******************************************************************************** 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/31/31.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10136 1.0000 500 10244 1.0000 500 10302 1.0000 500 10690 1.0000 500 10842 1.0000 500 1125 1.0000 500 11751 1.0000 500 11788 1.0000 500 1911 1.0000 500 24883 1.0000 500 25140 1.0000 500 25681 1.0000 500 25707 1.0000 500 261525 1.0000 500 262034 1.0000 500 262824 1.0000 500 263660 1.0000 500 263844 1.0000 500 268208 1.0000 500 3264 1.0000 500 4580 1.0000 500 5288 1.0000 500 5865 1.0000 500 5967 1.0000 500 9534 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/31/31.seqs.fa -oc motifs/31 -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= 25 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= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.221 G 0.240 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.221 G 0.240 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 25 llr = 266 E-value = 7.7e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :34:61121:5::22::325: pos.-specific C 24::1:::112::312121:2 probability G 721a:68:79:283:53:416 matrix T 115:32:81:38227465242 bits 2.2 2.0 * 1.7 * 1.5 * * Relative 1.3 * * * Entropy 1.1 * ** * ** (15.3 bits) 0.9 * * ** * ** 0.7 * ******* ** * * 0.4 * *********** *** ** 0.2 ************* ******* 0.0 --------------------- Multilevel GCTGAGGTGGATGCTGTTGAG consensus AA TT A TG G TGAATT sequence G T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10690 171 2.76e-11 AGTTTGAAAG GCAGAGGTGGATGGTGTAGAG AGGATGGCGA 262034 112 2.57e-08 GCAGAGGAGG TCAGAGGTGGCTGCTGGTGAG GTTGGCAAAT 24883 259 6.15e-08 GATATCGTAT CGTGAGGTGGTTGTTGTATTG CAGATGTTAA 5967 75 9.28e-08 GTGATCTACG GATGTTGTGGTTGGTGTATTG GATGGAGTTG 262824 112 9.28e-08 GGAGCTGCTG CTTGAGGTGGAGGATGTTGTG ACTTGTTTCT 10842 265 9.28e-08 TTCTACGAAC GATGCGGTGGATGCTCCTGAG GCAAGTGCAT 261525 67 3.31e-07 ATGAACTTTT GAGGAGGAGGATGTAGTAGTG CAGCGATGTT 3264 358 6.66e-07 AAAGGAGGTT GCTGTGATGGTGGCAGTTGAG CACGTCGATA 1125 158 1.04e-06 GGAATTGTAC GCTGAGGTCGAGGATCGTATC GAAGGAGTGT 5288 399 1.75e-06 GGATAGATGG GATGACGTGGCTTGTGTTGAC ACAGAGGGCT 268208 139 6.14e-06 GTTTCTTGGA GCCGTTGTGGTTGTGGTTGTG TTACACAGCC 4580 171 6.72e-06 GCTCGCCGTC GGAGAGGAGCTGGGTTGATAG GGTGTACTCT 263844 266 6.72e-06 GGCAAACTGT GCAGAAGTGGATTGTTATGTT GTTGAGTTGG 10244 339 6.72e-06 GTAAGCAGAG TGTGTGGTTGTTGGTGTTTGG TGTTGGTAGT 263660 285 8.02e-06 GGTTTGATAA GAAGAGGAGGATTCCTGTCTT CTTTGGACAT 1911 157 1.04e-05 TATCTCGAGG CCGGATGTGGAGGCCTTCAAG CTAGGTGCAC 11751 2 1.13e-05 T GCTGCTGTTGATGGTTCACAG CCCGCTGCAG 9534 73 1.34e-05 TGCTGATGGT GTTGTGGACGATGTCCTAGTG ATGGTAGGCG 25140 257 1.71e-05 TCATGAGACA GGAGAGATAGGTGATTTTAAG TACGTGCAGG 11788 340 1.71e-05 TCTGCTTACT GATGAGTTGCATGCTTGCAAT GATCATGTCA 5865 98 2.54e-05 GAATCAATGA GGTGAGCTTGTTGATCGTATC GTAATGCGAC 25681 229 3.18e-05 GTAGCAACGG CAAGATGAGGATGATTGGAGG AGGGTAGGTG 10302 14 3.97e-05 CGTGGGGGAG AAAGTAGTGGATTTTGTCGAC AGTATATATT 25707 412 1.17e-04 CTGCAAATCG GCAGTAGTAGCGGCAGTCCAT CCAACCAACC 10136 270 1.68e-04 CTGAATCAAA GGTGAGGTCACTGTATGTTGT TGCCTTGCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10690 2.8e-11 170_[+1]_309 262034 2.6e-08 111_[+1]_368 24883 6.1e-08 258_[+1]_221 5967 9.3e-08 74_[+1]_405 262824 9.3e-08 111_[+1]_368 10842 9.3e-08 264_[+1]_215 261525 3.3e-07 66_[+1]_413 3264 6.7e-07 357_[+1]_122 1125 1e-06 157_[+1]_322 5288 1.8e-06 398_[+1]_81 268208 6.1e-06 138_[+1]_341 4580 6.7e-06 170_[+1]_309 263844 6.7e-06 265_[+1]_214 10244 6.7e-06 338_[+1]_141 263660 8e-06 284_[+1]_195 1911 1e-05 156_[+1]_323 11751 1.1e-05 1_[+1]_478 9534 1.3e-05 72_[+1]_407 25140 1.7e-05 256_[+1]_223 11788 1.7e-05 339_[+1]_140 5865 2.5e-05 97_[+1]_382 25681 3.2e-05 228_[+1]_251 10302 4e-05 13_[+1]_466 25707 0.00012 411_[+1]_68 10136 0.00017 269_[+1]_210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=25 10690 ( 171) GCAGAGGTGGATGGTGTAGAG 1 262034 ( 112) TCAGAGGTGGCTGCTGGTGAG 1 24883 ( 259) CGTGAGGTGGTTGTTGTATTG 1 5967 ( 75) GATGTTGTGGTTGGTGTATTG 1 262824 ( 112) CTTGAGGTGGAGGATGTTGTG 1 10842 ( 265) GATGCGGTGGATGCTCCTGAG 1 261525 ( 67) GAGGAGGAGGATGTAGTAGTG 1 3264 ( 358) GCTGTGATGGTGGCAGTTGAG 1 1125 ( 158) GCTGAGGTCGAGGATCGTATC 1 5288 ( 399) GATGACGTGGCTTGTGTTGAC 1 268208 ( 139) GCCGTTGTGGTTGTGGTTGTG 1 4580 ( 171) GGAGAGGAGCTGGGTTGATAG 1 263844 ( 266) GCAGAAGTGGATTGTTATGTT 1 10244 ( 339) TGTGTGGTTGTTGGTGTTTGG 1 263660 ( 285) GAAGAGGAGGATTCCTGTCTT 1 1911 ( 157) CCGGATGTGGAGGCCTTCAAG 1 11751 ( 2) GCTGCTGTTGATGGTTCACAG 1 9534 ( 73) GTTGTGGACGATGTCCTAGTG 1 25140 ( 257) GGAGAGATAGGTGATTTTAAG 1 11788 ( 340) GATGAGTTGCATGCTTGCAAT 1 5865 ( 98) GGTGAGCTTGTTGATCGTATC 1 25681 ( 229) CAAGATGAGGATGATTGGAGG 1 10302 ( 14) AAAGTAGTGGATTTTGTCGAC 1 25707 ( 412) GCAGTAGTAGCGGCAGTCCAT 1 10136 ( 270) GGTGAGGTCACTGTATGTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 9.3948 E= 7.7e-007 -271 -47 158 -179 28 70 0 -179 45 -246 -158 91 -1129 -1129 206 -1129 128 -147 -1129 2 -113 -246 141 -46 -171 -246 181 -278 -39 -1129 -1129 153 -171 -88 150 -120 -271 -147 187 -1129 99 -47 -258 2 -1129 -1129 0 146 -1129 -1129 181 -79 -39 34 22 -20 -71 -88 -258 130 -1129 -47 100 38 -271 -147 41 102 9 -47 -258 91 -13 -88 87 -46 87 -1129 -100 53 -1129 -47 141 -46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 25 E= 7.7e-007 0.040000 0.160000 0.720000 0.080000 0.320000 0.360000 0.240000 0.080000 0.360000 0.040000 0.080000 0.520000 0.000000 0.000000 1.000000 0.000000 0.640000 0.080000 0.000000 0.280000 0.120000 0.040000 0.640000 0.200000 0.080000 0.040000 0.840000 0.040000 0.200000 0.000000 0.000000 0.800000 0.080000 0.120000 0.680000 0.120000 0.040000 0.080000 0.880000 0.000000 0.520000 0.160000 0.040000 0.280000 0.000000 0.000000 0.240000 0.760000 0.000000 0.000000 0.840000 0.160000 0.200000 0.280000 0.280000 0.240000 0.160000 0.120000 0.040000 0.680000 0.000000 0.160000 0.480000 0.360000 0.040000 0.080000 0.320000 0.560000 0.280000 0.160000 0.040000 0.520000 0.240000 0.120000 0.440000 0.200000 0.480000 0.000000 0.120000 0.400000 0.000000 0.160000 0.640000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[CAG][TA]G[AT][GT]G[TA]GG[AT][TG]G[CGTA]T[GT][TG][TA][GAT][AT][GT] -------------------------------------------------------------------------------- Time 5.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 15 llr = 204 E-value = 4.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 72345123:5::3:13::111 pos.-specific C 33455417a:9519354a169 probability G :53:::4::1:2::22::7:: matrix T ::111531:413613:6:13: bits 2.2 * * 2.0 * * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * * * * Entropy 1.1 * * * * ** * (19.6 bits) 0.9 * * ** * * *** * 0.7 ** *** **** ** ****** 0.4 ** *** ******* ****** 0.2 ****** ******* ****** 0.0 --------------------- Multilevel AGCCATGCCACCTCCCTCGCC consensus CCAACCTA T TA TAC T sequence AG A G GG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25681 447 1.13e-09 TACAAAAGGA AGCCCCCCCTCCTCACTCGCC GGTTCATCCA 24883 157 4.39e-09 CCTCATAGAG ACACACGCCTCCTCTCTCGAC GTACTCGTGA 10302 171 5.12e-09 CGGTACACTC AGCAACGACACCTCGGTCGCC ACTACTCTCA 262034 466 5.95e-09 ATCCGACAAC AGCAACACCACCACCGCCGCC AACAACAGCA 10244 454 1.09e-07 TATATTATCT AGGCCTTCCGCTCCTCCCGCC TTCTTCACAC 4580 447 2.13e-07 CTCCAGCGTC CCCCAAACCTCGACCCCCGTC GTGCTTGCAG 11788 90 2.33e-07 CTACGCCAAA AAACCTGACACGTCGACCGTC TACCCCGATA 1911 447 2.55e-07 GGGATAAATC CGGTCCGCCACTTCCCTCACC TCCCTCCCAA 5288 245 3.60e-07 CATTGGTTAT CGCCTTTCCACGTCGATCGTC TGCAAATGCC 11751 451 4.61e-07 TGAACTTCTA ACACACTACACTACTACCCCC TCTCCCCACA 263844 468 7.36e-07 CTGAAACTCT CCTACAGCCACCTTCCTCGTC TAGTCAAACA 263660 465 9.17e-07 CTGACACATC AACAATCACTCTTTTATCGCC AGTGGTCGCA 10690 473 9.17e-07 CAACGCAACC ACGCCTGCCTCCACACCCCCA TCCCACC 268208 88 2.32e-06 GTGTTGTGGC AGAACTTTCTCTCCCCTCTCC TCGGCCACAC 25707 380 2.61e-06 CCGTCATCCT CAGAATACCATCTCTGTCGAC TCTGCAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25681 1.1e-09 446_[+2]_33 24883 4.4e-09 156_[+2]_323 10302 5.1e-09 170_[+2]_309 262034 5.9e-09 465_[+2]_14 10244 1.1e-07 453_[+2]_26 4580 2.1e-07 446_[+2]_33 11788 2.3e-07 89_[+2]_390 1911 2.5e-07 446_[+2]_33 5288 3.6e-07 244_[+2]_235 11751 4.6e-07 450_[+2]_29 263844 7.4e-07 467_[+2]_12 263660 9.2e-07 464_[+2]_15 10690 9.2e-07 472_[+2]_7 268208 2.3e-06 87_[+2]_392 25707 2.6e-06 379_[+2]_100 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=15 25681 ( 447) AGCCCCCCCTCCTCACTCGCC 1 24883 ( 157) ACACACGCCTCCTCTCTCGAC 1 10302 ( 171) AGCAACGACACCTCGGTCGCC 1 262034 ( 466) AGCAACACCACCACCGCCGCC 1 10244 ( 454) AGGCCTTCCGCTCCTCCCGCC 1 4580 ( 447) CCCCAAACCTCGACCCCCGTC 1 11788 ( 90) AAACCTGACACGTCGACCGTC 1 1911 ( 447) CGGTCCGCCACTTCCCTCACC 1 5288 ( 245) CGCCTTTCCACGTCGATCGTC 1 11751 ( 451) ACACACTACACTACTACCCCC 1 263844 ( 468) CCTACAGCCACCTTCCTCGTC 1 263660 ( 465) AACAATCACTCTTTTATCGCC 1 10690 ( 473) ACGCCTGCCTCCACACCCCCA 1 268208 ( 88) AGAACTTTCTCTCCCCTCTCC 1 25707 ( 380) CAGAATACCATCTCTGTCGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 10.9177 E= 4.1e-005 134 59 -1055 -1055 -39 59 96 -1055 2 85 15 -205 61 127 -1055 -205 83 108 -1055 -205 -98 85 -1055 76 -39 -73 74 -5 2 159 -1055 -205 -1055 218 -1055 -1055 102 -1055 -185 53 -1055 208 -1055 -205 -1055 108 -26 27 2 -73 -1055 112 -1055 197 -1055 -105 -98 59 -26 27 2 127 -26 -1055 -1055 85 -1055 112 -1055 218 -1055 -1055 -198 -73 161 -205 -98 144 -1055 -5 -198 208 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 15 E= 4.1e-005 0.666667 0.333333 0.000000 0.000000 0.200000 0.333333 0.466667 0.000000 0.266667 0.400000 0.266667 0.066667 0.400000 0.533333 0.000000 0.066667 0.466667 0.466667 0.000000 0.066667 0.133333 0.400000 0.000000 0.466667 0.200000 0.133333 0.400000 0.266667 0.266667 0.666667 0.000000 0.066667 0.000000 1.000000 0.000000 0.000000 0.533333 0.000000 0.066667 0.400000 0.000000 0.933333 0.000000 0.066667 0.000000 0.466667 0.200000 0.333333 0.266667 0.133333 0.000000 0.600000 0.000000 0.866667 0.000000 0.133333 0.133333 0.333333 0.200000 0.333333 0.266667 0.533333 0.200000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.066667 0.133333 0.733333 0.066667 0.133333 0.600000 0.000000 0.266667 0.066667 0.933333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC][GCA][CAG][CA][AC][TC][GTA][CA]C[AT]C[CTG][TA]C[CTG][CAG][TC]CG[CT]C -------------------------------------------------------------------------------- Time 11.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 25 llr = 207 E-value = 6.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:2:18:25a1: pos.-specific C 1:23::2:4:41 probability G 28449::81::9 matrix T 5222:28:::5: bits 2.2 2.0 * 1.7 * 1.5 * * Relative 1.3 * * ** * * Entropy 1.1 * **** * * (11.9 bits) 0.9 * **** * * 0.7 * ******** 0.4 * ******** 0.2 ** ********* 0.0 ------------ Multilevel TGGGGATGAATG consensus A CC TC C C sequence G AT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10136 115 1.08e-07 TACAAACATG TGGGGATGCACG TTCGTCTCTT 262824 59 2.42e-07 ATTGATACAT TGGGGATGCATG GTTATTCGGC 10244 244 3.53e-06 CTTCGCGTAG TGTCGATGAATG TAGCGTCGGT 5288 449 5.34e-06 GAAATAGTGA TGGCGTTGAACG AGTATGTGAA 11788 255 5.34e-06 TTATCAGAAG GGCCGATGAACG GTGTGATGTA 262034 80 1.28e-05 TCGATGCCAT TGGTGTTGAATG GTCGGTAGAG 5865 169 1.42e-05 CGTAGTGTGG TGCCGATGGATG TATGCAGACG 3264 200 1.76e-05 TTGACGAAGA AGATGATGCACG TTGTCCATCG 25140 286 1.76e-05 AGTACGTGCA GGGCGACGAACG AGAATGTTGA 24883 122 1.76e-05 TCTCTTCCTC CGAGGATGAACG ATACCCACGC 263660 441 2.56e-05 GTAATGATTC TGTGGATACATG CACTGACACA 5967 48 3.49e-05 TTGTCAAGGC GGTGGACGAATG AAAATGTGAT 261525 285 3.88e-05 GGCAGACATC AGCGGATACACG TGCACATCGT 10690 295 7.41e-05 TTGAGTTGAG TTGCGATGGATG AGGTGGTTCA 11751 316 8.09e-05 TGTTGGAGAG TTGTGTTGCACG TTCGTTGTGC 10302 332 8.09e-05 CCTCGGCTTC TTTGGACGAACG GTATCTATTT 4580 143 1.04e-04 TTATTGTGGA TGGTGACGCATC GTACTGGCTC 9534 386 1.32e-04 TAATTGACAA AGAAGATGCATG TTATCCACCA 25681 266 1.32e-04 GGTGGGTGTT GGCGGTTGCAAG ACTCTCAGTG 263844 199 1.91e-04 AGTGATCGAA TGATGTTGAATC GTGATGGGTC 1911 435 1.91e-04 TGAAGTCGTT AGGGGATAAATC CGGTCCGCCA 1125 94 2.31e-04 CTTTCTTGGA GGCGAATGGACG TGGATACTGG 268208 478 4.00e-04 TCCAACAACA CGTCGTTGCAAG CTCTACGGTT 10842 378 4.97e-04 TCGTCTTGGG ATAGAATGAATG AGAGGTCTGC 25707 295 7.62e-04 GCAAAAATCC TGCTCACAAACG GCCAACATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10136 1.1e-07 114_[+3]_374 262824 2.4e-07 58_[+3]_430 10244 3.5e-06 243_[+3]_245 5288 5.3e-06 448_[+3]_40 11788 5.3e-06 254_[+3]_234 262034 1.3e-05 79_[+3]_409 5865 1.4e-05 168_[+3]_320 3264 1.8e-05 199_[+3]_289 25140 1.8e-05 285_[+3]_203 24883 1.8e-05 121_[+3]_367 263660 2.6e-05 440_[+3]_48 5967 3.5e-05 47_[+3]_441 261525 3.9e-05 284_[+3]_204 10690 7.4e-05 294_[+3]_194 11751 8.1e-05 315_[+3]_173 10302 8.1e-05 331_[+3]_157 4580 0.0001 142_[+3]_346 9534 0.00013 385_[+3]_103 25681 0.00013 265_[+3]_223 263844 0.00019 198_[+3]_290 1911 0.00019 434_[+3]_54 1125 0.00023 93_[+3]_395 268208 0.0004 477_[+3]_11 10842 0.0005 377_[+3]_111 25707 0.00076 294_[+3]_194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=25 10136 ( 115) TGGGGATGCACG 1 262824 ( 59) TGGGGATGCATG 1 10244 ( 244) TGTCGATGAATG 1 5288 ( 449) TGGCGTTGAACG 1 11788 ( 255) GGCCGATGAACG 1 262034 ( 80) TGGTGTTGAATG 1 5865 ( 169) TGCCGATGGATG 1 3264 ( 200) AGATGATGCACG 1 25140 ( 286) GGGCGACGAACG 1 24883 ( 122) CGAGGATGAACG 1 263660 ( 441) TGTGGATACATG 1 5967 ( 48) GGTGGACGAATG 1 261525 ( 285) AGCGGATACACG 1 10690 ( 295) TTGCGATGGATG 1 11751 ( 316) TTGTGTTGCACG 1 10302 ( 332) TTTGGACGAACG 1 4580 ( 143) TGGTGACGCATC 1 9534 ( 386) AGAAGATGCATG 1 25681 ( 266) GGCGGTTGCAAG 1 263844 ( 199) TGATGTTGAATC 1 1911 ( 435) AGGGGATAAATC 1 1125 ( 94) GGCGAATGGACG 1 268208 ( 478) CGTCGTTGCAAG 1 10842 ( 378) ATAGAATGAATG 1 25707 ( 295) TGCTCACAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 12225 bayes= 8.93074 E= 6.3e+000 -39 -147 -26 91 -1129 -1129 181 -79 -39 12 58 -46 -271 34 87 -20 -171 -246 187 -1129 153 -1129 -1129 -20 -1129 -15 -1129 153 -71 -1129 181 -1129 87 85 -100 -1129 193 -1129 -1129 -1129 -171 99 -1129 80 -1129 -88 187 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 25 E= 6.3e+000 0.200000 0.080000 0.200000 0.520000 0.000000 0.000000 0.840000 0.160000 0.200000 0.240000 0.360000 0.200000 0.040000 0.280000 0.440000 0.240000 0.080000 0.040000 0.880000 0.000000 0.760000 0.000000 0.000000 0.240000 0.000000 0.200000 0.000000 0.800000 0.160000 0.000000 0.840000 0.000000 0.480000 0.400000 0.120000 0.000000 1.000000 0.000000 0.000000 0.000000 0.080000 0.440000 0.000000 0.480000 0.000000 0.120000 0.880000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TAG]G[GCAT][GCT]G[AT][TC]G[AC]A[TC]G -------------------------------------------------------------------------------- Time 17.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10136 5.92e-05 114_[+3(1.08e-07)]_374 10244 7.68e-08 243_[+3(3.53e-06)]_83_\ [+1(6.72e-06)]_94_[+2(1.09e-07)]_26 10302 4.03e-07 13_[+1(3.97e-05)]_136_\ [+2(5.12e-09)]_140_[+3(8.09e-05)]_157 10690 9.48e-11 58_[+1(1.71e-05)]_19_[+1(5.28e-05)]_\ 51_[+1(2.76e-11)]_103_[+3(7.41e-05)]_166_[+2(9.17e-07)]_7 10842 3.45e-04 264_[+1(9.28e-08)]_215 1125 9.67e-04 157_[+1(1.04e-06)]_322 11751 7.46e-06 1_[+1(1.13e-05)]_293_[+3(8.09e-05)]_\ 123_[+2(4.61e-07)]_29 11788 5.20e-07 89_[+2(2.33e-07)]_144_\ [+3(5.34e-06)]_73_[+1(1.71e-05)]_140 1911 8.55e-06 156_[+1(1.04e-05)]_269_\ [+2(2.55e-07)]_33 24883 2.28e-10 121_[+3(1.76e-05)]_23_\ [+2(4.39e-09)]_81_[+1(6.15e-08)]_221 25140 3.88e-03 256_[+1(1.71e-05)]_8_[+3(1.76e-05)]_\ 203 25681 1.29e-07 228_[+1(3.18e-05)]_197_\ [+2(1.13e-09)]_8_[+2(7.31e-05)]_4 25707 1.48e-03 379_[+2(2.61e-06)]_100 261525 1.04e-04 66_[+1(3.31e-07)]_197_\ [+3(3.88e-05)]_204 262034 1.00e-10 79_[+3(1.28e-05)]_20_[+1(2.57e-08)]_\ 333_[+2(5.95e-09)]_14 262824 6.79e-07 58_[+3(2.42e-07)]_41_[+1(9.28e-08)]_\ 368 263660 3.68e-06 284_[+1(8.02e-06)]_135_\ [+3(2.56e-05)]_12_[+2(9.17e-07)]_15 263844 1.49e-05 265_[+1(6.72e-06)]_181_\ [+2(7.36e-07)]_12 268208 6.89e-05 87_[+2(2.32e-06)]_30_[+1(6.14e-06)]_\ 341 3264 8.42e-05 199_[+3(1.76e-05)]_146_\ [+1(6.66e-07)]_122 4580 2.93e-06 170_[+1(6.72e-06)]_255_\ [+2(2.13e-07)]_33 5288 9.78e-08 244_[+2(3.60e-07)]_133_\ [+1(1.75e-06)]_29_[+3(5.34e-06)]_40 5865 1.34e-03 97_[+1(2.54e-05)]_50_[+3(1.42e-05)]_\ 320 5967 6.78e-05 47_[+3(3.49e-05)]_15_[+1(9.28e-08)]_\ 3_[+1(2.54e-05)]_381 9534 1.42e-02 72_[+1(1.34e-05)]_407 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************