******************************************************************************** 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/9/9.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11224 1.0000 500 11656 1.0000 500 1626 1.0000 500 21105 1.0000 500 21958 1.0000 500 22024 1.0000 500 2227 1.0000 500 23519 1.0000 500 2378 1.0000 500 24343 1.0000 500 2441 1.0000 500 2497 1.0000 500 260799 1.0000 500 30979 1.0000 500 31951 1.0000 500 32209 1.0000 500 32285 1.0000 500 3308 1.0000 500 33926 1.0000 500 34158 1.0000 500 34510 1.0000 500 36557 1.0000 500 38322 1.0000 500 40148 1.0000 500 42368 1.0000 500 4915 1.0000 500 5545 1.0000 500 5830 1.0000 500 6138 1.0000 500 7806 1.0000 500 8122 1.0000 500 8587 1.0000 500 8877 1.0000 500 9133 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/9/9.seqs.fa -oc motifs/9 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.230 G 0.245 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.230 G 0.245 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 17 llr = 231 E-value = 2.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1:4131:3:::::412113: pos.-specific C 646571972a7:793962626 probability G 211::1:31::4:1:::62:2 matrix T 253125::5:363:4:11151 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 ** ** ** * Entropy 1.1 ** ***** * (19.6 bits) 0.8 * * ** ***** ** * 0.6 * *** ** ***** **** * 0.4 ******** ************ 0.2 ********************* 0.0 --------------------- Multilevel CTCCCTCCTCCTCCACCGCTC consensus CTA A GA TGT T AC AG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8877 458 4.12e-09 GATCTGCCAA CTCACTCCCCCTCCCCAGCAG GGTGAACCAC 11656 458 4.12e-09 GATCTGCCAA CTCACTCCCCCTCCCCAGCAG GGTGAACCAC 23519 10 1.53e-08 CCGGCGGGC GTCACACCACCGCCACCGATC CCCCCGTCTG 2497 366 7.48e-08 ATGCACTACC TCGCCTCCTCCTCCCCTCCTC TCTACCAAGG 34158 478 8.30e-08 ACCAACACGC CTCCCTCCTCTTCGTACCCTC GT 33926 443 8.30e-08 TTCGCATTTT GCTCCTCGTCCTCCTCCTCAC AGCTCTCATC 6138 259 9.20e-08 TCTACCTCCG CGTCCACCACCGCGACCGCTC CTAGTTCTTC 32285 456 1.24e-07 AGCTCCACAC GTCTTTCGTCTGCCTCCGCTC TACCAACTAT 260799 397 1.51e-07 GACGAGCGAG CTCCTGCGACCTTCACCCCTC CCTCCCTCCT 5830 456 2.21e-07 TCCCTCCTCG CCGTCTCCTCCGTCCACGCTC TCGCACACAT 34510 179 2.90e-07 CACACGAAAC CACACACGCCCTCCTCCGCCT CTTAAAAGAA 7806 443 3.17e-07 AATGATCGTG CCCAACCGTCCGTCTCCGGTC CTCGCCACAA 22024 168 7.33e-07 GATTGAGAGA CCCACTACGCCTCCTCCGATG ATGACTGTGT 32209 128 7.93e-07 AATGGTAGGA TCTCCACCTCTTCCACCGTCG GTGACAAAGG 40148 450 1.25e-06 ATACGATCAT CTTCAACCTCTGCCACACCAT TTCATTTCAA 30979 383 1.92e-06 GACCTTGATC TTCATCCCACCGTCCCAGGAC TGGTCCTCAT 4915 328 2.05e-06 GGTAGTGCTC CTTCCTCCACTTTCACTAGCC AGTTATCCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8877 4.1e-09 457_[+1]_22 11656 4.1e-09 457_[+1]_22 23519 1.5e-08 9_[+1]_470 2497 7.5e-08 365_[+1]_114 34158 8.3e-08 477_[+1]_2 33926 8.3e-08 442_[+1]_37 6138 9.2e-08 258_[+1]_221 32285 1.2e-07 455_[+1]_24 260799 1.5e-07 396_[+1]_83 5830 2.2e-07 455_[+1]_24 34510 2.9e-07 178_[+1]_301 7806 3.2e-07 442_[+1]_37 22024 7.3e-07 167_[+1]_312 32209 7.9e-07 127_[+1]_352 40148 1.3e-06 449_[+1]_30 30979 1.9e-06 382_[+1]_97 4915 2.1e-06 327_[+1]_152 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=17 8877 ( 458) CTCACTCCCCCTCCCCAGCAG 1 11656 ( 458) CTCACTCCCCCTCCCCAGCAG 1 23519 ( 10) GTCACACCACCGCCACCGATC 1 2497 ( 366) TCGCCTCCTCCTCCCCTCCTC 1 34158 ( 478) CTCCCTCCTCTTCGTACCCTC 1 33926 ( 443) GCTCCTCGTCCTCCTCCTCAC 1 6138 ( 259) CGTCCACCACCGCGACCGCTC 1 32285 ( 456) GTCTTTCGTCTGCCTCCGCTC 1 260799 ( 397) CTCCTGCGACCTTCACCCCTC 1 5830 ( 456) CCGTCTCCTCCGTCCACGCTC 1 34510 ( 179) CACACACGCCCTCCTCCGCCT 1 7806 ( 443) CCCAACCGTCCGTCTCCGGTC 1 22024 ( 168) CCCACTACGCCTCCTCCGATG 1 32209 ( 128) TCTCCACCTCTTCCACCGTCG 1 40148 ( 450) CTTCAACCTCTGCCACACCAT 1 30979 ( 383) TTCATCCCACCGTCCCAGGAC 1 4915 ( 328) CTTCCTCCACTTTCACTAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 11.2713 E= 2.3e-006 -1073 149 -47 -57 -216 62 -205 102 -1073 136 -105 17 64 103 -1073 -115 -117 162 -1073 -57 16 -96 -205 102 -216 203 -1073 -1073 -1073 162 27 -1073 16 -38 -205 85 -1073 212 -1073 -1073 -1073 162 -1073 17 -1073 -1073 75 117 -1073 162 -1073 17 -1073 194 -105 -1073 42 36 -1073 43 -117 194 -1073 -1073 -17 149 -1073 -115 -216 3 140 -215 -117 149 -47 -215 16 -38 -1073 102 -1073 149 -6 -115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 2.3e-006 0.000000 0.647059 0.176471 0.176471 0.058824 0.352941 0.058824 0.529412 0.000000 0.588235 0.117647 0.294118 0.411765 0.470588 0.000000 0.117647 0.117647 0.705882 0.000000 0.176471 0.294118 0.117647 0.058824 0.529412 0.058824 0.941176 0.000000 0.000000 0.000000 0.705882 0.294118 0.000000 0.294118 0.176471 0.058824 0.470588 0.000000 1.000000 0.000000 0.000000 0.000000 0.705882 0.000000 0.294118 0.000000 0.000000 0.411765 0.588235 0.000000 0.705882 0.000000 0.294118 0.000000 0.882353 0.117647 0.000000 0.352941 0.294118 0.000000 0.352941 0.117647 0.882353 0.000000 0.000000 0.235294 0.647059 0.000000 0.117647 0.058824 0.235294 0.647059 0.058824 0.117647 0.647059 0.176471 0.058824 0.294118 0.176471 0.000000 0.529412 0.000000 0.647059 0.235294 0.117647 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[TC][CT][CA]C[TA]C[CG][TA]C[CT][TG][CT]C[ATC]C[CA][GC]C[TA][CG] -------------------------------------------------------------------------------- Time 9.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 16 llr = 220 E-value = 2.7e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 24:::626:13:32191:391 pos.-specific C 11::1::31:1:11:111112 probability G 718883816939269:79616 matrix T 143221::4:3151::1:::1 bits 2.1 1.9 1.7 * * * * 1.5 * * ** * Relative 1.3 ** * * * ** * * Entropy 1.1 *** * * * ** * * (19.8 bits) 0.8 *** * ** * ** *** 0.6 * ******** * ****** 0.4 * ******** * ******** 0.2 ********************* 0.0 --------------------- Multilevel GAGGGAGAGGAGTGGAGGGAG consensus TT G CT G A A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8877 322 6.66e-11 ACCGTTAGCT GTGGGAGCTGTGTGGAGGAAG TATGTCAGTT 11656 322 6.66e-11 ACCGTTAGCT GTGGGAGCTGTGTGGAGGAAG TATGTCAGTT 21958 279 4.68e-09 TATGAAGAAG GAGGGAGAGGGGTGGAGCGAT GGATGTGTAA 42368 91 1.55e-08 TGTGATTCCC GTGGTGGACGGGAGGAGGGAG ATGGTGCACG 24343 197 4.56e-08 TGGGGACTTC AAGTTAGAGGTGAGGAGGGAC TCCTAAAAAG 5545 351 1.22e-07 AACGGGAACG ATGGGGACGGGGTAGAGGGAA GAGGAGGGCG 8122 107 1.46e-07 TGGAATATGC GAGTGAGCTGAGGCGACGGAG AGGATCAATT 30979 31 1.60e-07 GTCGTCTGCT GATGGGGCGGATTGGAGGAAC GTGGGGTAGC 31951 30 5.74e-07 ATTCGTCTCG GAGGTAGGTGTGACAAGGGAC TGTCATTAGA 11224 328 7.85e-07 GAGAGTCTTC AAGGGAGAGGAGTTGAAGGCT GTCGCTGTTA 40148 18 9.14e-07 TGGGAGTGGG GGTGCAGATGGGCAGAGGAAG CATCTTGTTG 2441 386 9.14e-07 ACCGACCGTC GAGGGAGAGGAGTGACTGGGG TGTTTGTCAT 1626 20 1.32e-06 AGGCCTCCGT GTGTGTGATACGAGGAGGAAG CAGAGGCAGA 4915 77 1.42e-06 TCTTATCTCT CTTGGGAAGGAGGAGAGGGAA CGGGAGATTG 260799 187 1.53e-06 TCTGTTGCTT TGTGGTAAGGGGTGGATGGAG GATATGGCTC 22024 220 1.53e-06 ACCATGTCGG GCGGGAGGGGTGGTGAAGCAG TGAGAGCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8877 6.7e-11 321_[+2]_158 11656 6.7e-11 321_[+2]_158 21958 4.7e-09 278_[+2]_201 42368 1.5e-08 90_[+2]_389 24343 4.6e-08 196_[+2]_283 5545 1.2e-07 350_[+2]_129 8122 1.5e-07 106_[+2]_373 30979 1.6e-07 30_[+2]_449 31951 5.7e-07 29_[+2]_450 11224 7.9e-07 327_[+2]_152 40148 9.1e-07 17_[+2]_462 2441 9.1e-07 385_[+2]_94 1626 1.3e-06 19_[+2]_460 4915 1.4e-06 76_[+2]_403 260799 1.5e-06 186_[+2]_293 22024 1.5e-06 219_[+2]_260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=16 8877 ( 322) GTGGGAGCTGTGTGGAGGAAG 1 11656 ( 322) GTGGGAGCTGTGTGGAGGAAG 1 21958 ( 279) GAGGGAGAGGGGTGGAGCGAT 1 42368 ( 91) GTGGTGGACGGGAGGAGGGAG 1 24343 ( 197) AAGTTAGAGGTGAGGAGGGAC 1 5545 ( 351) ATGGGGACGGGGTAGAGGGAA 1 8122 ( 107) GAGTGAGCTGAGGCGACGGAG 1 30979 ( 31) GATGGGGCGGATTGGAGGAAC 1 31951 ( 30) GAGGTAGGTGTGACAAGGGAC 1 11224 ( 328) AAGGGAGAGGAGTTGAAGGCT 1 40148 ( 18) GGTGCAGATGGGCAGAGGAAG 1 2441 ( 386) GAGGGAGAGGAGTGACTGGGG 1 1626 ( 20) GTGTGTGATACGAGGAGGAAG 1 4915 ( 77) CTTGGGAAGGAGGAGAGGGAA 1 260799 ( 187) TGTGGTAAGGGGTGGATGGAG 1 22024 ( 220) GCGGGAGGGGTGGTGAAGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 10.7305 E= 2.7e-006 -49 -188 149 -206 73 -188 -97 52 -1064 -1064 162 -7 -1064 -1064 173 -48 -1064 -188 162 -48 124 -1064 3 -106 -49 -1064 173 -1064 109 44 -97 -1064 -1064 -188 120 52 -208 -1064 194 -1064 24 -188 35 26 -1064 -1064 194 -206 -8 -188 -38 93 -49 -88 120 -106 -108 -1064 184 -1064 183 -188 -1064 -1064 -108 -188 149 -106 -1064 -188 194 -1064 24 -188 135 -1064 173 -188 -197 -1064 -108 -29 120 -106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 2.7e-006 0.187500 0.062500 0.687500 0.062500 0.437500 0.062500 0.125000 0.375000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.812500 0.187500 0.000000 0.062500 0.750000 0.187500 0.625000 0.000000 0.250000 0.125000 0.187500 0.000000 0.812500 0.000000 0.562500 0.312500 0.125000 0.000000 0.000000 0.062500 0.562500 0.375000 0.062500 0.000000 0.937500 0.000000 0.312500 0.062500 0.312500 0.312500 0.000000 0.000000 0.937500 0.062500 0.250000 0.062500 0.187500 0.500000 0.187500 0.125000 0.562500 0.125000 0.125000 0.000000 0.875000 0.000000 0.937500 0.062500 0.000000 0.000000 0.125000 0.062500 0.687500 0.125000 0.000000 0.062500 0.937500 0.000000 0.312500 0.062500 0.625000 0.000000 0.875000 0.062500 0.062500 0.000000 0.125000 0.187500 0.562500 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AT][GT]GG[AG]G[AC][GT]G[AGT]G[TA]GGAGG[GA]AG -------------------------------------------------------------------------------- Time 19.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 33 llr = 312 E-value = 3.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 736333::5:22:2::11: pos.-specific C :3221::22:1:::1::1: probability G 33:252:8142:6258135 matrix T 121216a:26584642855 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * * ** Entropy 1.1 ** * * ** * (13.6 bits) 0.8 * ** * * ** * 0.6 * * *** * ** ** * 0.4 * * *** * ****** * 0.2 * * *************** 0.0 ------------------- Multilevel AAAAGTTGATTTGTGGTTT consensus GCCGAA C GG T T GG sequence G T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 1626 173 2.27e-08 GAGGGGTTTG ACATATTGATTTGTGGTCT GGTGTGAAGC 36557 242 7.39e-08 CGATGGTTGA AACGGTTGCGTTGTGGTTT GTTGTTGTAG 8877 35 1.50e-07 AGACTAATGC AAAAAGTGATGTGTGGTGT CAAACTTGCG 11656 35 1.50e-07 AGACTAATGC AAAAAGTGATGTGTGGTGT CAAACTTGCG 2227 279 5.31e-07 CACGTCCAAC ACCTGTTCATTTGATGTTT GTTAGTAATT 9133 207 6.15e-07 CAGAAATAGT TAAAATTGATTTTTGGTTG TTTGATCTGT 34158 295 7.09e-07 ATCAGACAAA GTAGATTGAGATGTGGTGT GCTGAAAGTG 32285 330 9.37e-07 GGGTGAAATG AGAAGATGTGATGTGGTGG ACGAGAGATG 2441 316 1.07e-06 AGGATTACCC AGAGGATGAGTAGTGGTCT GTGCATGTTG 8587 332 2.05e-06 TGGCCATGAG ATAAGTTGTTGTTTCGTTG TGACGAGATG 31951 390 3.33e-06 AAATGGAAAG AAATGTTGTTATTTTGTAT TAAATTCGTA 38322 78 5.25e-06 GATGTCGTCG AGATGATGATGTTGTGTAT AAAGACGGTA 42368 292 6.53e-06 TTGACGGCAA ATCTCATGGTTTGTGGTTG CAAGACGAGA 32209 366 6.53e-06 CGTCGTGCGA ACATGGTGCGTTTGTGTGT TTGGATATTG 2378 384 1.21e-05 GTCTTCACGT GTCGGTTGGTGTGTTGTCG CCGTGACCTC 6138 114 1.34e-05 GATGCTGCTG ATCAGATGATGATGTGTTT GGCTGCTTTG 30979 176 1.47e-05 GCAAATGAGA GCTTCATGATTTGAGGTTG TTGATAATGT 21105 47 1.95e-05 AACAGCATTA ACACATTGATTAGTTTGTT GAATGGGCAA 4915 296 2.14e-05 TGGATACAAA AGCAGATGATTTGACGGTG AAAGGTAGTG 260799 256 2.14e-05 AGAGGAGGGG AGAGGGTGTGCTGATGTTG TCGGATTTTG 33926 248 2.80e-05 GTTGTTGTAA AGACTTTGGGTAGATGTTG AAGACGCTGG 8122 213 3.06e-05 TATGAGACTT GAACGTTCCTGTTTCGTGG TAGGGAATTC 7806 286 4.28e-05 TTTAACGTTA GAATGATGATGTCATGTGT ACTAGATCCT 5545 109 4.65e-05 ATAGGATGAT ATTGATTGAGATTTTGATT GTGGGGCGGC 23519 251 7.99e-05 AAGAGTGAGT ACTCATTCCTATGTGGATT GGTTTGGAAT 24343 165 9.25e-05 GAAAGGACAG GCAGCTTCAGTTTCGGTGG GCATGGGGAC 11224 208 9.25e-05 TTGCTAGGGG GGAGGTTTGGTTGTTGTAG AGTTAGTATT 34510 480 9.94e-05 CTGTTTGGAG TGACATTCATTATTGTTTT GA 3308 19 1.14e-04 ACAATAGCTC AATAGTTGCTTTGGGATCT TCGTTAACAA 21958 414 1.40e-04 ACTGTAATAG AAAAAGTCATCTATTGTGG GGACATTCCA 5830 333 1.60e-04 TTCGGAAGAC GCAATATGCGTTGTATTTG TCTAGTTCAT 40148 140 2.96e-04 CGTACAACAT GCCCTTTGATATTGGTGTT GCTACGATTC 22024 458 2.96e-04 TAACACATGG AGCATTTCTGAATTGTTTG TCTTACGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1626 2.3e-08 172_[+3]_309 36557 7.4e-08 241_[+3]_240 8877 1.5e-07 34_[+3]_447 11656 1.5e-07 34_[+3]_447 2227 5.3e-07 278_[+3]_203 9133 6.1e-07 206_[+3]_275 34158 7.1e-07 294_[+3]_187 32285 9.4e-07 329_[+3]_152 2441 1.1e-06 315_[+3]_166 8587 2.1e-06 331_[+3]_150 31951 3.3e-06 389_[+3]_92 38322 5.3e-06 77_[+3]_404 42368 6.5e-06 291_[+3]_190 32209 6.5e-06 365_[+3]_116 2378 1.2e-05 383_[+3]_98 6138 1.3e-05 113_[+3]_368 30979 1.5e-05 175_[+3]_306 21105 2e-05 46_[+3]_435 4915 2.1e-05 295_[+3]_186 260799 2.1e-05 255_[+3]_226 33926 2.8e-05 247_[+3]_234 8122 3.1e-05 212_[+3]_269 7806 4.3e-05 285_[+3]_196 5545 4.6e-05 108_[+3]_373 23519 8e-05 250_[+3]_231 24343 9.3e-05 164_[+3]_317 11224 9.3e-05 207_[+3]_274 34510 9.9e-05 479_[+3]_2 3308 0.00011 18_[+3]_463 21958 0.00014 413_[+3]_68 5830 0.00016 332_[+3]_149 40148 0.0003 139_[+3]_342 22024 0.0003 457_[+3]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=33 1626 ( 173) ACATATTGATTTGTGGTCT 1 36557 ( 242) AACGGTTGCGTTGTGGTTT 1 8877 ( 35) AAAAAGTGATGTGTGGTGT 1 11656 ( 35) AAAAAGTGATGTGTGGTGT 1 2227 ( 279) ACCTGTTCATTTGATGTTT 1 9133 ( 207) TAAAATTGATTTTTGGTTG 1 34158 ( 295) GTAGATTGAGATGTGGTGT 1 32285 ( 330) AGAAGATGTGATGTGGTGG 1 2441 ( 316) AGAGGATGAGTAGTGGTCT 1 8587 ( 332) ATAAGTTGTTGTTTCGTTG 1 31951 ( 390) AAATGTTGTTATTTTGTAT 1 38322 ( 78) AGATGATGATGTTGTGTAT 1 42368 ( 292) ATCTCATGGTTTGTGGTTG 1 32209 ( 366) ACATGGTGCGTTTGTGTGT 1 2378 ( 384) GTCGGTTGGTGTGTTGTCG 1 6138 ( 114) ATCAGATGATGATGTGTTT 1 30979 ( 176) GCTTCATGATTTGAGGTTG 1 21105 ( 47) ACACATTGATTAGTTTGTT 1 4915 ( 296) AGCAGATGATTTGACGGTG 1 260799 ( 256) AGAGGGTGTGCTGATGTTG 1 33926 ( 248) AGACTTTGGGTAGATGTTG 1 8122 ( 213) GAACGTTCCTGTTTCGTGG 1 7806 ( 286) GAATGATGATGTCATGTGT 1 5545 ( 109) ATTGATTGAGATTTTGATT 1 23519 ( 251) ACTCATTCCTATGTGGATT 1 24343 ( 165) GCAGCTTCAGTTTCGGTGG 1 11224 ( 208) GGAGGTTTGGTTGTTGTAG 1 34510 ( 480) TGACATTCATTATTGTTTT 1 3308 ( 19) AATAGTTGCTTTGGGATCT 1 21958 ( 414) AAAAAGTCATCTATTGTGG 1 5830 ( 333) GCAATATGCGTTGTATTTG 1 40148 ( 140) GCCCTTTGATATTGGTGTT 1 22024 ( 458) AGCATTTCTGAATTGTTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 16388 bayes= 8.98853 E= 3.5e-005 134 -1169 16 -211 5 25 16 -52 127 8 -1169 -111 34 -34 -1 -11 20 -134 99 -111 5 -1169 -69 114 -1169 -1169 -1169 193 -1169 -11 163 -311 105 -34 -101 -79 -1169 -1169 57 128 -32 -192 -1 89 -54 -1169 -1169 164 -312 -292 124 47 -54 -292 -69 128 -312 -134 99 59 -312 -1169 174 -79 -212 -1169 -143 170 -154 -92 16 98 -1169 -1169 89 106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 33 E= 3.5e-005 0.666667 0.000000 0.272727 0.060606 0.272727 0.272727 0.272727 0.181818 0.636364 0.242424 0.000000 0.121212 0.333333 0.181818 0.242424 0.242424 0.303030 0.090909 0.484848 0.121212 0.272727 0.000000 0.151515 0.575758 0.000000 0.000000 0.000000 1.000000 0.000000 0.212121 0.757576 0.030303 0.545455 0.181818 0.121212 0.151515 0.000000 0.000000 0.363636 0.636364 0.212121 0.060606 0.242424 0.484848 0.181818 0.000000 0.000000 0.818182 0.030303 0.030303 0.575758 0.363636 0.181818 0.030303 0.151515 0.636364 0.030303 0.090909 0.484848 0.393939 0.030303 0.000000 0.818182 0.151515 0.060606 0.000000 0.090909 0.848485 0.090909 0.121212 0.272727 0.515152 0.000000 0.000000 0.454545 0.545455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][ACG][AC][AGT][GA][TA]T[GC]A[TG][TGA]T[GT]T[GT]GT[TG][TG] -------------------------------------------------------------------------------- Time 28.46 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11224 4.93e-04 107_[+2(6.68e-05)]_79_\ [+3(9.25e-05)]_101_[+2(7.85e-07)]_152 11656 3.83e-15 34_[+3(1.50e-07)]_268_\ [+2(6.66e-11)]_115_[+1(4.12e-09)]_22 1626 2.14e-07 19_[+2(1.32e-06)]_132_\ [+3(2.27e-08)]_309 21105 4.50e-02 46_[+3(1.95e-05)]_435 21958 7.66e-07 57_[+1(5.26e-05)]_116_\ [+2(4.41e-06)]_63_[+2(4.68e-09)]_201 22024 5.68e-06 167_[+1(7.33e-07)]_31_\ [+2(1.53e-06)]_260 2227 4.87e-03 278_[+3(5.31e-07)]_203 23519 3.57e-05 9_[+1(1.53e-08)]_220_[+3(7.99e-05)]_\ 231 2378 2.77e-02 383_[+3(1.21e-05)]_98 24343 2.98e-05 164_[+3(9.25e-05)]_13_\ [+2(4.56e-08)]_283 2441 4.11e-06 315_[+3(1.07e-06)]_4_[+2(6.17e-05)]_\ 26_[+2(9.14e-07)]_94 2497 1.84e-03 365_[+1(7.48e-08)]_114 260799 1.36e-07 186_[+2(1.53e-06)]_48_\ [+3(2.14e-05)]_122_[+1(1.51e-07)]_83 30979 1.26e-07 30_[+2(1.60e-07)]_124_\ [+3(1.47e-05)]_188_[+1(1.92e-06)]_97 31951 2.39e-05 29_[+2(5.74e-07)]_339_\ [+3(3.33e-06)]_92 32209 3.93e-05 127_[+1(7.93e-07)]_217_\ [+3(6.53e-06)]_116 32285 5.42e-07 329_[+3(9.37e-07)]_107_\ [+1(1.24e-07)]_24 3308 2.40e-01 500 33926 2.35e-05 194_[+1(1.61e-05)]_32_\ [+3(2.80e-05)]_176_[+1(8.30e-08)]_37 34158 1.28e-06 294_[+3(7.09e-07)]_164_\ [+1(8.30e-08)]_2 34510 1.68e-04 178_[+1(2.90e-07)]_280_\ [+3(9.94e-05)]_2 36557 1.46e-04 51_[+2(9.77e-05)]_169_\ [+3(7.39e-08)]_240 38322 8.24e-03 77_[+3(5.25e-06)]_404 40148 5.80e-06 17_[+2(9.14e-07)]_411_\ [+1(1.25e-06)]_30 42368 4.04e-06 90_[+2(1.55e-08)]_180_\ [+3(6.53e-06)]_190 4915 1.35e-06 76_[+2(1.42e-06)]_198_\ [+3(2.14e-05)]_13_[+1(2.05e-06)]_152 5545 9.57e-05 108_[+3(4.65e-05)]_223_\ [+2(1.22e-07)]_129 5830 5.52e-04 455_[+1(2.21e-07)]_24 6138 1.54e-05 113_[+3(1.34e-05)]_126_\ [+1(9.20e-08)]_221 7806 3.43e-05 285_[+3(4.28e-05)]_138_\ [+1(3.17e-07)]_37 8122 4.76e-05 106_[+2(1.46e-07)]_85_\ [+3(3.06e-05)]_269 8587 7.97e-03 331_[+3(2.05e-06)]_150 8877 3.83e-15 34_[+3(1.50e-07)]_268_\ [+2(6.66e-11)]_115_[+1(4.12e-09)]_22 9133 3.25e-03 206_[+3(6.15e-07)]_275 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************