******************************************************************************** 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/128/128.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1216 1.0000 500 12164 1.0000 500 16039 1.0000 500 16613 1.0000 500 20865 1.0000 500 20975 1.0000 500 22843 1.0000 500 23457 1.0000 500 23748 1.0000 500 24683 1.0000 500 25356 1.0000 500 25811 1.0000 500 264827 1.0000 500 268606 1.0000 500 269532 1.0000 500 32230 1.0000 500 3331 1.0000 500 36937 1.0000 500 3929 1.0000 500 6207 1.0000 500 6286 1.0000 500 6458 1.0000 500 7584 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/128/128.seqs.fa -oc motifs/128 -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= 23 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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.232 G 0.242 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.232 G 0.242 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 23 llr = 252 E-value = 5.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1623187327437253113: pos.-specific C 433782:66354:8378129 probability G 3:1:1:1:2::2:::::33: matrix T 114:::12::1:3:2::421 bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * * * * * Entropy 1.1 *** ** * * (15.8 bits) 0.8 **** * ** ** * 0.6 * ******** ** ** * 0.4 * ************** * 0.2 ****************** * 0.0 -------------------- Multilevel CATCCAACCACCACACCTAC consensus GCCA C AACAATACA GG sequence G G T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 36937 376 3.59e-10 TCTCCCTTTA CATCCAAACACAACACCTGC AGCGACCACA 6458 263 1.84e-09 CAAAGCCGCT CCTCCCACCACCACACCTCC TCATCATCCT 20975 161 6.19e-08 GTTGCCTTCG CAAACAAACAACACCCCTGC GGCGTACAAT 25811 170 7.16e-08 ACACACCTAA CAGCCAACCACCAACACTAC ACTGGCCAAC 20865 139 7.16e-08 CCTACTTCCA CCTCCCACCACCACTCCCTC GCTTCGAGAG 268606 451 9.52e-08 TCTGCTTCGT CACCCAATCCAAACAACGTC CACGTCCAGC 16613 271 9.85e-07 CTGGAGGCTT CATCCAACGCCCTCTACATC ATCGGTTTGG 23748 150 1.22e-06 ATCGGTGACG AATCCATCCACATCAACGTC GCCATCATCA 264827 148 1.35e-06 GCCTTCTCCC GAACCACACCACACCCCGAC CGCTCGCCAA 22843 413 1.66e-06 TTTCGCGCCA CACCCAATCCAAACCCCTCT TCTCTCTCTG 6207 228 2.48e-06 TTGAGAGGCC GACCGAGACAACACACCAAC CCGCTGCCTT 1216 452 4.34e-06 TACATCCCCG ACCCCCAACCACACACAGAC CCAACCAACA 3929 36 4.75e-06 CCCCGATTTC GACAACACAACAACAACTGC AACACATCTC 25356 31 4.75e-06 CTTCTTGGTA CAACAAACGACGAACACGAC AACTACAACT 24683 154 7.96e-06 CTGCACCTCG CCTACCATCATATCACCGTC TCAACGTGCC 6286 226 1.19e-05 CGTGGCACCT TTTCCAAAGAACAATCCTCC TTCAAGCGGT 269532 475 1.29e-05 TGGGAAATGT GAAAAAACACAAACAACAAC CAAAAC 7584 465 1.62e-05 ACTACCCTCT GCTCCATTCCACTAACCCCC CAGAGCACAG 3331 256 1.62e-05 GTTGGCTCGT GACACAACGACAACTCAGGT GCACCGAGTT 16039 76 3.06e-05 TGGATGAACT ACTCCAACGATGTCACGTAC CCGTAACTCG 12164 462 3.27e-05 ACGTATCATT GCTCCAGCAAAGAATGCTGC TCTTGACGGT 23457 293 7.71e-05 CTGGATTGGC TTGACAACAACGTCACAGGC TGAACCTTTT 32230 326 1.12e-04 ACTAGATACA GAGCGAGCAGCGACCCCCCC TTTACCTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36937 3.6e-10 375_[+1]_105 6458 1.8e-09 262_[+1]_218 20975 6.2e-08 160_[+1]_320 25811 7.2e-08 169_[+1]_311 20865 7.2e-08 138_[+1]_342 268606 9.5e-08 450_[+1]_30 16613 9.8e-07 270_[+1]_210 23748 1.2e-06 149_[+1]_331 264827 1.4e-06 147_[+1]_333 22843 1.7e-06 412_[+1]_68 6207 2.5e-06 227_[+1]_253 1216 4.3e-06 451_[+1]_29 3929 4.7e-06 35_[+1]_445 25356 4.7e-06 30_[+1]_450 24683 8e-06 153_[+1]_327 6286 1.2e-05 225_[+1]_255 269532 1.3e-05 474_[+1]_6 7584 1.6e-05 464_[+1]_16 3331 1.6e-05 255_[+1]_225 16039 3.1e-05 75_[+1]_405 12164 3.3e-05 461_[+1]_19 23457 7.7e-05 292_[+1]_188 32230 0.00011 325_[+1]_155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=23 36937 ( 376) CATCCAAACACAACACCTGC 1 6458 ( 263) CCTCCCACCACCACACCTCC 1 20975 ( 161) CAAACAAACAACACCCCTGC 1 25811 ( 170) CAGCCAACCACCAACACTAC 1 20865 ( 139) CCTCCCACCACCACTCCCTC 1 268606 ( 451) CACCCAATCCAAACAACGTC 1 16613 ( 271) CATCCAACGCCCTCTACATC 1 23748 ( 150) AATCCATCCACATCAACGTC 1 264827 ( 148) GAACCACACCACACCCCGAC 1 22843 ( 413) CACCCAATCCAAACCCCTCT 1 6207 ( 228) GACCGAGACAACACACCAAC 1 1216 ( 452) ACCCCCAACCACACACAGAC 1 3929 ( 36) GACAACACAACAACAACTGC 1 25356 ( 31) CAACAAACGACGAACACGAC 1 24683 ( 154) CCTACCATCATATCACCGTC 1 6286 ( 226) TTTCCAAAGAACAATCCTCC 1 269532 ( 475) GAAAAAACACAAACAACAAC 1 7584 ( 465) GCTCCATTCCACTAACCCCC 1 3331 ( 256) GACACAACGACAACTCAGGT 1 16039 ( 76) ACTCCAACGATGTCACGTAC 1 12164 ( 462) GCTCCAGCAAAGAATGCTGC 1 23457 ( 293) TTGACAACAACGTCACAGGC 1 32230 ( 326) GAGCGAGCAGCGACCCCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 11063 bayes= 9.97259 E= 5.8e-009 -100 91 52 -161 122 39 -1117 -161 -58 17 -89 71 0 167 -1117 -1117 -100 175 -148 -1117 159 -9 -1117 -1117 150 -241 -89 -161 0 129 -1117 -61 -26 129 -16 -1117 132 39 -247 -1117 74 104 -1117 -161 42 91 -16 -1117 150 -1117 -1117 -2 -26 175 -1117 -1117 100 17 -1117 -29 22 149 -247 -1117 -100 183 -247 -1117 -100 -83 52 56 22 -9 11 -29 -1117 198 -1117 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 23 E= 5.8e-009 0.130435 0.434783 0.347826 0.086957 0.608696 0.304348 0.000000 0.086957 0.173913 0.260870 0.130435 0.434783 0.260870 0.739130 0.000000 0.000000 0.130435 0.782609 0.086957 0.000000 0.782609 0.217391 0.000000 0.000000 0.739130 0.043478 0.130435 0.086957 0.260870 0.565217 0.000000 0.173913 0.217391 0.565217 0.217391 0.000000 0.652174 0.304348 0.043478 0.000000 0.434783 0.478261 0.000000 0.086957 0.347826 0.434783 0.217391 0.000000 0.739130 0.000000 0.000000 0.260870 0.217391 0.782609 0.000000 0.000000 0.521739 0.260870 0.000000 0.217391 0.304348 0.652174 0.043478 0.000000 0.130435 0.826087 0.043478 0.000000 0.130435 0.130435 0.347826 0.391304 0.304348 0.217391 0.260870 0.217391 0.000000 0.913043 0.000000 0.086957 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][AC][TC][CA]C[AC]A[CA][CAG][AC][CA][CAG][AT][CA][ACT][CA]C[TG][AGCT]C -------------------------------------------------------------------------------- Time 5.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 18 llr = 216 E-value = 3.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 213123331111:11:31:: pos.-specific C ::2317::1:11147::2:6 probability G 61436:26:82193:a1:a1 matrix T 28122:519177:22:67:3 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 ** * * * Entropy 1.1 * ** * * * (17.3 bits) 0.8 * * *** * ** *** 0.6 ** * **** * ****** 0.4 ** ********* ****** 0.2 ******************** 0.0 -------------------- Multilevel GTGCGCTGTGTTGCCGTTGC consensus A AG AAA GT AC T sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 6286 108 2.88e-10 CTGGAGTGAA ATGCGCAGTGTTGGCGTTGC TGGTAGCGTT 268606 99 3.15e-08 TGCTGCCCAG GTCAGATATGTTGTCGTTGC TGTTGTTGTG 32230 152 7.63e-08 TCTCATTATT GTTCGAAGTGTTGCAGATGC AGAGGTGTCG 23457 139 2.39e-07 GTTGGTCGGC GTATGCAATGGTGTCGTCGT AAGAATCAGC 20975 136 2.96e-07 CGCGAAAAAG GAACGCTTTGTTGCTGTTGC CTTCGCAAAC 16613 11 4.05e-07 GGTGCGGTAG TTAGGATGTGTTGCAGTTGG ACGGCATGAG 6207 44 5.47e-07 AATAATCAAC GTTGTATGTGTTGCTGTCGT TGGGCCGTTG 3929 349 7.33e-07 CGTAGAATAC ATCCACTGTGTTGCTGGTGT AATACAATGT 7584 58 8.06e-07 ATTGGGGAGA GTGTGCTATTCTGACGTTGC TCTCTGCTCC 264827 239 1.53e-06 CAGTGGAACT GTAGACAAAGTGGCCGATGC CTCGTTGGAT 269532 259 1.67e-06 GCTCATGAAA GTGCCCAGTGGTCTCGTTGG ACTGGAATAA 22843 179 2.16e-06 ATCCTTTTTC GGAGTCAATGGGGCCGATGC GAAGGACGGA 12164 193 2.16e-06 TAGTGTGGAC ATGTGATGTGTACGCGATGT ACACATGATG 36937 255 3.26e-06 TTTGTGTTTC GTGTGCGGTGACGTTGTTGT TAGATGCCGT 16039 256 3.82e-06 CTGAGGTGGG GAGGCAGGTGTTGGCGAAGC ACGAGGAACT 3331 310 7.51e-06 AGTAGCATCA ATGCACTATTCAGCCGTCGC ATCATAGCAC 23748 35 1.07e-05 TGTTTGAAGG TTCGTCTGCATTGGCGATGC ATGCATTGGA 6458 5 1.14e-05 ATGG TGGAGCGGTGTCGGCGGCGC GGCGGCTCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6286 2.9e-10 107_[+2]_373 268606 3.2e-08 98_[+2]_382 32230 7.6e-08 151_[+2]_329 23457 2.4e-07 138_[+2]_342 20975 3e-07 135_[+2]_345 16613 4e-07 10_[+2]_470 6207 5.5e-07 43_[+2]_437 3929 7.3e-07 348_[+2]_132 7584 8.1e-07 57_[+2]_423 264827 1.5e-06 238_[+2]_242 269532 1.7e-06 258_[+2]_222 22843 2.2e-06 178_[+2]_302 12164 2.2e-06 192_[+2]_288 36937 3.3e-06 254_[+2]_226 16039 3.8e-06 255_[+2]_225 3331 7.5e-06 309_[+2]_171 23748 1.1e-05 34_[+2]_446 6458 1.1e-05 4_[+2]_476 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=18 6286 ( 108) ATGCGCAGTGTTGGCGTTGC 1 268606 ( 99) GTCAGATATGTTGTCGTTGC 1 32230 ( 152) GTTCGAAGTGTTGCAGATGC 1 23457 ( 139) GTATGCAATGGTGTCGTCGT 1 20975 ( 136) GAACGCTTTGTTGCTGTTGC 1 16613 ( 11) TTAGGATGTGTTGCAGTTGG 1 6207 ( 44) GTTGTATGTGTTGCTGTCGT 1 3929 ( 349) ATCCACTGTGTTGCTGGTGT 1 7584 ( 58) GTGTGCTATTCTGACGTTGC 1 264827 ( 239) GTAGACAAAGTGGCCGATGC 1 269532 ( 259) GTGCCCAGTGGTCTCGTTGG 1 22843 ( 179) GGAGTCAATGGGGCCGATGC 1 12164 ( 193) ATGTGATGTGTACGCGATGT 1 36937 ( 255) GTGTGCGGTGACGTTGTTGT 1 16039 ( 256) GAGGCAGGTGTTGGCGAAGC 1 3331 ( 310) ATGCACTATTCAGCCGTCGC 1 23748 ( 35) TTCGTCTGCATTGGCGATGC 1 6458 ( 5) TGGAGCGGTGTCGGCGGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 11063 bayes= 9.39569 E= 3.3e-004 -23 -1081 134 -67 -123 -1081 -112 155 9 -48 88 -125 -123 52 46 -26 -64 -106 120 -67 35 152 -1081 -1081 35 -1081 -54 91 35 -1081 134 -225 -223 -206 -1081 174 -223 -1081 178 -125 -223 -106 -54 133 -123 -106 -112 133 -1081 -106 188 -1081 -223 94 20 -26 -123 152 -1081 -26 -1081 -1081 205 -1081 35 -1081 -112 107 -223 -6 -1081 144 -1081 -1081 205 -1081 -1081 140 -112 7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 18 E= 3.3e-004 0.222222 0.000000 0.611111 0.166667 0.111111 0.000000 0.111111 0.777778 0.277778 0.166667 0.444444 0.111111 0.111111 0.333333 0.333333 0.222222 0.166667 0.111111 0.555556 0.166667 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.166667 0.500000 0.333333 0.000000 0.611111 0.055556 0.055556 0.055556 0.000000 0.888889 0.055556 0.000000 0.833333 0.111111 0.055556 0.111111 0.166667 0.666667 0.111111 0.111111 0.111111 0.666667 0.000000 0.111111 0.888889 0.000000 0.055556 0.444444 0.277778 0.222222 0.111111 0.666667 0.000000 0.222222 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.111111 0.555556 0.055556 0.222222 0.000000 0.722222 0.000000 0.000000 1.000000 0.000000 0.000000 0.611111 0.111111 0.277778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]T[GA][CGT]G[CA][TA][GA]TGTTG[CGT][CT]G[TA][TC]G[CT] -------------------------------------------------------------------------------- Time 11.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 13 llr = 167 E-value = 2.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3::1::2::13:1::21: pos.-specific C 5:122:::::2:21::1:: probability G 4255:283:a2151a55:7 matrix T 15547825a:5638:5293 bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 ** * * Relative 1.3 ** ** * * Entropy 1.1 ** ** ** ** (18.6 bits) 0.8 * *** ** *** ** 0.6 * ******** * *** ** 0.4 ********** ***** ** 0.2 ******************* 0.0 ------------------- Multilevel CTGGTTGTTGTTGTGTGTG consensus GATTC TG GAT GA T sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 7584 187 1.39e-09 CGTTCTCGTG CTTTCTGTTGTTGTGGGTG GATACACATC 264827 91 6.36e-08 TTTGTTTGTC CTTGTTGTTGATCTGTTTG ACGTTTATTA 20865 56 1.02e-07 TCGTTCGGAC GTTCTTTTTGCTGTGTGTG GCGCCAACGA 23457 113 1.76e-07 TCCTGATACA CTGGTTGGTGGGGTGGGTT GGTCGGCGTA 25811 23 2.65e-07 AGGTCGACTG TTGGTTTGTGGTGTGTGTG GTACCGCGGC 16039 14 4.26e-07 TGGAATGGAG CTGGATGATGTAGTGGATG CGCAGGTGAC 12164 134 4.66e-07 AAAAGACAGT GAGTTTGTTGTATTGGCTT GTTTTGTTTA 3331 76 6.07e-07 TGCTGCCATG GTTGCTGTTGTAGTGTAAG CGTTGTGTTT 32230 368 9.19e-07 GACGTGCTGG CATTTTGATGTTCCGTTTG CTCTGACACG 23748 345 9.19e-07 GTGGAGGAGA GAGTTGTGTGTATTGTGTG TTTGTGACGT 16613 363 9.19e-07 CGGTTTGTGA CGTCCTGTTGTTCTGGATT CGGTCATCTT 268606 41 2.07e-06 ATATGAATGG GGGGTTGGTGCTTAGTTTG TGTAGCAGTT 6458 36 7.69e-06 GCGGCTCGGG CACTTGGTTGGTTGGGGTT CCGTTGGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7584 1.4e-09 186_[+3]_295 264827 6.4e-08 90_[+3]_391 20865 1e-07 55_[+3]_426 23457 1.8e-07 112_[+3]_369 25811 2.6e-07 22_[+3]_459 16039 4.3e-07 13_[+3]_468 12164 4.7e-07 133_[+3]_348 3331 6.1e-07 75_[+3]_406 32230 9.2e-07 367_[+3]_114 23748 9.2e-07 344_[+3]_137 16613 9.2e-07 362_[+3]_119 268606 2.1e-06 40_[+3]_441 6458 7.7e-06 35_[+3]_446 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=13 7584 ( 187) CTTTCTGTTGTTGTGGGTG 1 264827 ( 91) CTTGTTGTTGATCTGTTTG 1 20865 ( 56) GTTCTTTTTGCTGTGTGTG 1 23457 ( 113) CTGGTTGGTGGGGTGGGTT 1 25811 ( 23) TTGGTTTGTGGTGTGTGTG 1 16039 ( 14) CTGGATGATGTAGTGGATG 1 12164 ( 134) GAGTTTGTTGTATTGGCTT 1 3331 ( 76) GTTGCTGTTGTAGTGTAAG 1 32230 ( 368) CATTTTGATGTTCCGTTTG 1 23748 ( 345) GAGTTGTGTGTATTGTGTG 1 16613 ( 363) CGTCCTGTTGTTCTGGATT 1 268606 ( 41) GGGGTTGGTGCTTAGTTTG 1 6458 ( 36) CACTTGGTTGGTTGGGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 11086 bayes= 9.48959 E= 2.1e+001 -1035 122 67 -178 24 -1035 -65 102 -1035 -159 93 80 -1035 -59 93 53 -176 -1 -1035 138 -1035 -1035 -65 167 -1035 -1035 167 -20 -76 -1035 35 102 -1035 -1035 -1035 191 -1035 -1035 205 -1035 -176 -59 -7 102 24 -1035 -165 121 -1035 -1 93 21 -176 -159 -165 153 -1035 -1035 205 -1035 -1035 -1035 93 102 -18 -159 93 -20 -176 -1035 -1035 180 -1035 -1035 152 21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 13 E= 2.1e+001 0.000000 0.538462 0.384615 0.076923 0.307692 0.000000 0.153846 0.538462 0.000000 0.076923 0.461538 0.461538 0.000000 0.153846 0.461538 0.384615 0.076923 0.230769 0.000000 0.692308 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 0.769231 0.230769 0.153846 0.000000 0.307692 0.538462 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.076923 0.153846 0.230769 0.538462 0.307692 0.000000 0.076923 0.615385 0.000000 0.230769 0.461538 0.307692 0.076923 0.076923 0.076923 0.769231 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.461538 0.538462 0.230769 0.076923 0.461538 0.230769 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 0.692308 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][TA][GT][GT][TC]T[GT][TG]TG[TG][TA][GTC]TG[TG][GAT]T[GT] -------------------------------------------------------------------------------- Time 17.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1216 7.17e-03 451_[+1(4.34e-06)]_29 12164 7.63e-07 133_[+3(4.66e-07)]_40_\ [+2(2.16e-06)]_249_[+1(3.27e-05)]_19 16039 1.11e-06 13_[+3(4.26e-07)]_43_[+1(3.06e-05)]_\ 160_[+2(3.82e-06)]_225 16613 1.27e-08 10_[+2(4.05e-07)]_240_\ [+1(9.85e-07)]_72_[+3(9.19e-07)]_119 20865 2.93e-07 55_[+3(1.02e-07)]_64_[+1(7.16e-08)]_\ 342 20975 1.25e-07 135_[+2(2.96e-07)]_5_[+1(6.19e-08)]_\ 320 22843 6.41e-05 178_[+2(2.16e-06)]_214_\ [+1(1.66e-06)]_68 23457 9.23e-08 112_[+3(1.76e-07)]_7_[+2(2.39e-07)]_\ 134_[+1(7.71e-05)]_188 23748 3.06e-07 34_[+2(1.07e-05)]_95_[+1(1.22e-06)]_\ 175_[+3(9.19e-07)]_137 24683 1.46e-02 153_[+1(7.96e-06)]_327 25356 1.76e-02 30_[+1(4.75e-06)]_450 25811 8.15e-07 22_[+3(2.65e-07)]_128_\ [+1(7.16e-08)]_311 264827 4.95e-09 69_[+3(5.15e-05)]_2_[+3(6.36e-08)]_\ 38_[+1(1.35e-06)]_71_[+2(1.53e-06)]_242 268606 2.91e-10 40_[+3(2.07e-06)]_39_[+2(3.15e-08)]_\ 332_[+1(9.52e-08)]_30 269532 6.20e-05 258_[+2(1.67e-06)]_196_\ [+1(1.29e-05)]_6 32230 2.05e-07 16_[+3(3.46e-05)]_116_\ [+2(7.63e-08)]_196_[+3(9.19e-07)]_114 3331 1.58e-06 75_[+3(6.07e-07)]_161_\ [+1(1.62e-05)]_34_[+2(7.51e-06)]_85_[+3(6.39e-05)]_67 36937 3.07e-09 110_[+1(4.75e-06)]_124_\ [+2(3.26e-06)]_101_[+1(3.59e-10)]_105 3929 1.82e-05 35_[+1(4.75e-06)]_293_\ [+2(7.33e-07)]_132 6207 3.12e-05 43_[+2(5.47e-07)]_164_\ [+1(2.48e-06)]_253 6286 1.01e-07 107_[+2(2.88e-10)]_98_\ [+1(1.19e-05)]_255 6458 5.95e-09 4_[+2(1.14e-05)]_11_[+3(7.69e-06)]_\ 170_[+1(1.64e-07)]_18_[+1(1.84e-09)]_218 7584 7.85e-10 57_[+2(8.06e-07)]_109_\ [+3(1.39e-09)]_91_[+3(2.24e-05)]_149_[+1(1.62e-05)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************