827 ( 148) AGCGTTGACTGTGACA 1 44959 ( 37) AGCGTACACAGTGAAT 1 21116 ( 276) AACACACACCGTGAGA 1 47099 ( 199) GTGTTTTACTGACAGT 1 28551 ( 164) GGCGTTTACTGTTAGC 1 49132 ( 349) GACACGGACTGTGAGA 1 46612 ( 292) AAGACTCTCCGTGAGT 1 34564 ( 376) AGAATTGACAGTGATA 1 8363 ( 282) GGGTTTCACATTGAAT 1 36420 ( 455) AACTCTGAGCGTCAAT 1 8720 ( 392) GTGTGTTGCAGTCACT 1 51005 ( 116) CACTGTCACTGATACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 21340 bayes= 10.1784 E= 1.9e-005 52 28 49 -1145 90 -188 32 -53 20 81 13 -1145 66 -1145 -36 73 -1145 28 32 61 -180 -1145 -268 179 -1145 102 -10 -5 184 -1145 -168 -285 -1145 187 -268 -1145 90 -89 -1145 61 -1145 -1145 207 -285 -180 -1145 -1145 185 -1145 92 64 -85 201 -1145 -1145 -1145 1 -89 132 -285 20 -130 -1145 123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 28 E= 1.9e-005 0.357143 0.321429 0.321429 0.000000 0.464286 0.071429 0.285714 0.178571 0.285714 0.464286 0.250000 0.000000 0.392857 0.000000 0.178571 0.428571 0.000000 0.321429 0.285714 0.392857 0.071429 0.000000 0.035714 0.892857 0.000000 0.535714 0.214286 0.250000 0.892857 0.000000 0.071429 0.035714 0.000000 0.964286 0.035714 0.000000 0.464286 0.142857 0.000000 0.392857 0.000000 0.000000 0.964286 0.035714 0.071429 0.000000 0.000000 0.928571 0.000000 0.500000 0.357143 0.142857 1.000000 0.000000 0.000000 0.000000 0.250000 0.142857 0.571429 0.035714 0.285714 0.107143 0.000000 0.607143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACG][AG][CAG][TA][TCG]T[CTG]AC[AT]GT[CG]A[GA][TA] -------------------------------------------------------------------------------- Time 19.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 18 llr = 201 E-value = 1.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 454:1::211:8:4: pos.-specific C ::49:12126::73: probability G 6:119:3853a::28 matrix T :5:::95:2::2312 bits 2.1 * 1.9 * * 1.7 ** * 1.5 *** * Relative 1.3 *** ** * Entropy 1.1 ** *** * *** * (16.1 bits) 0.9 ** *** * *** * 0.6 ****** * **** * 0.4 ******** **** * 0.2 *************** 0.0 --------------- Multilevel GAACGTTGGCGACAG consensus ATC G TG TTCT sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 27838 70 1.99e-08 CCCCCACCCG GAACGTTGGGGACAG CGAAAACGGA 49647 310 1.68e-07 GCCGAGGCCG AACCGTTGCCGACAG CACGTTGCCG 18475 14 2.37e-07 GAGACACGAG AACCGTTGGCGTCCG AGTTCGGGTG 20948 201 5.61e-07 CCTACCCACC ATCCGTCGGCGATCG GCGACGAGGA 27039 303 9.01e-07 TCGCTACATA GTACGTGAGGGACAG GAACATACAT 17198 266 1.42e-06 CATCACTGAC GTCCGTTCGCGACCG AAGGATCCCA 20508 280 1.76e-06 AAGTCGTCAC AACGGTCGGCGACCG ATCGTCGGTG 54971 132 2.18e-06 AGCGTCGTTG GTCCGTGGCAGACAG ACATTGCTGC 28551 428 2.39e-06 TGTGAAAGAA AAACGTTGTCGATAT GAGTTCCAAA 42757 280 4.13e-06 CAAAAACTAT GTACGTGAACGACGG CACGTGTTGG 32272 358 5.75e-06 TGAACACAGA AAACATTGCCGACAG CCGACAATGG 49086 199 6.21e-06 TGGTGGTTCC GACCGTGGTGGTTCG TTCGTCTCCG 43658 61 7.27e-06 ATCTGACCCC GTACGTTGGGGTTGT CATCCCACCA 9411 293 7.84e-06 TGCCGGTAGT GAACGCCGTCGACCG CGGCGGCATC 36420 74 9.10e-06 TAACAGTAAG ATGCGTTGGGGATGT TTTTTGGATG 20167 434 9.79e-06 GGTAGTGACG AAACGTTAAAGACAG CCTTCTTCAT 50520 235 9.79e-06 TTGGTGTCGT GTCCGTCGTCGTCTG TCCCTGTTCC 38015 33 1.29e-05 GTGGGGTCCG GTGGGTGGGCGACGT TGTCGCTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27838 2e-08 69_[+2]_416 49647 1.7e-07 309_[+2]_176 18475 2.4e-07 13_[+2]_472 20948 5.6e-07 200_[+2]_285 27039 9e-07 302_[+2]_183 17198 1.4e-06 265_[+2]_220 20508 1.8e-06 279_[+2]_206 54971 2.2e-06 131_[+2]_354 28551 2.4e-06 427_[+2]_58 42757 4.1e-06 279_[+2]_206 32272 5.7e-06 357_[+2]_128 49086 6.2e-06 198_[+2]_287 43658 7.3e-06 60_[+2]_425 9411 7.8e-06 292_[+2]_193 36420 9.1e-06 73_[+2]_412 20167 9.8e-06 433_[+2]_52 50520 9.8e-06 234_[+2]_251 38015 1.3e-05 32_[+2]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=18 27838 ( 70) GAACGTTGGGGACAG 1 49647 ( 310) AACCGTTGCCGACAG 1 18475 ( 14) AACCGTTGGCGTCCG 1 20948 ( 201) ATCCGTCGGCGATCG 1 27039 ( 303) GTACGTGAGGGACAG 1 17198 ( 266) GTCCGTTCGCGACCG 1 20508 ( 280) AACGGTCGGCGACCG 1 54971 ( 132) GTCCGTGGCAGACAG 1 28551 ( 428) AAACGTTGTCGATAT 1 42757 ( 280) GTACGTGAACGACGG 1 32272 ( 358) AAACATTGCCGACAG 1 49086 ( 199) GACCGTGGTGGTTCG 1 43658 ( 61) GTACGTTGGGGTTGT 1 9411 ( 293) GAACGCCGTCGACCG 1 36420 ( 74) ATGCGTTGGGGATGT 1 20167 ( 434) AAACGTTAAAGACAG 1 50520 ( 235) GTCCGTCGTCGTCTG 1 38015 ( 33) GTGGGTGGGCGACGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 21384 bayes= 11.0616 E= 1.5e+001 84 -1081 128 -1081 101 -1081 -1081 95 84 75 -104 -1081 -1081 175 -104 -1081 -216 -1081 204 -1081 -1081 -225 -1081 187 -1081 -25 28 95 -58 -225 176 -1081 -116 -66 113 -22 -116 121 28 -1081 -1081 -1081 213 -1081 164 -1081 -1081 -22 -1081 145 -1081 11 64 34 -4 -221 -1081 -1081 176 -22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 18 E= 1.5e+001 0.444444 0.000000 0.555556 0.000000 0.500000 0.000000 0.000000 0.500000 0.444444 0.444444 0.111111 0.000000 0.000000 0.888889 0.111111 0.000000 0.055556 0.000000 0.944444 0.000000 0.000000 0.055556 0.000000 0.944444 0.000000 0.222222 0.277778 0.500000 0.166667 0.055556 0.777778 0.000000 0.111111 0.166667 0.500000 0.222222 0.111111 0.611111 0.277778 0.000000 0.000000 0.000000 1.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.000000 0.722222 0.000000 0.277778 0.388889 0.333333 0.222222 0.055556 0.000000 0.000000 0.777778 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][AT][AC]CGT[TGC]G[GT][CG]G[AT][CT][ACG][GT] -------------------------------------------------------------------------------- Time 37.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 11 llr = 164 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 6513937:5:a5739:95568 pos.-specific C 1:43::18:7:5351a:5121 probability G 2:52::1253:::2::1:3:1 matrix T 15:3171::::::1::::22: bits 2.1 1.9 * * 1.7 * * 1.5 * * *** Relative 1.3 * * * *** Entropy 1.1 * ** ****** **** * (21.5 bits) 0.9 * ** ****** **** * 0.6 ** ********* **** ** 0.4 *** ********* **** ** 0.2 *** ***************** 0.0 --------------------- Multilevel AAGAATACGCAAACACAAAAA consensus TCC A AG CCA CG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 48371 393 8.89e-10 TTCCACACAT ATATATACGCACACACAAAAA TATATATACA 14827 323 1.10e-08 GTAAGCCCAA ATGCATACGCAACACCAAAAA GTAGAATATT 20948 327 1.22e-08 GAACGATACC AACAATACACAACGACACACA AACATTGAGT 19341 145 2.04e-08 CACGGTGTGT GTGAATAGGGAAAAACAAGAA TTACATGGTA 54754 431 3.30e-08 TTACAGATAA AACAATCCACAAACACACGTA TCCTATCTCA 38015 205 8.68e-08 CCAACCCGTT CACGATACACACACACACTCA CTCCAACACC 21116 229 1.10e-07 TCTATTTCCA AAGTTATCGCAAACACACGAA CTCCCCGGGA 44959 426 1.28e-07 CATTCCAAAG AAGCAAACGGACCGACACAAC TCGAGTCGTT 9411 477 1.61e-07 GCGAGAAGTC GTGCAAGCGCAAAAACAACAA GGA 42757 173 2.16e-07 TGCTTACACT TAGTATAGAGACACACGAAAA GCACTCCGGA 17198 393 3.93e-07 GAGTCTGTTG ATCGATACACACATACAATTG CTGCAAGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48371 8.9e-10 392_[+3]_87 14827 1.1e-08 322_[+3]_157 20948 1.2e-08 326_[+3]_153 19341 2e-08 144_[+3]_335 54754 3.3e-08 430_[+3]_49 38015 8.7e-08 204_[+3]_275 21116 1.1e-07 228_[+3]_251 44959 1.3e-07 425_[+3]_54 9411 1.6e-07 476_[+3]_3 42757 2.2e-07 172_[+3]_307 17198 3.9e-07 392_[+3]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=11 48371 ( 393) ATATATACGCACACACAAAAA 1 14827 ( 323) ATGCATACGCAACACCAAAAA 1 20948 ( 327) AACAATACACAACGACACACA 1 19341 ( 145) GTGAATAGGGAAAAACAAGAA 1 54754 ( 431) AACAATCCACAAACACACGTA 1 38015 ( 205) CACGATACACACACACACTCA 1 21116 ( 229) AAGTTATCGCAAACACACGAA 1 44959 ( 426) AAGCAAACGGACCGACACAAC 1 9411 ( 477) GTGCAAGCGCAAAAACAACAA 1 42757 ( 173) TAGTATAGAGACACACGAAAA 1 17198 ( 393) ATCGATACACACATACAATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 10.4584 E= 1.7e+002 135 -154 -33 -150 113 -1010 -1010 82 -145 46 125 -1010 13 5 -33 8 187 -1010 -1010 -150 13 -1010 -1010 149 155 -154 -133 -150 -1010 163 -33 -1010 87 -1010 125 -1010 -1010 146 25 -1010 201 -1010 -1010 -1010 113 78 -1010 -1010 155 5 -1010 -1010 13 78 -33 -150 187 -154 -1010 -1010 -1010 192 -1010 -1010 187 -1010 -133 -1010 113 78 -1010 -1010 87 -154 25 -51 135 -54 -1010 -51 172 -154 -133 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 1.7e+002 0.636364 0.090909 0.181818 0.090909 0.545455 0.000000 0.000000 0.454545 0.090909 0.363636 0.545455 0.000000 0.272727 0.272727 0.181818 0.272727 0.909091 0.000000 0.000000 0.090909 0.272727 0.000000 0.000000 0.727273 0.727273 0.090909 0.090909 0.090909 0.000000 0.818182 0.181818 0.000000 0.454545 0.000000 0.545455 0.000000 0.000000 0.727273 0.272727 0.000000 1.000000 0.000000 0.000000 0.000000 0.545455 0.454545 0.000000 0.000000 0.727273 0.272727 0.000000 0.000000 0.272727 0.454545 0.181818 0.090909 0.909091 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.545455 0.454545 0.000000 0.000000 0.454545 0.090909 0.272727 0.181818 0.636364 0.181818 0.000000 0.181818 0.818182 0.090909 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[AT][GC][ACT]A[TA]AC[GA][CG]A[AC][AC][CA]ACA[AC][AG]AA -------------------------------------------------------------------------------- Time 55.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17198 1.34e-08 265_[+2(1.42e-06)]_31_\ [+1(6.85e-07)]_65_[+3(3.93e-07)]_87 42566 9.26e-01 500 8720 1.95e-03 133_[+3(2.77e-06)]_237_\ [+1(5.02e-05)]_93 42757 1.56e-05 172_[+3(2.16e-07)]_86_\ [+2(4.13e-06)]_206 24820 3.77e-03 157_[+1(2.52e-06)]_327 9411 3.15e-05 292_[+2(7.84e-06)]_169_\ [+3(1.61e-07)]_3 8363 1.62e-01 281_[+1(2.41e-05)]_203 36420 4.43e-03 73_[+2(9.10e-06)]_366_\ [+1(4.44e-05)]_30 46612 5.22e-02 291_[+1(2.24e-05)]_193 20948 4.37e-10 86_[+1(1.38e-06)]_[+1(8.87e-05)]_82_\ [+2(5.61e-07)]_111_[+3(1.22e-08)]_153 36711 2.68e-05 25_[+2(6.47e-05)]_320_\ [+1(2.15e-08)]_124 51005 2.39e-02 115_[+1(5.66e-05)]_369 21116 4.38e-05 228_[+3(1.10e-07)]_26_\ [+1(1.65e-05)]_209 47099 7.12e-02 198_[+1(1.78e-05)]_286 28551 8.90e-04 163_[+1(2.08e-05)]_27_\ [+2(3.39e-05)]_206_[+2(2.39e-06)]_58 28737 1.34e-05 95_[+1(3.46e-07)]_8_[+1(1.46e-08)]_\ 365 54754 6.92e-04 430_[+3(3.30e-08)]_49 37835 3.22e-01 500 38015 3.31e-08 32_[+2(1.29e-05)]_157_\ [+3(8.68e-08)]_128_[+1(6.75e-05)]_30_[+1(9.22e-07)]_85 14827 2.98e-06 147_[+1(1.21e-05)]_159_\ [+3(1.10e-08)]_157 48371 1.67e-05 392_[+3(8.89e-10)]_87 48822 1.15e-02 109_[+1(2.52e-06)]_375 43658 8.52e-03 60_[+2(7.27e-06)]_425 43732 6.15e-03 144_[+1(7.93e-07)]_340 43774 1.30e-02 162_[+1(1.05e-06)]_322 54971 3.95e-03 131_[+2(2.18e-06)]_354 55122 1.30e-02 357_[+1(3.42e-06)]_127 18475 5.20e-06 13_[+2(2.37e-07)]_125_\ [+1(1.57e-06)]_331 50520 3.07e-03 234_[+2(9.79e-06)]_251 55215 2.55e-02 466_[+1(5.09e-06)]_18 19341 4.30e-06 47_[+1(6.00e-05)]_81_[+3(2.04e-08)]_\ 208_[+1(7.25e-06)]_111 7614 4.82e-01 500 44959 1.87e-06 36_[+1(1.41e-05)]_298_\ [+2(4.88e-05)]_60_[+3(1.28e-07)]_54 19690 4.30e-03 95_[+1(4.61e-06)]_27_[+1(9.22e-07)]_\ 346 27039 3.65e-03 302_[+2(9.01e-07)]_183 20167 1.49e-04 83_[+1(3.42e-06)]_334_\ [+2(9.79e-06)]_52 20508 1.92e-02 279_[+2(1.76e-06)]_206 27838 6.10e-05 69_[+2(1.99e-08)]_416 43838 2.35e-02 254_[+1(1.21e-05)]_230 32272 4.97e-03 357_[+2(5.75e-06)]_128 49086 3.08e-02 198_[+2(6.21e-06)]_287 49132 7.54e-02 348_[+1(2.24e-05)]_136 49647 5.85e-04 309_[+2(1.68e-07)]_176 34564 7.31e-03 375_[+1(2.41e-05)]_109 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************