******************************************************************************** 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/302/302.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10552 1.0000 500 10938 1.0000 500 11965 1.0000 500 14322 1.0000 500 1591 1.0000 500 15961 1.0000 500 19963 1.0000 500 20752 1.0000 500 20962 1.0000 500 20972 1.0000 500 21234 1.0000 500 21665 1.0000 500 2218 1.0000 500 22978 1.0000 500 2321 1.0000 500 23932 1.0000 500 24017 1.0000 500 24164 1.0000 500 24820 1.0000 500 24858 1.0000 500 25205 1.0000 500 25357 1.0000 500 262677 1.0000 500 263456 1.0000 500 264732 1.0000 500 2666 1.0000 500 269633 1.0000 500 269976 1.0000 500 28825 1.0000 500 2941 1.0000 500 31783 1.0000 500 3250 1.0000 500 36958 1.0000 500 3706 1.0000 500 38469 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/302/302.seqs.fa -oc motifs/302 -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= 35 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= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.237 G 0.237 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.237 G 0.237 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 27 llr = 278 E-value = 1.5e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1::11::42::3213 pos.-specific C 42::1::12::::::: probability G 42:a3:7812647712 matrix T 25a:493:2646:175 bits 2.1 ** 1.9 ** 1.7 ** * 1.5 ** * Relative 1.2 ** *** Entropy 1.0 ** *** ** (14.9 bits) 0.8 ** *** ***** 0.6 * ** *** ****** 0.4 * ** *** ****** 0.2 **************** 0.0 ---------------- Multilevel CTTGTTGGATGTGGTT consensus GC G T C TGA A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 20962 86 5.51e-08 GGTAGCGGCG GTTGCTGGATGGGGTT GCTTTGTGGT 2218 97 6.70e-08 GAGGAAGTCC TTTGTTGGATGTAGTT TGTCAGGCGA 15961 322 6.70e-08 ACGATATCTA CGTGGTGGATGTGGTA GTCAATGAGA 264732 112 7.65e-07 TGCAGGGTGC CCTGCTGGGTGGGGTT GGGGGTCTGC 262677 112 7.65e-07 TGCAGGGTGC CCTGCTGGGTGGGGTT GGGGGTCTGC 2666 198 1.00e-06 ATACAGTGAA TTTGTTTGCTTTGGTA GTCATCCAAT 269976 347 1.14e-06 CGGTGTCTGC TCTGGTGGTTTGGGTT GACTTCGGGG 263456 162 1.66e-06 TTTTCATTGT CTTGTTTGGTTTGGAT ACTGCTAATC 24820 206 1.87e-06 TGACGATGTT GTTGTTGGATGTGGGC GAATCGGAAT 2321 352 2.97e-06 GTGTCAAGTG GTTGATGCCTTGGGTT CGCCTTGATC 38469 231 4.11e-06 GGTAAAGGCT CGTGTTTGTAGTGGTA GGGCGATGAG 36958 78 6.81e-06 CATCTGATTT GGTGGTGGAGGGGATG TTTCTTGCTA 23932 252 7.49e-06 AAGAAAGGGT GTTGTTGGCTGGAAAT TTCATTTCGA 24164 321 8.24e-06 AGGTACGCAA GCTGATTGTTTGGGTG ATGTGTTTTA 19963 430 9.90e-06 CCTGGCAATA CTTGGTTGCTCGGGTG CGACACCGAT 3706 234 1.18e-05 GCGGCACACT CTTGTTGGATGCGTTG CAGCTCATCC 21234 54 1.29e-05 AGAAAGCAAC CTTGTTGGAATTGTAT TAGCTTCAAT 28825 177 1.53e-05 CATCATTGTC GGTGGTGGTGTTGGGG GAATGGACCG 25205 240 1.53e-05 TCTCCGTGGT CTTGTTTCCGGTAGTA GGCGTCGACT 24017 32 1.53e-05 AAAGGTAGGC GCTGATGGAGGGAGGT TGGAGAAAGA 10552 253 1.53e-05 TCTCCGTGGT CTTGTTTCCGGTAGTA GGCGTCGACT 24858 330 1.66e-05 AAAATCGAGG GTTGTAGGATTGAATT CTAAACGACG 25357 189 2.28e-05 CGATGTATCA CATGATGGGAGTAGTT CTCCTTCGCA 2941 99 2.46e-05 GTTGCCGCAC TGTGGTTGAAGTGGGA TGGGGTGGAA 1591 141 3.29e-05 GCCTACATAC TTTGTAGGAATTAGTA CAAAGATGTG 20752 36 4.62e-05 CCACTACACG GATGGTGAATGTGATT TGAGTCGGTA 31783 47 6.71e-05 ATCTTCCAAT CCTGGTGCTTTTGAAG CTCATTTGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20962 5.5e-08 85_[+1]_399 2218 6.7e-08 96_[+1]_388 15961 6.7e-08 321_[+1]_163 264732 7.6e-07 111_[+1]_373 262677 7.6e-07 111_[+1]_373 2666 1e-06 197_[+1]_287 269976 1.1e-06 346_[+1]_138 263456 1.7e-06 161_[+1]_323 24820 1.9e-06 205_[+1]_279 2321 3e-06 351_[+1]_133 38469 4.1e-06 230_[+1]_254 36958 6.8e-06 77_[+1]_407 23932 7.5e-06 251_[+1]_233 24164 8.2e-06 320_[+1]_164 19963 9.9e-06 429_[+1]_55 3706 1.2e-05 233_[+1]_251 21234 1.3e-05 53_[+1]_431 28825 1.5e-05 176_[+1]_308 25205 1.5e-05 239_[+1]_245 24017 1.5e-05 31_[+1]_453 10552 1.5e-05 252_[+1]_232 24858 1.7e-05 329_[+1]_155 25357 2.3e-05 188_[+1]_296 2941 2.5e-05 98_[+1]_386 1591 3.3e-05 140_[+1]_344 20752 4.6e-05 35_[+1]_449 31783 6.7e-05 46_[+1]_438 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=27 20962 ( 86) GTTGCTGGATGGGGTT 1 2218 ( 97) TTTGTTGGATGTAGTT 1 15961 ( 322) CGTGGTGGATGTGGTA 1 264732 ( 112) CCTGCTGGGTGGGGTT 1 262677 ( 112) CCTGCTGGGTGGGGTT 1 2666 ( 198) TTTGTTTGCTTTGGTA 1 269976 ( 347) TCTGGTGGTTTGGGTT 1 263456 ( 162) CTTGTTTGGTTTGGAT 1 24820 ( 206) GTTGTTGGATGTGGGC 1 2321 ( 352) GTTGATGCCTTGGGTT 1 38469 ( 231) CGTGTTTGTAGTGGTA 1 36958 ( 78) GGTGGTGGAGGGGATG 1 23932 ( 252) GTTGTTGGCTGGAAAT 1 24164 ( 321) GCTGATTGTTTGGGTG 1 19963 ( 430) CTTGGTTGCTCGGGTG 1 3706 ( 234) CTTGTTGGATGCGTTG 1 21234 ( 54) CTTGTTGGAATTGTAT 1 28825 ( 177) GGTGGTGGTGTTGGGG 1 25205 ( 240) CTTGTTTCCGGTAGTA 1 24017 ( 32) GCTGATGGAGGGAGGT 1 10552 ( 253) CTTGTTTCCGGTAGTA 1 24858 ( 330) GTTGTAGGATTGAATT 1 25357 ( 189) CATGATGGGAGTAGTT 1 2941 ( 99) TGTGGTTGAAGTGGGA 1 1591 ( 141) TTTGTAGGAATTAGTA 1 20752 ( 36) GATGGTGAATGTGATT 1 31783 ( 47) CCTGGTGCTTTTGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 9.86371 E= 1.5e-008 -1140 90 64 -45 -188 -10 -36 103 -1140 -1140 -1140 198 -1140 -1140 208 -1140 -88 -110 32 81 -188 -1140 -1140 187 -1140 -1140 157 23 -287 -68 178 -1140 71 -10 -68 -45 -55 -1140 -36 131 -1140 -268 132 55 -1140 -268 78 113 12 -1140 157 -1140 -55 -1140 164 -177 -88 -1140 -68 147 -7 -268 -9 93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 27 E= 1.5e-008 0.000000 0.444444 0.370370 0.185185 0.074074 0.222222 0.185185 0.518519 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.148148 0.111111 0.296296 0.444444 0.074074 0.000000 0.000000 0.925926 0.000000 0.000000 0.703704 0.296296 0.037037 0.148148 0.814815 0.000000 0.444444 0.222222 0.148148 0.185185 0.185185 0.000000 0.185185 0.629630 0.000000 0.037037 0.592593 0.370370 0.000000 0.037037 0.407407 0.555556 0.296296 0.000000 0.703704 0.000000 0.185185 0.000000 0.740741 0.074074 0.148148 0.000000 0.148148 0.703704 0.259259 0.037037 0.222222 0.481481 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][TC]TG[TG]T[GT]G[AC]T[GT][TG][GA]GT[TAG] -------------------------------------------------------------------------------- Time 11.00 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 16 llr = 201 E-value = 2.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :31::::11:1:::1 pos.-specific C 9:981389:65:4a1 probability G 11:::13:::16::1 matrix T :7:396::94346:8 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * ** * Relative 1.2 * *** *** * Entropy 1.0 * *** **** *** (18.1 bits) 0.8 ***** **** **** 0.6 ********** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CTCCTTCCTCCGTCT consensus A T CG TTTC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 25205 116 7.44e-09 CATGAACTTC CTCCTCCCTCTGTCT GTTGAAAGAT 10552 130 7.44e-09 CATGAACTTC CTCCTCCCTCTGTCT GTTGAAAGAT 19963 335 1.45e-08 GACGAAGACC CTCCTCCCTCTGCCT CTGAGCTCTC 264732 406 7.32e-08 TACGTCAAAT CACCTTCCTCGGTCT AACAGCGCCC 262677 406 7.32e-08 TACGTCAAAT CACCTTCCTCGGTCT AACAGCGCCC 11965 445 1.29e-07 CCTTCTGTGT CTCTTTCCTTCTCCT CGCTTCCGTC 3706 470 1.94e-07 AGGGGAGGGG CTCTTGCCTCTGTCT TGCTCCTCCT 14322 418 3.63e-07 CATTAAACTT GTCCTTCCTTCGCCT CCCAACGCCC 263456 41 1.59e-06 CAGAATCTCT CACCTTGCTTCTTCG GACTCTCGAG 21665 289 1.72e-06 GCAGATGACG CTCCTCGCTCCTCCA TCGACCCCTC 20972 347 2.87e-06 GTTGAACTGG CTACTCCCATCTTCT CAAATCAACA 2321 368 3.28e-06 GCCTTGGGTT CGCCTTGATCTGTCT GTCCTTCACA 23932 450 4.00e-06 GCACAAGGCA CTCCCTCCACCGTCC ACCACTACCG 24858 28 4.27e-06 TTTCTCAACG CTCTTGCATTCTCCT TCTTGCGCAC 269633 404 4.55e-06 TGCTTCTCCC CTCCCTCCTCATTCG TCGAAGGAGA 24164 150 4.55e-06 TCCACTGTAC CAATTTGCTTCGCCT TTATGGTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25205 7.4e-09 115_[+2]_370 10552 7.4e-09 129_[+2]_356 19963 1.4e-08 334_[+2]_151 264732 7.3e-08 405_[+2]_80 262677 7.3e-08 405_[+2]_80 11965 1.3e-07 444_[+2]_41 3706 1.9e-07 469_[+2]_16 14322 3.6e-07 417_[+2]_68 263456 1.6e-06 40_[+2]_445 21665 1.7e-06 288_[+2]_197 20972 2.9e-06 346_[+2]_139 2321 3.3e-06 367_[+2]_118 23932 4e-06 449_[+2]_36 24858 4.3e-06 27_[+2]_458 269633 4.5e-06 403_[+2]_82 24164 4.5e-06 149_[+2]_336 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=16 25205 ( 116) CTCCTCCCTCTGTCT 1 10552 ( 130) CTCCTCCCTCTGTCT 1 19963 ( 335) CTCCTCCCTCTGCCT 1 264732 ( 406) CACCTTCCTCGGTCT 1 262677 ( 406) CACCTTCCTCGGTCT 1 11965 ( 445) CTCTTTCCTTCTCCT 1 3706 ( 470) CTCTTGCCTCTGTCT 1 14322 ( 418) GTCCTTCCTTCGCCT 1 263456 ( 41) CACCTTGCTTCTTCG 1 21665 ( 289) CTCCTCGCTCCTCCA 1 20972 ( 347) CTACTCCCATCTTCT 1 2321 ( 368) CGCCTTGATCTGTCT 1 23932 ( 450) CTCCCTCCACCGTCC 1 24858 ( 28) CTCTTGCATTCTCCT 1 269633 ( 404) CTCCCTCCTCATTCG 1 24164 ( 150) CAATTTGCTTCGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 17010 bayes= 10.7902 E= 2.4e-007 -1064 198 -192 -1064 -12 -1064 -192 144 -112 188 -1064 -1064 -1064 166 -1064 -2 -1064 -93 -1064 179 -1064 40 -92 115 -1064 166 8 -1064 -112 188 -1064 -1064 -112 -1064 -1064 179 -1064 140 -1064 57 -212 107 -92 30 -1064 -1064 140 57 -1064 66 -1064 130 -1064 207 -1064 -1064 -212 -192 -92 157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 16 E= 2.4e-007 0.000000 0.937500 0.062500 0.000000 0.250000 0.000000 0.062500 0.687500 0.125000 0.875000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.125000 0.000000 0.875000 0.000000 0.312500 0.125000 0.562500 0.000000 0.750000 0.250000 0.000000 0.125000 0.875000 0.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.625000 0.000000 0.375000 0.062500 0.500000 0.125000 0.312500 0.000000 0.000000 0.625000 0.375000 0.000000 0.375000 0.000000 0.625000 0.000000 1.000000 0.000000 0.000000 0.062500 0.062500 0.125000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TA]C[CT]T[TC][CG]CT[CT][CT][GT][TC]CT -------------------------------------------------------------------------------- Time 21.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 24 llr = 267 E-value = 3.9e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 6:295:645361a547 pos.-specific C 484:58:63549:462 probability G ::41:24:12:::::: matrix T :2:::::::::::1:1 bits 2.1 1.9 * 1.7 ** 1.5 * * ** Relative 1.2 * * * ** Entropy 1.0 ** ***** ** * (16.0 bits) 0.8 ** ***** *** ** 0.6 ** ***** ****** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel ACCAACACACACAACA consensus CTG C GACAC CA sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 264732 163 5.35e-08 CGCAAACAAC CCCACCACCCCCACCA CGGCCATGGC 262677 163 5.35e-08 CGCAAACAAC CCCACCACCCCCACCA CGGCCATGGC 20752 473 6.88e-08 ACACGAGATG CCGACCACACACACAA GGCCCCCTAA 3250 459 3.84e-07 ACCTTCAAGA CCAAACACAGACACCA TTCACCATAC 24820 459 3.84e-07 CCTCTTCTTC ACGACCGCAACCACAA AATACGTGCT 19963 290 4.45e-07 AAACAAAACA CCCAACACCGACACAA CAACACTACA 25205 90 5.72e-07 TTCTCAACCA ACCACCGCGCACACAA CATGAACTTC 10552 104 5.72e-07 TTCTCAACCA ACCACCGCGCACACAA CATGAACTTC 20962 200 9.48e-07 CTGGTGACCG ACGGCCAAACACACCA GGCAGAAGCC 31783 384 1.08e-06 GAAGCCGGAG ACGAACGACCACAACC TCTCTCCACA 24017 162 1.90e-06 CGACCACTCG ACGACGAACAACAACA CTGCCATCCT 21665 481 2.11e-06 CACCAGAGCA ACAGCCAAACACAACA CCAT 1591 357 2.33e-06 TCTTGATTGA CCCACCGCAGCCATCA GTGAACACAC 24164 413 2.86e-06 TTTCTGTAAC CCGGACGAACCCAACA CACAGACCCA 269976 477 3.45e-06 AGCCCTCCCT CCAAAGGCACACAAAA ACCGCAAC 14322 483 6.23e-06 CATCATTACC CTCAACACAACCATCA AC 2218 370 8.46e-06 GCTACTCCCT CCAAACGCGCACAAAC AAGAAGCGTC 24858 350 9.79e-06 TGAATTCTAA ACGACGGAAAACAACT CCAGGTTACT 20972 50 9.79e-06 TACACATCAT ATCAACACAACAAACA TGATAAGAAG 28825 204 1.05e-05 AATGGACCGA ATGAACAACAACAAAC ACTCTCGAGG 21234 482 1.56e-05 CATCCTGCAA ACCAACACCTCCAAAT CCA 2941 451 1.76e-05 CGAGTGTACC ATCAACAACGTCAACA TCAAGTGGAT 25357 148 3.02e-05 AACGTCGACG ACAACCGATGCCAACC AATAATAAAA 22978 163 5.89e-05 ATGAATTTGA ATGAAGACAAAAACCT ACAGCAATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264732 5.4e-08 162_[+3]_322 262677 5.4e-08 162_[+3]_322 20752 6.9e-08 472_[+3]_12 3250 3.8e-07 458_[+3]_26 24820 3.8e-07 458_[+3]_26 19963 4.5e-07 289_[+3]_195 25205 5.7e-07 89_[+3]_395 10552 5.7e-07 103_[+3]_381 20962 9.5e-07 199_[+3]_285 31783 1.1e-06 383_[+3]_101 24017 1.9e-06 161_[+3]_323 21665 2.1e-06 480_[+3]_4 1591 2.3e-06 356_[+3]_128 24164 2.9e-06 412_[+3]_72 269976 3.4e-06 476_[+3]_8 14322 6.2e-06 482_[+3]_2 2218 8.5e-06 369_[+3]_115 24858 9.8e-06 349_[+3]_135 20972 9.8e-06 49_[+3]_435 28825 1e-05 203_[+3]_281 21234 1.6e-05 481_[+3]_3 2941 1.8e-05 450_[+3]_34 25357 3e-05 147_[+3]_337 22978 5.9e-05 162_[+3]_322 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=24 264732 ( 163) CCCACCACCCCCACCA 1 262677 ( 163) CCCACCACCCCCACCA 1 20752 ( 473) CCGACCACACACACAA 1 3250 ( 459) CCAAACACAGACACCA 1 24820 ( 459) ACGACCGCAACCACAA 1 19963 ( 290) CCCAACACCGACACAA 1 25205 ( 90) ACCACCGCGCACACAA 1 10552 ( 104) ACCACCGCGCACACAA 1 20962 ( 200) ACGGCCAAACACACCA 1 31783 ( 384) ACGAACGACCACAACC 1 24017 ( 162) ACGACGAACAACAACA 1 21665 ( 481) ACAGCCAAACACAACA 1 1591 ( 357) CCCACCGCAGCCATCA 1 24164 ( 413) CCGGACGAACCCAACA 1 269976 ( 477) CCAAAGGCACACAAAA 1 14322 ( 483) CTCAACACAACCATCA 1 2218 ( 370) CCAAACGCGCACAAAC 1 24858 ( 350) ACGACGGAAAACAACT 1 20972 ( 50) ATCAACACAACAAACA 1 28825 ( 204) ATGAACAACAACAAAC 1 21234 ( 482) ACCAACACCTCCAAAT 1 2941 ( 451) ATCAACAACGTCAACA 1 25357 ( 148) ACAACCGATGCCAACC 1 22978 ( 163) ATGAAGACAAAAACCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 10.5647 E= 3.9e-010 110 81 -1123 -1123 -1123 174 -1123 -28 -39 81 66 -1123 168 -1123 -92 -1123 88 107 -1123 -1123 -1123 181 -51 -1123 110 -1123 81 -1123 46 140 -1123 -1123 88 49 -92 -260 10 95 -19 -260 110 66 -1123 -260 -171 195 -1123 -1123 188 -1123 -1123 -1123 88 81 -1123 -160 46 140 -1123 -1123 138 -51 -1123 -102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 3.9e-010 0.583333 0.416667 0.000000 0.000000 0.000000 0.791667 0.000000 0.208333 0.208333 0.416667 0.375000 0.000000 0.875000 0.000000 0.125000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.583333 0.000000 0.416667 0.000000 0.375000 0.625000 0.000000 0.000000 0.500000 0.333333 0.125000 0.041667 0.291667 0.458333 0.208333 0.041667 0.583333 0.375000 0.000000 0.041667 0.083333 0.916667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.416667 0.000000 0.083333 0.375000 0.625000 0.000000 0.000000 0.708333 0.166667 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC][CT][CGA]A[AC]C[AG][CA][AC][CAG][AC]CA[AC][CA]A -------------------------------------------------------------------------------- Time 32.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10552 2.63e-09 103_[+3(5.72e-07)]_10_\ [+2(7.44e-09)]_108_[+1(1.53e-05)]_232 10938 5.06e-01 500 11965 1.89e-03 444_[+2(1.29e-07)]_41 14322 1.84e-05 417_[+2(3.63e-07)]_50_\ [+3(6.23e-06)]_2 1591 4.24e-05 140_[+1(3.29e-05)]_200_\ [+3(2.33e-06)]_14_[+2(3.86e-05)]_99 15961 1.18e-03 321_[+1(6.70e-08)]_163 19963 2.59e-09 261_[+3(6.30e-05)]_12_\ [+3(4.45e-07)]_29_[+2(1.45e-08)]_80_[+1(9.90e-06)]_55 20752 5.77e-05 35_[+1(4.62e-05)]_244_\ [+3(3.32e-05)]_161_[+3(6.88e-08)]_12 20962 5.75e-07 85_[+1(5.51e-08)]_98_[+3(9.48e-07)]_\ 41_[+3(5.09e-05)]_228 20972 5.36e-04 49_[+3(9.79e-06)]_281_\ [+2(2.87e-06)]_139 21234 2.15e-03 53_[+1(1.29e-05)]_412_\ [+3(1.56e-05)]_3 21665 1.96e-05 288_[+2(1.72e-06)]_177_\ [+3(2.11e-06)]_4 2218 1.75e-05 96_[+1(6.70e-08)]_257_\ [+3(8.46e-06)]_115 22978 7.69e-02 162_[+3(5.89e-05)]_322 2321 2.20e-04 351_[+1(2.97e-06)]_[+2(3.28e-06)]_\ 118 23932 5.29e-04 251_[+1(7.49e-06)]_182_\ [+2(4.00e-06)]_36 24017 4.75e-04 31_[+1(1.53e-05)]_114_\ [+3(1.90e-06)]_323 24164 2.26e-06 149_[+2(4.55e-06)]_156_\ [+1(8.24e-06)]_76_[+3(2.86e-06)]_72 24820 1.80e-05 205_[+1(1.87e-06)]_237_\ [+3(3.84e-07)]_26 24858 1.19e-05 27_[+2(4.27e-06)]_287_\ [+1(1.66e-05)]_4_[+3(9.79e-06)]_135 25205 2.63e-09 89_[+3(5.72e-07)]_10_[+2(7.44e-09)]_\ 109_[+1(1.53e-05)]_245 25357 7.54e-04 147_[+3(3.02e-05)]_25_\ [+1(2.28e-05)]_296 262677 1.51e-10 111_[+1(7.65e-07)]_35_\ [+3(5.35e-08)]_5_[+3(2.60e-05)]_206_[+2(7.32e-08)]_80 263456 2.48e-05 40_[+2(1.59e-06)]_106_\ [+1(1.66e-06)]_323 264732 1.51e-10 111_[+1(7.65e-07)]_35_\ [+3(5.35e-08)]_5_[+3(2.60e-05)]_206_[+2(7.32e-08)]_80 2666 6.08e-03 197_[+1(1.00e-06)]_287 269633 1.09e-02 403_[+2(4.55e-06)]_82 269976 8.19e-05 183_[+3(1.76e-05)]_147_\ [+1(1.14e-06)]_114_[+3(3.45e-06)]_8 28825 1.73e-03 176_[+1(1.53e-05)]_11_\ [+3(1.05e-05)]_281 2941 2.81e-03 98_[+1(2.46e-05)]_336_\ [+3(1.76e-05)]_34 31783 2.16e-04 46_[+1(6.71e-05)]_321_\ [+3(1.08e-06)]_101 3250 7.32e-04 458_[+3(3.84e-07)]_26 36958 7.56e-02 77_[+1(6.81e-06)]_407 3706 6.38e-05 233_[+1(1.18e-05)]_220_\ [+2(1.94e-07)]_16 38469 3.93e-02 88_[+1(3.78e-05)]_107_\ [+1(8.45e-05)]_3_[+1(4.11e-06)]_254 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************