******************************************************************************** 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/397/397.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1118 1.0000 500 11522 1.0000 500 2017 1.0000 500 20674 1.0000 500 2118 1.0000 500 2182 1.0000 500 21843 1.0000 500 22124 1.0000 500 22524 1.0000 500 22549 1.0000 500 22637 1.0000 500 22935 1.0000 500 23346 1.0000 500 23366 1.0000 500 23598 1.0000 500 24250 1.0000 500 24328 1.0000 500 24682 1.0000 500 25288 1.0000 500 25622 1.0000 500 25702 1.0000 500 261539 1.0000 500 261639 1.0000 500 267971 1.0000 500 268232 1.0000 500 269705 1.0000 500 2742 1.0000 500 3266 1.0000 500 40496 1.0000 500 40728 1.0000 500 4909 1.0000 500 5273 1.0000 500 6558 1.0000 500 6603 1.0000 500 7819 1.0000 500 8460 1.0000 500 9195 1.0000 500 9677 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/397/397.seqs.fa -oc motifs/397 -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= 38 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= 19000 N= 38 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.225 G 0.240 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.225 G 0.240 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 36 llr = 302 E-value = 3.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4256a:96286 pos.-specific C 71543:a::8:2 probability G 131::::::::1 matrix T 23211::14:21 bits 2.2 * 1.9 * 1.7 ** 1.5 *** Relative 1.3 *** ** Entropy 1.1 * *** ** (12.1 bits) 0.9 * ****** 0.6 * ******** 0.4 * ********* 0.2 ************ 0.0 ------------ Multilevel CACAAACAACAA consensus G CC T C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9195 475 6.62e-08 CATCAGACGC CACAAACAACAA ACAAACCATA 2017 21 6.89e-07 TTCTACTATT CGCACACAACAA TAGCAAATCG 268232 33 2.13e-06 GAAGCAGCAG CAACAACAACAA CAACAATACT 23598 329 3.09e-06 ACGGAGAGGA CGACAACAACAA CGGCGATGGT 23346 394 3.92e-06 ATGAATGACA CATAAACATCAA CTGCTTCTAC 23366 96 4.76e-06 TGGTATTCAA CTCTAACAACAA GACATGAAAG 8460 305 5.54e-06 AGATCCACTA TGCAAACAACAA GTTACCTGAG 269705 310 7.85e-06 CAACCAGTGT TTCCAACAACAA GAGCTCTGCA 25288 441 9.18e-06 CTCAACAAAA CACAAACATAAA TATTCATTGC 22637 423 9.18e-06 AGCGAGAGCC CTCACACAACAG CGTCGAACTC 24250 468 1.18e-05 ACTTCTCCGG CACACACATCAG CAATCCATTG 22524 477 1.18e-05 ACAAGGTTCA CGTACACATCAA CCGAACACTC 2182 337 1.18e-05 ATAAGCACCA CCCCCACAACAA CCCCGCACTC 4909 436 1.33e-05 AGATTAAATG GACAAACATCAA ACGAGGGGAA 6558 479 1.80e-05 TACACGCATC CATCAACAACTA ACGCTGCACA 7819 272 2.51e-05 GACCCCAAGG CAGCAACATCAC AAGACGAACT 267971 168 2.51e-05 CCTGCGTGTT TGTAAACAACAA TAGAGTTAAT 2742 404 2.85e-05 ACCGTAAGGT CTACAACAACTA AAATATCAAG 1118 319 2.85e-05 CCTAGTTACA TACCAACATCAC GACATCCTCT 261539 28 3.22e-05 TCATTCTCGT CTCCAACATCTC GTATGCGTCA 11522 164 4.57e-05 CAGCTCGTAT CGCTCACATCAC AATGACGGAC 40496 442 5.13e-05 CTTAATCGTC CTACCACAACTA ACTGTAGTCT 22935 378 5.13e-05 CTTGGTCTCG CTCACACATCTC ACATCCGAAC 5273 309 1.03e-04 CTTCATATCT CCCCAACAAAAC GTGAGTTGAA 40728 408 1.11e-04 AACGTTTATT CACTAACAAAAG TCAAACAAAA 24682 485 1.21e-04 TGCTAGCTCA GAAACACAACAC CAAC 21843 136 1.42e-04 GTTTCCATTG CGGAAACAAAAG TTGCTTCTTC 24328 300 2.27e-04 CCATCTTCAA GACAAACTTCAA CATGGCCTCC 2118 451 2.42e-04 CTAGGTGTGG CTGAAACATATA TCTTGTGATC 22549 484 3.09e-04 ATCGATCTTC TGTATACAACAC CGAGT 3266 481 3.28e-04 CTAGTTCGTT TGCCCGCAACAA TATCCAAC 20674 216 3.48e-04 CTATCACATC GATCAACAACTG TTCTTATTCA 22124 297 3.69e-04 AATTATTGTC CTTCCACAAAAT CGGCCAATCG 9677 266 4.19e-04 GCAGGATCAA CTCTAACACAAA CGACGATAAA 6603 460 4.19e-04 ATATAATCGC CGAATACTACAA CCAGAACGGC 25702 456 4.45e-04 CTTGACCCCT CAGATACATCAT AGAAGAATCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9195 6.6e-08 474_[+1]_14 2017 6.9e-07 20_[+1]_468 268232 2.1e-06 32_[+1]_456 23598 3.1e-06 328_[+1]_160 23346 3.9e-06 393_[+1]_95 23366 4.8e-06 95_[+1]_393 8460 5.5e-06 304_[+1]_184 269705 7.8e-06 309_[+1]_179 25288 9.2e-06 440_[+1]_48 22637 9.2e-06 422_[+1]_66 24250 1.2e-05 467_[+1]_21 22524 1.2e-05 476_[+1]_12 2182 1.2e-05 336_[+1]_152 4909 1.3e-05 435_[+1]_53 6558 1.8e-05 478_[+1]_10 7819 2.5e-05 271_[+1]_217 267971 2.5e-05 167_[+1]_321 2742 2.9e-05 403_[+1]_85 1118 2.9e-05 318_[+1]_170 261539 3.2e-05 27_[+1]_461 11522 4.6e-05 163_[+1]_325 40496 5.1e-05 441_[+1]_47 22935 5.1e-05 377_[+1]_111 5273 0.0001 308_[+1]_180 40728 0.00011 407_[+1]_81 24682 0.00012 484_[+1]_4 21843 0.00014 135_[+1]_353 24328 0.00023 299_[+1]_189 2118 0.00024 450_[+1]_38 22549 0.00031 483_[+1]_5 3266 0.00033 480_[+1]_8 20674 0.00035 215_[+1]_273 22124 0.00037 296_[+1]_192 9677 0.00042 265_[+1]_223 6603 0.00042 459_[+1]_29 25702 0.00044 455_[+1]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=36 9195 ( 475) CACAAACAACAA 1 2017 ( 21) CGCACACAACAA 1 268232 ( 33) CAACAACAACAA 1 23598 ( 329) CGACAACAACAA 1 23346 ( 394) CATAAACATCAA 1 23366 ( 96) CTCTAACAACAA 1 8460 ( 305) TGCAAACAACAA 1 269705 ( 310) TTCCAACAACAA 1 25288 ( 441) CACAAACATAAA 1 22637 ( 423) CTCACACAACAG 1 24250 ( 468) CACACACATCAG 1 22524 ( 477) CGTACACATCAA 1 2182 ( 337) CCCCCACAACAA 1 4909 ( 436) GACAAACATCAA 1 6558 ( 479) CATCAACAACTA 1 7819 ( 272) CAGCAACATCAC 1 267971 ( 168) TGTAAACAACAA 1 2742 ( 404) CTACAACAACTA 1 1118 ( 319) TACCAACATCAC 1 261539 ( 28) CTCCAACATCTC 1 11522 ( 164) CGCTCACATCAC 1 40496 ( 442) CTACCACAACTA 1 22935 ( 378) CTCACACATCTC 1 5273 ( 309) CCCCAACAAAAC 1 40728 ( 408) CACTAACAAAAG 1 24682 ( 485) GAAACACAACAC 1 21843 ( 136) CGGAAACAAAAG 1 24328 ( 300) GACAAACTTCAA 1 2118 ( 451) CTGAAACATATA 1 22549 ( 484) TGTATACAACAC 1 3266 ( 481) TGCCCGCAACAA 1 20674 ( 216) GATCAACAACTG 1 22124 ( 297) CTTCCACAAAAT 1 9677 ( 266) CTCTAACACAAA 1 6603 ( 460) CGAATACTACAA 1 25702 ( 456) CAGATACATCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18582 bayes= 9.14345 E= 3.0e-005 -1181 168 -111 -68 54 -202 21 5 -68 123 -111 -46 90 79 -1181 -127 119 44 -1181 -168 186 -1181 -311 -1181 -1181 215 -1181 -1181 182 -1181 -1181 -227 119 -301 -1181 43 -46 184 -1181 -1181 159 -1181 -1181 -46 113 -2 -79 -227 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 36 E= 3.0e-005 0.000000 0.722222 0.111111 0.166667 0.388889 0.055556 0.277778 0.277778 0.166667 0.527778 0.111111 0.194444 0.500000 0.388889 0.000000 0.111111 0.611111 0.305556 0.000000 0.083333 0.972222 0.000000 0.027778 0.000000 0.000000 1.000000 0.000000 0.000000 0.944444 0.000000 0.000000 0.055556 0.611111 0.027778 0.000000 0.361111 0.194444 0.805556 0.000000 0.000000 0.805556 0.000000 0.000000 0.194444 0.583333 0.222222 0.138889 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AGT]C[AC][AC]ACA[AT]CA[AC] -------------------------------------------------------------------------------- Time 12.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 38 llr = 325 E-value = 1.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 632133:1::611132 pos.-specific C :22::2::2::4::21 probability G 42186165:a2:9616 matrix T 136::4458:25:341 bits 2.2 1.9 * 1.7 * * 1.5 * * Relative 1.3 * ** * Entropy 1.1 * * ** * (12.3 bits) 0.9 ** * ** ** 0.6 * ** **** *** 0.4 * ** ******** * 0.2 * ************** 0.0 ---------------- Multilevel ATTGGTGGTGATGGTG consensus GA AATT GC TAA sequence C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 6603 64 6.86e-08 GCTGCAGGTT GTTGGATGTGATGGTG GGGGATGAAC 261639 244 1.17e-07 CGTTGTGGAG AGTGATGTTGACGGTG ATGTCTGAGA 22549 26 1.13e-06 TTGATTTGCA AATAGAGGTGATGGTG AGATGATGTT 268232 61 2.20e-06 TACTACTACG ACTGGTGGTGATGATG CTGAGTTTGA 261539 405 2.20e-06 AGTTCAATTC AATGGCTTTGGCGGAG GCGGCATGGA 269705 206 3.00e-06 AGTTACAATA ACTGATGGTGGTGGTA AGACGAAGTC 22637 183 3.48e-06 TCATTGCCAT GTTGGTTGTGATGGAT GATGTGATGA 7819 348 4.03e-06 GGCTGAGAGA AAAGGTGTTGGCGTTG ACAGCGTGGC 22935 171 6.96e-06 AGCACGATAT GATGGATGTGACGATG AGAACCGAAC 9677 36 7.92e-06 CGTTGACAGT AATGATTTTGTCGGTA GTAGATACAA 25288 267 9.00e-06 TGATCGAGCC GTCGACGTTGACGTTG CGTCAACGCG 6558 118 1.02e-05 CGAGCAAGAC ACTGAAGGCGATGTAG TGGGGGAGGT 25702 128 1.02e-05 TGACCATTGT GTTGGTGATGATGGTA TGCATCCATT 20674 105 1.02e-05 ATCTCATGGC GTTGGTTTTGATGGGA GTACTGCTGA 23366 297 1.15e-05 TGTTAGTGTA GAAGGATGTGATGGAA TGTAGAATGT 2742 101 1.63e-05 TCCTCCCTCG TCTGGCTGTGTTGGTG ATAGCTTTCA 40728 309 2.52e-05 GAAGTTGAGT GTTGAAGTTGAAGTAG CATTCCAACA 25622 230 2.52e-05 TCGGTGAGAA GACGGTGTCGACGTCG TCGGCCGCCA 5273 52 3.43e-05 AATGACGACG ACCGACGATGACGGTG CACGACGTCT 2118 416 3.78e-05 GCATGAGACT AGGAGAGGTGATGTAG AAGAGGGATC 24682 353 4.58e-05 GGATCGGTGT GTAGGAGTTGGAGGAG GTCGGTGAGG 21843 317 4.58e-05 TTTGCGAATG TGCGGTGTTGATGGTT TCCCTTCCAC 11522 240 4.58e-05 GAGCCGTGTG GATGGTTGCGGTGGCA GCGAGGAAGG 1118 90 4.58e-05 AGGCCAGAGC ATCGGCGGTGTTGTGG TTTGACGGGA 23598 3 5.03e-05 TT AGGGGTGTTGATGTGA GTTTTGATGA 2017 346 5.03e-05 CAAGTCAGGT AGAGAATGTGGCGTCG ATTGGAACAG 9195 16 6.04e-05 GTTGTGGCAC AAGGGCGTCGTCGGCG GCTGTTGACA 2182 53 6.60e-05 CATCAGAGAG ATTGGAGGTGGCAGAT GGTACCAATG 22524 149 9.30e-05 GAGGGGAGAA GGGGAAGTTGGCGGAT CGTGTCCACT 22124 219 1.19e-04 TGTCCATCAC ACTGCAGTTGTCGGCA ACCGTCGGAG 3266 69 1.50e-04 AAGCGGCATC GCTAGGTTTGACGTCA AACGCCGACT 267971 195 1.61e-04 TTAATAAATA ACAGAGTGTGTCGGTC ACTTCTGCCC 8460 19 2.16e-04 GAAGTGCAGA AGCAGGGTTGAAGGAG CTGAGCGAGG 24328 151 2.65e-04 GCGGCAGCGA GTTGGTTTTCATGTTC TCGTTTCGGT 24250 175 3.67e-04 CTTGTGAACG AAGGAATTCGTTGGAT CAATTTTTTG 40496 68 4.15e-04 GTTTCTTCTC TCTGGCGGCGACATCG GAGGTTAATA 23346 156 8.99e-04 AGGAGGTATC ATTCTTGGTGACAGTG ATCAGGCTGA 4909 229 1.04e-03 AAGACGCTGT AGAAAGTGTGTTGTTC AACCAGTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6603 6.9e-08 63_[+2]_421 261639 1.2e-07 243_[+2]_241 22549 1.1e-06 25_[+2]_459 268232 2.2e-06 60_[+2]_424 261539 2.2e-06 404_[+2]_80 269705 3e-06 205_[+2]_279 22637 3.5e-06 182_[+2]_302 7819 4e-06 347_[+2]_137 22935 7e-06 170_[+2]_314 9677 7.9e-06 35_[+2]_449 25288 9e-06 266_[+2]_218 6558 1e-05 117_[+2]_367 25702 1e-05 127_[+2]_357 20674 1e-05 104_[+2]_380 23366 1.2e-05 296_[+2]_188 2742 1.6e-05 100_[+2]_384 40728 2.5e-05 308_[+2]_176 25622 2.5e-05 229_[+2]_255 5273 3.4e-05 51_[+2]_433 2118 3.8e-05 415_[+2]_69 24682 4.6e-05 352_[+2]_132 21843 4.6e-05 316_[+2]_168 11522 4.6e-05 239_[+2]_245 1118 4.6e-05 89_[+2]_395 23598 5e-05 2_[+2]_482 2017 5e-05 345_[+2]_139 9195 6e-05 15_[+2]_469 2182 6.6e-05 52_[+2]_432 22524 9.3e-05 148_[+2]_336 22124 0.00012 218_[+2]_266 3266 0.00015 68_[+2]_416 267971 0.00016 194_[+2]_290 8460 0.00022 18_[+2]_466 24328 0.00027 150_[+2]_334 24250 0.00037 174_[+2]_310 40496 0.00042 67_[+2]_417 23346 0.0009 155_[+2]_329 4909 0.001 228_[+2]_256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=38 6603 ( 64) GTTGGATGTGATGGTG 1 261639 ( 244) AGTGATGTTGACGGTG 1 22549 ( 26) AATAGAGGTGATGGTG 1 268232 ( 61) ACTGGTGGTGATGATG 1 261539 ( 405) AATGGCTTTGGCGGAG 1 269705 ( 206) ACTGATGGTGGTGGTA 1 22637 ( 183) GTTGGTTGTGATGGAT 1 7819 ( 348) AAAGGTGTTGGCGTTG 1 22935 ( 171) GATGGATGTGACGATG 1 9677 ( 36) AATGATTTTGTCGGTA 1 25288 ( 267) GTCGACGTTGACGTTG 1 6558 ( 118) ACTGAAGGCGATGTAG 1 25702 ( 128) GTTGGTGATGATGGTA 1 20674 ( 105) GTTGGTTTTGATGGGA 1 23366 ( 297) GAAGGATGTGATGGAA 1 2742 ( 101) TCTGGCTGTGTTGGTG 1 40728 ( 309) GTTGAAGTTGAAGTAG 1 25622 ( 230) GACGGTGTCGACGTCG 1 5273 ( 52) ACCGACGATGACGGTG 1 2118 ( 416) AGGAGAGGTGATGTAG 1 24682 ( 353) GTAGGAGTTGGAGGAG 1 21843 ( 317) TGCGGTGTTGATGGTT 1 11522 ( 240) GATGGTTGCGGTGGCA 1 1118 ( 90) ATCGGCGGTGTTGTGG 1 23598 ( 3) AGGGGTGTTGATGTGA 1 2017 ( 346) AGAGAATGTGGCGTCG 1 9195 ( 16) AAGGGCGTCGTCGGCG 1 2182 ( 53) ATTGGAGGTGGCAGAT 1 22524 ( 149) GGGGAAGTTGGCGGAT 1 22124 ( 219) ACTGCAGTTGTCGGCA 1 3266 ( 69) GCTAGGTTTGACGTCA 1 267971 ( 195) ACAGAGTGTGTCGGTC 1 8460 ( 19) AGCAGGGTTGAAGGAG 1 24328 ( 151) GTTGGTTTTCATGTTC 1 24250 ( 175) AAGGAATTCGTTGGAT 1 40496 ( 68) TCTGGCGGCGACATCG 1 23346 ( 156) ATTCTTGGTGACAGTG 1 4909 ( 229) AGAAAGTGTGTTGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 18430 bayes= 8.91886 E= 1.6e-004 105 -1189 62 -176 -2 7 -19 11 -76 -51 -87 104 -102 -309 181 -1189 24 -309 140 -334 36 -29 -119 46 -1189 -1189 134 56 -234 -1189 98 82 -1189 -51 -1189 165 -1189 -309 202 -1189 111 -1189 -19 -35 -176 99 -1189 82 -176 -1189 194 -1189 -234 -1189 134 35 11 -29 -160 74 -18 -151 120 -103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 38 E= 1.6e-004 0.552632 0.000000 0.368421 0.078947 0.263158 0.236842 0.210526 0.289474 0.157895 0.157895 0.131579 0.552632 0.131579 0.026316 0.842105 0.000000 0.315789 0.026316 0.631579 0.026316 0.342105 0.184211 0.105263 0.368421 0.000000 0.000000 0.605263 0.394737 0.052632 0.000000 0.473684 0.473684 0.000000 0.157895 0.000000 0.842105 0.000000 0.026316 0.973684 0.000000 0.578947 0.000000 0.210526 0.210526 0.078947 0.447368 0.000000 0.473684 0.078947 0.000000 0.921053 0.000000 0.052632 0.000000 0.605263 0.342105 0.289474 0.184211 0.078947 0.447368 0.236842 0.078947 0.552632 0.131579 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][TACG]TG[GA][TA][GT][GT]TG[AGT][TC]G[GT][TA][GA] -------------------------------------------------------------------------------- Time 25.23 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 38 llr = 306 E-value = 6.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 4:1621:::7:1 pos.-specific C 477355:a8347 probability G ::21::3:::2: matrix T 231:347:2:32 bits 2.2 * 1.9 * 1.7 * 1.5 ** Relative 1.3 ** Entropy 1.1 * **** (11.6 bits) 0.9 *** **** * 0.6 ********* * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACCACCTCCACC consensus CT CTTG CTT sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 269705 459 1.69e-07 GAAGAGCCAC ACCACTTCCACC ACCCTTCCAT 7819 376 5.89e-07 AGCGTGGCTT TCCACCTCCACC TTGCTCTTTA 6558 248 7.23e-07 TAAGATCTGT CCCACTTCCAGC GCTCTGAGCA 8460 476 1.86e-06 TTAGTGGCAA CCCACCTCCACT TCTCAATCTG 23598 287 5.84e-06 CCGTGGGCAG ACCACCGCCCGC AAGCCGAAAG 22549 351 6.90e-06 CTCGTGAAAC ACCACCTCTACC GACGTCGGGA 25288 303 1.48e-05 TTGAACACCG CCCCTCTCCCTC GATCTGCAAT 3266 89 1.68e-05 ACGTCAAACG CCGACTTCCAGC TGGCTAGAGT 261639 13 2.18e-05 AGCACCCTTC ACCAATGCCCCC TCATTCTGCT 261539 487 2.49e-05 AACGTGGATT CTCACCTCCAGT AC 40728 467 2.81e-05 GACCGTCGTC CCCACCGCCACA GTACAAAGCA 2118 214 3.19e-05 GAAGTCACAA TCCACAGCCACC AGCGCCCAAC 9195 78 3.59e-05 ACACCAAGCT ATCATTGCCATC TGGGAGAGAC 24328 396 3.59e-05 CCATTTGCAA ATCACATCCATC CATTGATGCA 5273 288 4.01e-05 GGAGGTATTG ACTACTTCCACC TTCATATCTC 24250 98 4.01e-05 ACAGGTTCAA CCGAACTCCATC TCAAAGACAG 2017 477 4.01e-05 CGCTCTCTAT ATCAACGCCATC AGCTCCAATA 11522 71 5.03e-05 TACGAACAAT CCACCTTCCACC AAAGAGCCTT 1118 475 5.61e-05 CAAAACATCA ACCCTTTCCATT TGCAAATCAC 2742 150 6.91e-05 GACGATTCTT TCCGCTGCCACC GAAGCAACTC 22637 134 6.91e-05 CTGCCTCCTG ATCCTCTCCCGC CGTTGCCTCG 4909 9 8.44e-05 GAGAACGA ACAATCGCCACC CGTCAAGGAT 22524 359 8.44e-05 TGGGTTCGGC ATCAAATCCACC ACTGAGTCCA 23346 231 1.03e-04 ACGCAATCCT CTCCTATCCACC GGTATTCGGC 22124 2 1.13e-04 C ATCCCCTCCCGT CTTGACGTTG 268232 307 1.35e-04 CATATCGGCT CTCCTTTCCATT GGCGACGATT 24682 95 1.35e-04 TACACAGTAT CCCCATTCCCTT GATAGAATTC 2182 392 1.47e-04 ACCGAATAAT ACCATCGCTCGC GTCATCTTTT 22935 427 1.60e-04 CGAAGTAGCT CCCATTGCCCCA ACCAATCGAC 40496 370 2.05e-04 TTCTCACTGC TCGACCTCCCGT GGCTTGCTGT 267971 254 2.05e-04 CCTTCGTCGA CTACTCTCCACC ACGAGAGTAC 25702 437 2.21e-04 ATCTACATGC ACCATCTCTCTT GACCCCTCAG 20674 199 2.21e-04 AACAACCTGT CTCAACGCTATC ACATCGATCA 21843 338 2.98e-04 TGGTTTCCCT TCCACTGCTCCT TCGTTGCAAA 25622 246 3.20e-04 GTCGACGTCG TCGGCCGCCATC ATTCTTCCTC 6603 344 5.00e-04 TTTCGTCTCT TCTCATTCCATC GCCCAGCACT 23366 11 8.04e-04 AAAATAATGA ATGCCTTCCCTA TACTGATTTC 9677 192 8.81e-04 GATATCATCG TCGGCTTCTAGC ACAAAGCAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269705 1.7e-07 458_[+3]_30 7819 5.9e-07 375_[+3]_113 6558 7.2e-07 247_[+3]_241 8460 1.9e-06 475_[+3]_13 23598 5.8e-06 286_[+3]_202 22549 6.9e-06 350_[+3]_138 25288 1.5e-05 302_[+3]_186 3266 1.7e-05 88_[+3]_400 261639 2.2e-05 12_[+3]_476 261539 2.5e-05 486_[+3]_2 40728 2.8e-05 466_[+3]_22 2118 3.2e-05 213_[+3]_275 9195 3.6e-05 77_[+3]_411 24328 3.6e-05 395_[+3]_93 5273 4e-05 287_[+3]_201 24250 4e-05 97_[+3]_391 2017 4e-05 476_[+3]_12 11522 5e-05 70_[+3]_418 1118 5.6e-05 474_[+3]_14 2742 6.9e-05 149_[+3]_339 22637 6.9e-05 133_[+3]_355 4909 8.4e-05 8_[+3]_480 22524 8.4e-05 358_[+3]_130 23346 0.0001 230_[+3]_258 22124 0.00011 1_[+3]_487 268232 0.00013 306_[+3]_182 24682 0.00013 94_[+3]_394 2182 0.00015 391_[+3]_97 22935 0.00016 426_[+3]_62 40496 0.00021 369_[+3]_119 267971 0.00021 253_[+3]_235 25702 0.00022 436_[+3]_52 20674 0.00022 198_[+3]_290 21843 0.0003 337_[+3]_151 25622 0.00032 245_[+3]_243 6603 0.0005 343_[+3]_145 23366 0.0008 10_[+3]_478 9677 0.00088 191_[+3]_297 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=38 269705 ( 459) ACCACTTCCACC 1 7819 ( 376) TCCACCTCCACC 1 6558 ( 248) CCCACTTCCAGC 1 8460 ( 476) CCCACCTCCACT 1 23598 ( 287) ACCACCGCCCGC 1 22549 ( 351) ACCACCTCTACC 1 25288 ( 303) CCCCTCTCCCTC 1 3266 ( 89) CCGACTTCCAGC 1 261639 ( 13) ACCAATGCCCCC 1 261539 ( 487) CTCACCTCCAGT 1 40728 ( 467) CCCACCGCCACA 1 2118 ( 214) TCCACAGCCACC 1 9195 ( 78) ATCATTGCCATC 1 24328 ( 396) ATCACATCCATC 1 5273 ( 288) ACTACTTCCACC 1 24250 ( 98) CCGAACTCCATC 1 2017 ( 477) ATCAACGCCATC 1 11522 ( 71) CCACCTTCCACC 1 1118 ( 475) ACCCTTTCCATT 1 2742 ( 150) TCCGCTGCCACC 1 22637 ( 134) ATCCTCTCCCGC 1 4909 ( 9) ACAATCGCCACC 1 22524 ( 359) ATCAAATCCACC 1 23346 ( 231) CTCCTATCCACC 1 22124 ( 2) ATCCCCTCCCGT 1 268232 ( 307) CTCCTTTCCATT 1 24682 ( 95) CCCCATTCCCTT 1 2182 ( 392) ACCATCGCTCGC 1 22935 ( 427) CCCATTGCCCCA 1 40496 ( 370) TCGACCTCCCGT 1 267971 ( 254) CTACTCTCCACC 1 25702 ( 437) ACCATCTCTCTT 1 20674 ( 199) CTCAACGCTATC 1 21843 ( 338) TCCACTGCTCCT 1 25622 ( 246) TCGGCCGCCATC 1 6603 ( 344) TCTCATTCCATC 1 23366 ( 11) ATGCCTTCCCTA 1 9677 ( 192) TCGGCTTCTAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18582 bayes= 9.12593 E= 6.2e-003 65 71 -1189 -35 -1189 160 -1189 24 -176 166 -60 -235 124 36 -160 -1189 -54 123 -1189 11 -134 107 -1189 65 -1189 -1189 51 130 -1189 215 -1189 -1189 -1189 190 -1189 -76 136 49 -1189 -1189 -1189 90 -2 35 -176 160 -1189 -18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 38 E= 6.2e-003 0.421053 0.368421 0.000000 0.210526 0.000000 0.684211 0.000000 0.315789 0.078947 0.710526 0.157895 0.052632 0.631579 0.289474 0.078947 0.000000 0.184211 0.526316 0.000000 0.289474 0.105263 0.473684 0.000000 0.421053 0.000000 0.000000 0.342105 0.657895 0.000000 1.000000 0.000000 0.000000 0.000000 0.842105 0.000000 0.157895 0.684211 0.315789 0.000000 0.000000 0.000000 0.421053 0.236842 0.342105 0.078947 0.684211 0.000000 0.236842 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [ACT][CT]C[AC][CT][CT][TG]CC[AC][CTG][CT] -------------------------------------------------------------------------------- Time 36.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1118 6.69e-04 89_[+2(4.58e-05)]_213_\ [+1(2.85e-05)]_144_[+3(5.61e-05)]_14 11522 9.05e-04 70_[+3(5.03e-05)]_81_[+1(4.57e-05)]_\ 64_[+2(4.58e-05)]_245 2017 2.20e-05 20_[+1(6.89e-07)]_313_\ [+2(5.03e-05)]_115_[+3(4.01e-05)]_12 20674 4.36e-03 104_[+2(1.02e-05)]_380 2118 2.05e-03 213_[+3(3.19e-05)]_190_\ [+2(3.78e-05)]_69 2182 9.61e-04 52_[+2(6.60e-05)]_268_\ [+1(1.18e-05)]_152 21843 3.75e-03 316_[+2(4.58e-05)]_168 22124 1.86e-02 500 22524 8.08e-04 148_[+2(9.30e-05)]_194_\ [+3(8.44e-05)]_106_[+1(1.18e-05)]_12 22549 3.41e-05 25_[+2(1.13e-06)]_309_\ [+3(6.90e-06)]_138 22637 3.31e-05 133_[+3(6.91e-05)]_37_\ [+2(3.48e-06)]_224_[+1(9.18e-06)]_66 22935 5.33e-04 29_[+2(5.52e-05)]_125_\ [+2(6.96e-06)]_191_[+1(5.13e-05)]_111 23346 2.14e-03 393_[+1(3.92e-06)]_95 23366 3.79e-04 95_[+1(4.76e-06)]_189_\ [+2(1.15e-05)]_188 23598 1.52e-05 2_[+2(5.03e-05)]_268_[+3(5.84e-06)]_\ 30_[+1(3.09e-06)]_160 24250 1.31e-03 97_[+3(4.01e-05)]_358_\ [+1(1.18e-05)]_21 24328 9.91e-03 395_[+3(3.59e-05)]_93 24682 4.40e-03 352_[+2(4.58e-05)]_132 25288 1.99e-05 91_[+1(6.27e-05)]_163_\ [+2(9.00e-06)]_20_[+3(1.48e-05)]_126_[+1(9.18e-06)]_48 25622 4.03e-02 229_[+2(2.52e-05)]_255 25702 5.21e-03 127_[+2(1.02e-05)]_357 261539 2.73e-05 27_[+1(3.22e-05)]_365_\ [+2(2.20e-06)]_66_[+3(2.49e-05)]_2 261639 5.84e-05 12_[+3(2.18e-05)]_219_\ [+2(1.17e-07)]_241 267971 4.74e-03 167_[+1(2.51e-05)]_302_\ [+1(9.45e-05)]_7 268232 1.08e-05 32_[+1(2.13e-06)]_16_[+2(2.20e-06)]_\ 82_[+1(2.01e-05)]_330 269705 1.17e-07 205_[+2(3.00e-06)]_88_\ [+1(7.85e-06)]_137_[+3(1.69e-07)]_30 2742 3.34e-04 100_[+2(1.63e-05)]_33_\ [+3(6.91e-05)]_139_[+2(7.86e-05)]_87_[+1(2.85e-05)]_85 3266 4.61e-03 88_[+3(1.68e-05)]_400 40496 1.67e-02 441_[+1(5.13e-05)]_47 40728 7.05e-04 308_[+2(2.52e-05)]_142_\ [+3(2.81e-05)]_22 4909 5.44e-03 8_[+3(8.44e-05)]_415_[+1(1.33e-05)]_\ 53 5273 1.15e-03 51_[+2(3.43e-05)]_220_\ [+3(4.01e-05)]_201 6558 2.76e-06 117_[+2(1.02e-05)]_114_\ [+3(7.23e-07)]_219_[+1(1.80e-05)]_10 6603 1.42e-04 63_[+2(6.86e-08)]_421 7819 1.35e-06 271_[+1(2.51e-05)]_64_\ [+2(4.03e-06)]_12_[+3(5.89e-07)]_113 8460 3.23e-05 304_[+1(5.54e-06)]_159_\ [+3(1.86e-06)]_13 9195 2.92e-06 15_[+2(6.04e-05)]_46_[+3(3.59e-05)]_\ 276_[+1(8.70e-05)]_97_[+1(6.62e-08)]_14 9677 1.09e-02 35_[+2(7.92e-06)]_449 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************