******************************************************************************** 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/87/87.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11387 1.0000 500 1230 1.0000 500 12637 1.0000 500 14942 1.0000 500 2085 1.0000 500 21233 1.0000 500 23058 1.0000 500 23201 1.0000 500 23496 1.0000 500 23994 1.0000 500 24333 1.0000 500 261781 1.0000 500 262204 1.0000 500 262526 1.0000 500 262574 1.0000 500 28217 1.0000 500 2844 1.0000 500 3085 1.0000 500 3158 1.0000 500 32706 1.0000 500 34878 1.0000 500 35189 1.0000 500 35420 1.0000 500 36373 1.0000 500 37523 1.0000 500 3928 1.0000 500 40206 1.0000 500 5775 1.0000 500 6686 1.0000 500 6816 1.0000 500 8387 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/87/87.seqs.fa -oc motifs/87 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.244 G 0.233 T 0.254 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.244 G 0.233 T 0.254 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 25 llr = 295 E-value = 1.1e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :44:6426327528:a7126 pos.-specific C 8:2a14817824827:1751 probability G :4::31:1::1:::2:212: matrix T 224::1:2:::11::::2:2 bits 2.1 * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * * Entropy 1.1 * * * ** **** (17.0 bits) 0.8 * * * *** ***** 0.6 * * * ********** * 0.4 ** ** ************** 0.2 ******************** 0.0 -------------------- Multilevel CGACAACACCAACACAACCA consensus TAT GC AACC G G AT sequence TC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 23994 183 3.71e-09 TTTGCAATGA TGCCAACACCACCACAACGA AAGTACCGAC 5775 431 1.13e-08 CTTTCTAACA CAACAACTCCATCACAACCA CTCACTCATA 40206 331 1.31e-08 ATCAAACAAG CTACGCCACCACCACAATGA CGGCCGTTAG 2085 455 3.09e-08 CAAGCCACAC CGTCTCCTCCACCACAACCA CCGATCAGCA 23201 480 3.54e-08 ATATCAGCGG CTTCAACAACACAACAACAA A 261781 63 7.75e-08 ATGTTCAGAG CTCCACCAACAACACAATCT AAACAGGAGG 6686 34 8.78e-08 ACCACATCAT CATCATCAACAACACAATAA CAATAAACTC 28217 273 1.43e-07 CGCATCAAGC CAACAACACCAACAAAGCGA CTTACCAATA 2844 302 3.53e-07 GCTCCCAACG CATCAACACACACACAGCAT TGGCCACATT 11387 413 5.98e-07 TCCTCTCGGT CGTCGCCACAACCCCAACCG CAACCAAAAG 3158 349 6.62e-07 CAAGCAGCAC CACCCCCACCCACCCAACAA ACAACGCCTA 8387 477 8.09e-07 CCTCCTACTT CGGCACCTCCACCACAGCCC CACC 12637 457 8.09e-07 TCTGCAACAA TATCAACACCAACAGACGCA ACAAATACCA 37523 160 2.07e-06 TTGGTTGTGT TGTCGCCGACAACACACCGT GGGAGAGTAA 32706 54 3.20e-06 CCCTCCAAAG CGACACAACCGCAACAACAC GACATGGAAG 6816 389 3.48e-06 TTTCCTCGGC CGACGACGACAACAGAGACT AAGCGGCCCT 35189 358 3.78e-06 ACAGCTCTAG TATCATCAACCAACCAACCA ACCTTCGTTC 3085 450 6.61e-06 ACAACATTGA CAACGAAACAGATACAACAA CAACTTAGAC 24333 329 7.13e-06 CCAGACAACG CTACACCCCCGCTACAGCGT ATCACAGCCG 34878 32 8.29e-06 ACGGAGGTGG CGACCGTACAAACAGAACCA GGACCCCTTT 36373 368 8.93e-06 CTTCGTATGG CTACAGCCCCCCACGAACCA TTGTTAACAA 262204 187 1.11e-05 ACGACGACGA CGACGAACACAACAGACGCA ACGCTTCCTC 1230 68 1.11e-05 ACCCCCAACA TACCATCACAACCTCAATCA CTAACCTCCA 21233 467 1.92e-05 CCACCTTAGC AGCCGACGACACCACAAAGT CTCGCTTCAT 14942 199 2.48e-05 TTTGCTAATG CTTCGAATCCCTCAGAACTA GCATTGACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23994 3.7e-09 182_[+1]_298 5775 1.1e-08 430_[+1]_50 40206 1.3e-08 330_[+1]_150 2085 3.1e-08 454_[+1]_26 23201 3.5e-08 479_[+1]_1 261781 7.8e-08 62_[+1]_418 6686 8.8e-08 33_[+1]_447 28217 1.4e-07 272_[+1]_208 2844 3.5e-07 301_[+1]_179 11387 6e-07 412_[+1]_68 3158 6.6e-07 348_[+1]_132 8387 8.1e-07 476_[+1]_4 12637 8.1e-07 456_[+1]_24 37523 2.1e-06 159_[+1]_321 32706 3.2e-06 53_[+1]_427 6816 3.5e-06 388_[+1]_92 35189 3.8e-06 357_[+1]_123 3085 6.6e-06 449_[+1]_31 24333 7.1e-06 328_[+1]_152 34878 8.3e-06 31_[+1]_449 36373 8.9e-06 367_[+1]_113 262204 1.1e-05 186_[+1]_294 1230 1.1e-05 67_[+1]_413 21233 1.9e-05 466_[+1]_14 14942 2.5e-05 198_[+1]_282 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=25 23994 ( 183) TGCCAACACCACCACAACGA 1 5775 ( 431) CAACAACTCCATCACAACCA 1 40206 ( 331) CTACGCCACCACCACAATGA 1 2085 ( 455) CGTCTCCTCCACCACAACCA 1 23201 ( 480) CTTCAACAACACAACAACAA 1 261781 ( 63) CTCCACCAACAACACAATCT 1 6686 ( 34) CATCATCAACAACACAATAA 1 28217 ( 273) CAACAACACCAACAAAGCGA 1 2844 ( 302) CATCAACACACACACAGCAT 1 11387 ( 413) CGTCGCCACAACCCCAACCG 1 3158 ( 349) CACCCCCACCCACCCAACAA 1 8387 ( 477) CGGCACCTCCACCACAGCCC 1 12637 ( 457) TATCAACACCAACAGACGCA 1 37523 ( 160) TGTCGCCGACAACACACCGT 1 32706 ( 54) CGACACAACCGCAACAACAC 1 6816 ( 389) CGACGACGACAACAGAGACT 1 35189 ( 358) TATCATCAACCAACCAACCA 1 3085 ( 450) CAACGAAACAGATACAACAA 1 24333 ( 329) CTACACCCCCGCTACAGCGT 1 34878 ( 32) CGACCGTACAAACAGAACCA 1 36373 ( 368) CTACAGCCCCCCACGAACCA 1 262204 ( 187) CGACGAACACAACAGACGCA 1 1230 ( 68) TACCATCACAACCTCAATCA 1 21233 ( 467) AGCCGACGACACCACAAAGT 1 14942 ( 199) CTTCGAATCCCTCAGAACTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14911 bayes= 9.70856 E= 1.1e-013 -275 164 -1129 -34 42 -1129 78 -8 57 -29 -254 50 -1129 203 -1129 -1129 106 -161 46 -266 71 56 -154 -108 -75 171 -1129 -266 116 -102 -95 -67 25 148 -1129 -1129 -43 171 -1129 -1129 134 -29 -95 -1129 83 85 -1129 -167 -75 164 -1129 -167 157 -61 -1129 -266 -275 156 5 -1129 189 -1129 -1129 -1129 134 -102 -22 -1129 -175 148 -154 -67 -17 97 5 -266 125 -161 -254 -8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 25 E= 1.1e-013 0.040000 0.760000 0.000000 0.200000 0.360000 0.000000 0.400000 0.240000 0.400000 0.200000 0.040000 0.360000 0.000000 1.000000 0.000000 0.000000 0.560000 0.080000 0.320000 0.040000 0.440000 0.360000 0.080000 0.120000 0.160000 0.800000 0.000000 0.040000 0.600000 0.120000 0.120000 0.160000 0.320000 0.680000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.680000 0.200000 0.120000 0.000000 0.480000 0.440000 0.000000 0.080000 0.160000 0.760000 0.000000 0.080000 0.800000 0.160000 0.000000 0.040000 0.040000 0.720000 0.240000 0.000000 1.000000 0.000000 0.000000 0.000000 0.680000 0.120000 0.200000 0.000000 0.080000 0.680000 0.080000 0.160000 0.240000 0.480000 0.240000 0.040000 0.640000 0.080000 0.040000 0.240000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][GAT][ATC]C[AG][AC]CA[CA][CA][AC][AC]CA[CG]A[AG]C[CAG][AT] -------------------------------------------------------------------------------- Time 7.70 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 16 llr = 213 E-value = 2.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1116::1:1312:3:28:331 pos.-specific C :3:::4:4:133:11:::3:: probability G 828:8634936384983a379 matrix T 14143:63:3:3321:::11: bits 2.1 * 1.9 * 1.7 * * 1.5 * ** * * Relative 1.3 * * * ** * * Entropy 1.1 * **** * * **** * (19.2 bits) 0.8 * **** * * * **** ** 0.6 * ***** * * * **** ** 0.4 * ******* * * **** ** 0.2 ********* * ****** ** 0.0 --------------------- Multilevel GTGAGGTCGAGTGGGGAGCGG consensus C TTCGG TCCTA G GA sequence T G G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 2085 174 1.63e-09 ATTCACGCTC GCGAGCTCGTCCGAGGAGAGG ATCGTTGCGA 40206 214 2.68e-09 TTCCAGAGAA GTGAGGTCGACCGAGGAGTGG ATTGGAGGTG 12637 273 6.61e-09 CTTTTGAGTG GTGTGCTCGTCGGCGGAGCGG TTCAAGTGAT 2844 29 5.03e-08 TCGGGCTTCG GCTAGCTCGCGTTGGGAGCGG CGGTCGGCCG 23201 27 5.63e-08 TCATTTCGAG GTGAGGTGAGGCGAGGAGGAG GTTTGTGAAG 6686 259 7.02e-08 GGCGTTGATT GTGTGCGTGTGTGGTGAGGGG AAGTGGGAGG 23058 314 9.65e-08 GTGTTGAAGG GAGTTGTTGTGTGTGGGGGGG GAGCAATGGT 8387 208 5.61e-07 TGGTGTTGGT GTGATGTTGTGATGGAAGAAG ACTCGAGAGA 24333 55 5.61e-07 GTGTGTCAAC TCTAGCTCGGGGGGGGGGCAG CTCCAAAGTA 35420 117 1.05e-06 TTGTTGGACT GCGTGGGGGCCTTTGGAGGGA TCGACGCGGA 3158 131 1.05e-06 TCTGTCCCAC GAAATCGGGAGAGAGGGGGGG AGTATACTAT 32706 247 1.13e-06 ATGCAAGTGG TGGTGCTGGAGAGAGGAGCAA CATTATGAAG 5775 256 1.31e-06 GATGATACTA GTGAGGGGGGAGGGCAAGAGG AGGCAGGCGA 35189 276 1.41e-06 GAGGAGGAAG AGAATGAGGAGTGGGGAGAGG AAGAATGTGA 3928 149 2.43e-06 ATTGTCTTCT AGGAGGTTGGACGTGGAGCTG TGAGTGTAGA 6816 27 2.59e-06 AGGACCGATG GCGTGGACGAGGTCGAGGTGG TGGCGACAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2085 1.6e-09 173_[+2]_306 40206 2.7e-09 213_[+2]_266 12637 6.6e-09 272_[+2]_207 2844 5e-08 28_[+2]_451 23201 5.6e-08 26_[+2]_453 6686 7e-08 258_[+2]_221 23058 9.6e-08 313_[+2]_166 8387 5.6e-07 207_[+2]_272 24333 5.6e-07 54_[+2]_425 35420 1.1e-06 116_[+2]_363 3158 1.1e-06 130_[+2]_349 32706 1.1e-06 246_[+2]_233 5775 1.3e-06 255_[+2]_224 35189 1.4e-06 275_[+2]_204 3928 2.4e-06 148_[+2]_331 6816 2.6e-06 26_[+2]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=16 2085 ( 174) GCGAGCTCGTCCGAGGAGAGG 1 40206 ( 214) GTGAGGTCGACCGAGGAGTGG 1 12637 ( 273) GTGTGCTCGTCGGCGGAGCGG 1 2844 ( 29) GCTAGCTCGCGTTGGGAGCGG 1 23201 ( 27) GTGAGGTGAGGCGAGGAGGAG 1 6686 ( 259) GTGTGCGTGTGTGGTGAGGGG 1 23058 ( 314) GAGTTGTTGTGTGTGGGGGGG 1 8387 ( 208) GTGATGTTGTGATGGAAGAAG 1 24333 ( 55) TCTAGCTCGGGGGGGGGGCAG 1 35420 ( 117) GCGTGGGGGCCTTTGGAGGGA 1 3158 ( 131) GAAATCGGGAGAGAGGGGGGG 1 32706 ( 247) TGGTGCTGGAGAGAGGAGCAA 1 5775 ( 256) GTGAGGGGGGAGGGCAAGAGG 1 35189 ( 276) AGAATGAGGAGTGGGGAGAGG 1 3928 ( 149) AGGAGGTTGGACGTGGAGCTG 1 6816 ( 27) GCGTGGACGAGGTCGAGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 11.1824 E= 2.6e-005 -111 -1064 169 -102 -111 36 -31 56 -111 -1064 169 -102 121 -1064 -1064 56 -1064 -1064 169 -2 -1064 84 127 -1064 -111 -1064 10 130 -1064 62 69 -2 -210 -1064 201 -1064 21 -97 10 30 -111 3 143 -1064 -52 3 10 30 -1064 -1064 169 -2 21 -97 69 -44 -1064 -196 191 -202 -52 -1064 180 -1064 148 -1064 10 -1064 -1064 -1064 210 -1064 -11 36 43 -102 -11 -1064 156 -202 -111 -1064 191 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 2.6e-005 0.125000 0.000000 0.750000 0.125000 0.125000 0.312500 0.187500 0.375000 0.125000 0.000000 0.750000 0.125000 0.625000 0.000000 0.000000 0.375000 0.000000 0.000000 0.750000 0.250000 0.000000 0.437500 0.562500 0.000000 0.125000 0.000000 0.250000 0.625000 0.000000 0.375000 0.375000 0.250000 0.062500 0.000000 0.937500 0.000000 0.312500 0.125000 0.250000 0.312500 0.125000 0.250000 0.625000 0.000000 0.187500 0.250000 0.250000 0.312500 0.000000 0.000000 0.750000 0.250000 0.312500 0.125000 0.375000 0.187500 0.000000 0.062500 0.875000 0.062500 0.187500 0.000000 0.812500 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.312500 0.312500 0.125000 0.250000 0.000000 0.687500 0.062500 0.125000 0.000000 0.875000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TC]G[AT][GT][GC][TG][CGT]G[ATG][GC][TCG][GT][GA]GG[AG]G[CGA][GA]G -------------------------------------------------------------------------------- Time 15.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 20 llr = 234 E-value = 2.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :51:4313222::8::21761 pos.-specific C 1121:3:21::11:2133125 probability G 921a22a3572192:6643:4 matrix T 138:43:33279:184:2:31 bits 2.1 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 * * * ** * Entropy 1.1 * * * ** * (16.9 bits) 0.8 * ** * ****** 0.6 * ** * ******** ** 0.4 * *** * ******** *** 0.2 ***** * ************* 0.0 --------------------- Multilevel GATGACGTGGTTGATGGGAAC consensus T TT AT CTCCGTG sequence GA G T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35420 164 6.28e-10 TGGCGTAGTC GATGACGCGTTTGATGGGAAC CAGGATCTTC 12637 140 9.01e-10 TATGGTGGCG GATGTAGTTGTTGATGGCGAC AATGGTACTT 36373 247 1.28e-07 TCTGGAAAGA GATGATGTGAATGATGGGCAC ACTGCGCGTT 11387 206 1.44e-07 CTCATTGAAT GATGAAGGAGTTGGTTGTATG AACAGGGATG 3085 235 4.26e-07 AGTATGATCA GCTGTTGTTGTTGACGAGATG CACCGATGCA 8387 109 5.78e-07 TGCTGCGGTG GACGTCGCAGTTGGTGCGGAG TGTTTTTCCC 262204 10 5.78e-07 GTGGACATT GTTGGCGTGGTTGTTCGTATC GATATCCGCC 23058 158 6.38e-07 TGGGTGGAAT GGTGTGAGGGTTGATTGGACC CGAACGATCT 6686 206 1.49e-06 GGCGGATGTG GATGTAGTGGTGGACGCTACG GGGGCTGCGT 262526 294 1.49e-06 CGTGACCAAC GATGACGACGTCGACGCCGAC TCCTCCGATA 32706 271 1.63e-06 GGAGCAACAT TATGAAGAGTGTGATTGCGAG TACAATGTAC 40206 97 1.95e-06 GGCTGCCATC GCTGATGATGTTGATGAGACT GGAAAGCGAC 2844 67 2.53e-06 CCGCTGTTTC GGTGGGGACGTTCATGGTGAG TGTTGTGAAG 14942 3 3.25e-06 TA GGTGGGGAGGTTGATCCAAAA TTGGCGACAA 35189 5 4.51e-06 GAGC GAAGAAGGGGACGATTCCAAC AAACAATCAT 6816 68 8.33e-06 ATGGCGAGGT GTCCATGCTGTTGGTTGGATG TTGAAGCCGG 3928 253 8.33e-06 CTGATGAAGA CATGTTGTGTATGTTGGCATC CGATGAAGAG 28217 169 1.04e-05 ACAACTGGGT TTGGTTGGGGTTGATTGACAC CGGTAAGTTC 3158 294 1.38e-05 AACGCGTGTG GTTGGCGGTAGTCATTGCAAA GCAGCACGAA 21233 93 1.47e-05 GCTCGTCTAT GTCGTCGCAAGTGACGAGAAG AAATCACAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35420 6.3e-10 163_[+3]_316 12637 9e-10 139_[+3]_340 36373 1.3e-07 246_[+3]_233 11387 1.4e-07 205_[+3]_274 3085 4.3e-07 234_[+3]_245 8387 5.8e-07 108_[+3]_371 262204 5.8e-07 9_[+3]_470 23058 6.4e-07 157_[+3]_322 6686 1.5e-06 205_[+3]_274 262526 1.5e-06 293_[+3]_186 32706 1.6e-06 270_[+3]_209 40206 2e-06 96_[+3]_383 2844 2.5e-06 66_[+3]_413 14942 3.3e-06 2_[+3]_477 35189 4.5e-06 4_[+3]_475 6816 8.3e-06 67_[+3]_412 3928 8.3e-06 252_[+3]_227 28217 1e-05 168_[+3]_311 3158 1.4e-05 293_[+3]_186 21233 1.5e-05 92_[+3]_387 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=20 35420 ( 164) GATGACGCGTTTGATGGGAAC 1 12637 ( 140) GATGTAGTTGTTGATGGCGAC 1 36373 ( 247) GATGATGTGAATGATGGGCAC 1 11387 ( 206) GATGAAGGAGTTGGTTGTATG 1 3085 ( 235) GCTGTTGTTGTTGACGAGATG 1 8387 ( 109) GACGTCGCAGTTGGTGCGGAG 1 262204 ( 10) GTTGGCGTGGTTGTTCGTATC 1 23058 ( 158) GGTGTGAGGGTTGATTGGACC 1 6686 ( 206) GATGTAGTGGTGGACGCTACG 1 262526 ( 294) GATGACGACGTCGACGCCGAC 1 32706 ( 271) TATGAAGAGTGTGATTGCGAG 1 40206 ( 97) GCTGATGATGTTGATGAGACT 1 2844 ( 67) GGTGGGGACGTTCATGGTGAG 1 14942 ( 3) GGTGGGGAGGTTGATCCAAAA 1 35189 ( 5) GAAGAAGGGGACGATTCCAAC 1 6816 ( 68) GTCCATGCTGTTGGTTGGATG 1 3928 ( 253) CATGTTGTGTATGTTGGCATC 1 28217 ( 169) TTGGTTGGGGTTGATTGACAC 1 3158 ( 294) GTTGGCGGTAGTCATTGCAAA 1 21233 ( 93) GTCGTCGCAAGTGACGAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 10.4816 E= 2.8e-002 -1097 -229 187 -134 89 -129 -63 -2 -243 -70 -221 156 -1097 -229 203 -1097 57 -1097 -22 65 -11 30 -63 24 -243 -1097 203 -1097 -11 -29 10 24 -84 -129 110 -2 -84 -1097 159 -76 -84 -1097 -63 146 -1097 -129 -221 174 -1097 -129 195 -1097 148 -1097 -63 -134 -1097 -29 -1097 165 -1097 -129 124 46 -84 3 137 -1097 -143 30 78 -34 127 -129 10 -1097 116 -70 -1097 -2 -143 88 78 -234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 2.8e-002 0.000000 0.050000 0.850000 0.100000 0.500000 0.100000 0.150000 0.250000 0.050000 0.150000 0.050000 0.750000 0.000000 0.050000 0.950000 0.000000 0.400000 0.000000 0.200000 0.400000 0.250000 0.300000 0.150000 0.300000 0.050000 0.000000 0.950000 0.000000 0.250000 0.200000 0.250000 0.300000 0.150000 0.100000 0.500000 0.250000 0.150000 0.000000 0.700000 0.150000 0.150000 0.000000 0.150000 0.700000 0.000000 0.100000 0.050000 0.850000 0.000000 0.100000 0.900000 0.000000 0.750000 0.000000 0.150000 0.100000 0.000000 0.200000 0.000000 0.800000 0.000000 0.100000 0.550000 0.350000 0.150000 0.250000 0.600000 0.000000 0.100000 0.300000 0.400000 0.200000 0.650000 0.100000 0.250000 0.000000 0.600000 0.150000 0.000000 0.250000 0.100000 0.450000 0.400000 0.050000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT]TG[ATG][CTA]G[TAGC][GT]GTTGA[TC][GT][GC][GCT][AG][AT][CG] -------------------------------------------------------------------------------- Time 22.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11387 2.38e-06 205_[+3(1.44e-07)]_186_\ [+1(5.98e-07)]_68 1230 2.71e-02 67_[+1(1.11e-05)]_413 12637 3.50e-13 139_[+3(9.01e-10)]_112_\ [+2(6.61e-09)]_163_[+1(8.09e-07)]_24 14942 5.46e-04 2_[+3(3.25e-06)]_175_[+1(2.48e-05)]_\ 282 2085 4.91e-10 6_[+1(3.20e-06)]_147_[+2(1.63e-09)]_\ 260_[+1(3.09e-08)]_26 21233 1.81e-03 92_[+3(1.47e-05)]_353_\ [+1(1.92e-05)]_14 23058 1.79e-06 157_[+3(6.38e-07)]_135_\ [+2(9.65e-08)]_166 23201 9.10e-09 26_[+2(5.63e-08)]_432_\ [+1(3.54e-08)]_1 23496 3.86e-01 500 23994 2.68e-05 182_[+1(3.71e-09)]_6_[+1(9.61e-06)]_\ 272 24333 1.53e-05 54_[+2(5.61e-07)]_207_\ [+1(8.09e-05)]_26_[+1(7.13e-06)]_89_[+1(9.38e-05)]_43 261781 9.03e-04 62_[+1(7.75e-08)]_418 262204 6.93e-05 9_[+3(5.78e-07)]_156_[+1(1.11e-05)]_\ 294 262526 1.18e-02 155_[+3(5.78e-05)]_117_\ [+3(1.49e-06)]_186 262574 1.22e-01 500 28217 1.36e-05 168_[+3(1.04e-05)]_83_\ [+1(1.43e-07)]_208 2844 1.82e-09 28_[+2(5.03e-08)]_17_[+3(2.53e-06)]_\ 74_[+1(9.84e-05)]_120_[+1(3.53e-07)]_179 3085 3.80e-05 234_[+3(4.26e-07)]_194_\ [+1(6.61e-06)]_31 3158 2.49e-07 130_[+2(1.05e-06)]_142_\ [+3(1.38e-05)]_34_[+1(6.62e-07)]_132 32706 1.61e-07 53_[+1(3.20e-06)]_173_\ [+2(1.13e-06)]_3_[+3(1.63e-06)]_182_[+1(1.37e-05)]_7 34878 1.66e-02 31_[+1(8.29e-06)]_449 35189 5.73e-07 4_[+3(4.51e-06)]_250_[+2(1.41e-06)]_\ 61_[+1(3.78e-06)]_123 35420 3.41e-08 116_[+2(1.05e-06)]_26_\ [+3(6.28e-10)]_316 36373 2.47e-05 246_[+3(1.28e-07)]_100_\ [+1(8.93e-06)]_113 37523 1.75e-02 159_[+1(2.07e-06)]_321 3928 2.51e-04 148_[+2(2.43e-06)]_83_\ [+3(8.33e-06)]_227 40206 4.26e-12 96_[+3(1.95e-06)]_96_[+2(2.68e-09)]_\ 96_[+1(1.31e-08)]_17_[+1(4.10e-06)]_113 5775 5.97e-08 255_[+2(1.31e-06)]_154_\ [+1(1.13e-08)]_50 6686 4.18e-10 33_[+1(8.78e-08)]_152_\ [+3(1.49e-06)]_32_[+2(7.02e-08)]_221 6816 1.60e-06 26_[+2(2.59e-06)]_20_[+3(8.33e-06)]_\ 300_[+1(3.48e-06)]_92 8387 9.30e-09 108_[+3(5.78e-07)]_78_\ [+2(5.61e-07)]_17_[+2(7.77e-05)]_210_[+1(8.09e-07)]_4 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************