******************************************************************************** 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/335/335.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10490 1.0000 500 10581 1.0000 500 11162 1.0000 500 12403 1.0000 500 1303 1.0000 500 14225 1.0000 500 20609 1.0000 500 20832 1.0000 500 21532 1.0000 500 21622 1.0000 500 24150 1.0000 500 24515 1.0000 500 24744 1.0000 500 24919 1.0000 500 25015 1.0000 500 25267 1.0000 500 25748 1.0000 500 25873 1.0000 500 2628 1.0000 500 269391 1.0000 500 269520 1.0000 500 270332 1.0000 500 3394 1.0000 500 37497 1.0000 500 37758 1.0000 500 38171 1.0000 500 6726 1.0000 500 6924 1.0000 500 8344 1.0000 500 8405 1.0000 500 985 1.0000 500 9941 1.0000 500 bd1935 1.0000 500 bd923 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/335/335.seqs.fa -oc motifs/335 -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 0.255 C 0.224 G 0.252 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.224 G 0.252 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 34 llr = 337 E-value = 3.2e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:::3::13::12:2:21:3: pos.-specific C 162851871496376234524 probability G 13:2:11:1112:121:1213 matrix T 6:8:29125611511654443 bits 2.2 1.9 1.7 1.5 Relative 1.3 * * Entropy 1.1 *** *** * (14.3 bits) 0.9 *** *** ** * 0.6 *** *** ** * * * 0.4 ******* ******** * 0.2 ********************* 0.0 --------------------- Multilevel TCTCCTCCTTCCTCCTTCCTC consensus GC A TAC GC CCTTAG sequence T A A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 985 429 4.44e-09 TGACATCTCC TCTCTTCCTTCCTCCGTCTTG CCTCTGCCAA bd923 9 2.34e-08 AGCCACGA CGTCCTCCGTCCTCCTCCTTG CCTCTCTCGC 9941 414 2.74e-08 TGCATGTATT TGTCCTCCCTCCTCCTCGTTC ACCCGTACCT 37758 349 3.31e-07 TATTTTATGA TCTGATCCTTCTCCCTTCGTG ATATTCCGTT 10490 166 4.24e-07 AATGACACGG TGTCCTCCATCGTCGTTATAT CGTTAGAAGA 6924 351 1.37e-06 ATTTATATTA TCCCCTGTATCCTCCTCCCGT CCGTCCTTTC 24919 319 1.37e-06 ACACTTAGCC CCTCAGCCCCCCCCCTATCTG TTGCCCCTCG 14225 30 1.37e-06 ATCTAGATGA TCTGCTGTTTCCTCCTACCCT CCGCATACTA 6726 392 1.70e-06 AAATTCTTAC TCTCTTATTCCCTCCTCTTTG TTACAACATC 8344 384 2.11e-06 CTGCCAGCTG TCTCTTCCTTCTCTCTTTTGC ACAGCATCAA 37497 444 3.22e-06 CAAAAACAGG AGCCTTCCTCTCCCCTTCCAG ACAGAAACCT 270332 445 3.22e-06 CAAAAACAGG AGCCTTCCTCTCCCCTTCCAG ACAGAAACCT 269391 95 3.57e-06 CGACGCATCA CGTCCTGCTTCGTCGTCCGTC GGCGTCGTCC 20832 371 3.57e-06 GCCTACAATT CCTCTTCCCCCCATCTCTCAT CTCTGATGTG 3394 459 3.96e-06 AAGACTTCCA TGTCCTCCTTCAACTCTCGTT CCACCTCCTA 24515 451 4.38e-06 ACAATTCTGC TCTTATCCATCCACCCATCCG ACTAATCCAT 1303 406 5.34e-06 CCCACAAGAA GCTCCCCCCCCCCCCGCCCGC GAAGACAATG 21622 435 7.88e-06 GAAGAACGAA ACTCGGCCTGCCTCCTTCCAC CCTACAAACG 21532 196 8.66e-06 GTAGGACTTG ACTCCTCCATCTCCATCAGCC GAAGTTGATG 11162 471 9.52e-06 CACACCTTGT TATCCTCCACCCACATTGTCG TCACCACCA 38171 213 1.26e-05 CCGAAGTACT CGCCCTCCTCGCTCACTTTCC ACAATCCGAT 8405 433 1.65e-05 GCTACTACTC TCTCTTTCACCACCACTGCTC AAGCCGACGC 269520 180 1.96e-05 ATGGCAGTGT TGCCATCCGCCGTGCTATGTT CATCGTGTGG 25748 383 1.96e-05 CGTGGTTGAA GCTGCTCCTTCCCGCCAAGAT TTCTTCGAAG bd1935 323 2.33e-05 TGGGAGAGAG TGTGCTCTGCCCACGGTTTAC GTAGTATGCC 25015 205 2.54e-05 CGAATACCAC TCTCCTCTTTGGTGCTGCCAT ACTGTTGTTA 20609 380 2.77e-05 CATGTTGTTG TCTCCTCCACCGCTACACCAA CAACCAAGTC 25267 55 4.19e-05 GAAGTAGGCA TCCCATTCATCATCTTCTTCG TCGTAGGGTG 25873 122 4.54e-05 TAGTGCTCAT GCTCACTCTCCGTCGTTTCGC TTGCACTTAA 24744 257 5.75e-05 TGAGAATGTG GCCCCTCAATCGACGCTTTTT TCCCTCAATC 2628 79 6.72e-05 TAGAGATGAC ACACATCCGTCCACAGCTCTG TATCGCACGA 12403 285 6.72e-05 AATAGACCTT TCTCATCAATCATACTAACAC CATTGCAAAC 10581 218 7.83e-05 CAACTTGCCT TCTGCGTTTGCCTGCTTCCAC AACCACAACC 24150 67 1.85e-04 CTTTGGAACC GGTGATCTTTGCTGGCTCTTC TTGGTGAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 985 4.4e-09 428_[+1]_51 bd923 2.3e-08 8_[+1]_471 9941 2.7e-08 413_[+1]_66 37758 3.3e-07 348_[+1]_131 10490 4.2e-07 165_[+1]_314 6924 1.4e-06 350_[+1]_129 24919 1.4e-06 318_[+1]_161 14225 1.4e-06 29_[+1]_450 6726 1.7e-06 391_[+1]_88 8344 2.1e-06 383_[+1]_96 37497 3.2e-06 443_[+1]_36 270332 3.2e-06 444_[+1]_35 269391 3.6e-06 94_[+1]_385 20832 3.6e-06 370_[+1]_109 3394 4e-06 458_[+1]_21 24515 4.4e-06 450_[+1]_29 1303 5.3e-06 405_[+1]_74 21622 7.9e-06 434_[+1]_45 21532 8.7e-06 195_[+1]_284 11162 9.5e-06 470_[+1]_9 38171 1.3e-05 212_[+1]_267 8405 1.6e-05 432_[+1]_47 269520 2e-05 179_[+1]_300 25748 2e-05 382_[+1]_97 bd1935 2.3e-05 322_[+1]_157 25015 2.5e-05 204_[+1]_275 20609 2.8e-05 379_[+1]_100 25267 4.2e-05 54_[+1]_425 25873 4.5e-05 121_[+1]_358 24744 5.8e-05 256_[+1]_223 2628 6.7e-05 78_[+1]_401 12403 6.7e-05 284_[+1]_195 10581 7.8e-05 217_[+1]_262 24150 0.00019 66_[+1]_413 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=34 985 ( 429) TCTCTTCCTTCCTCCGTCTTG 1 bd923 ( 9) CGTCCTCCGTCCTCCTCCTTG 1 9941 ( 414) TGTCCTCCCTCCTCCTCGTTC 1 37758 ( 349) TCTGATCCTTCTCCCTTCGTG 1 10490 ( 166) TGTCCTCCATCGTCGTTATAT 1 6924 ( 351) TCCCCTGTATCCTCCTCCCGT 1 24919 ( 319) CCTCAGCCCCCCCCCTATCTG 1 14225 ( 30) TCTGCTGTTTCCTCCTACCCT 1 6726 ( 392) TCTCTTATTCCCTCCTCTTTG 1 8344 ( 384) TCTCTTCCTTCTCTCTTTTGC 1 37497 ( 444) AGCCTTCCTCTCCCCTTCCAG 1 270332 ( 445) AGCCTTCCTCTCCCCTTCCAG 1 269391 ( 95) CGTCCTGCTTCGTCGTCCGTC 1 20832 ( 371) CCTCTTCCCCCCATCTCTCAT 1 3394 ( 459) TGTCCTCCTTCAACTCTCGTT 1 24515 ( 451) TCTTATCCATCCACCCATCCG 1 1303 ( 406) GCTCCCCCCCCCCCCGCCCGC 1 21622 ( 435) ACTCGGCCTGCCTCCTTCCAC 1 21532 ( 196) ACTCCTCCATCTCCATCAGCC 1 11162 ( 471) TATCCTCCACCCACATTGTCG 1 38171 ( 213) CGCCCTCCTCGCTCACTTTCC 1 8405 ( 433) TCTCTTTCACCACCACTGCTC 1 269520 ( 180) TGCCATCCGCCGTGCTATGTT 1 25748 ( 383) GCTGCTCCTTCCCGCCAAGAT 1 bd1935 ( 323) TGTGCTCTGCCCACGGTTTAC 1 25015 ( 205) TCTCCTCTTTGGTGCTGCCAT 1 20609 ( 380) TCTCCTCCACCGCTACACCAA 1 25267 ( 55) TCCCATTCATCATCTTCTTCG 1 25873 ( 122) GCTCACTCTCCGTCGTTTCGC 1 24744 ( 257) GCCCCTCAATCGACGCTTTTT 1 2628 ( 79) ACACATCCGTCCACAGCTCTG 1 12403 ( 285) TCTCATCAATCATACTAACAC 1 10581 ( 218) TCTGCGTTTGCCTGCTTCCAC 1 24150 ( 67) GGTGATCTTTGCTGGCTCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 8.97356 E= 3.2e-009 -80 -61 -78 106 -312 153 36 -1173 -312 -12 -1173 151 -1173 182 -52 -318 5 116 -310 -38 -1173 -193 -151 167 -312 177 -151 -119 -212 171 -1173 -38 20 -93 -110 81 -1173 77 -210 106 -1173 193 -151 -219 -112 139 -29 -160 -31 39 -1173 90 -312 171 -78 -160 -53 139 -52 -219 -1173 7 -110 127 -31 39 -310 81 -112 98 -151 40 -1173 107 -52 40 34 -35 -110 51 -312 77 36 -2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 34 E= 3.2e-009 0.147059 0.147059 0.147059 0.558824 0.029412 0.647059 0.323529 0.000000 0.029412 0.205882 0.000000 0.764706 0.000000 0.794118 0.176471 0.029412 0.264706 0.500000 0.029412 0.205882 0.000000 0.058824 0.088235 0.852941 0.029412 0.764706 0.088235 0.117647 0.058824 0.735294 0.000000 0.205882 0.294118 0.117647 0.117647 0.470588 0.000000 0.382353 0.058824 0.558824 0.000000 0.852941 0.088235 0.058824 0.117647 0.588235 0.205882 0.088235 0.205882 0.294118 0.000000 0.500000 0.029412 0.735294 0.147059 0.088235 0.176471 0.588235 0.176471 0.058824 0.000000 0.235294 0.117647 0.647059 0.205882 0.294118 0.029412 0.470588 0.117647 0.441176 0.088235 0.352941 0.000000 0.470588 0.176471 0.352941 0.323529 0.176471 0.117647 0.382353 0.029412 0.382353 0.323529 0.264706 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CG][TC]C[CAT]TC[CT][TA][TC]C[CG][TCA]CC[TC][TCA][CT][CT][TA][CGT] -------------------------------------------------------------------------------- Time 10.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 28 llr = 299 E-value = 1.0e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1321:31:4::::33:4413 pos.-specific C :1:1:::::3:2:::1:12: probability G 45389219156:94185236 matrix T 515:15815348136:1351 bits 2.2 1.9 1.7 1.5 * * Relative 1.3 * * ** Entropy 1.1 ** ** *** * (15.4 bits) 0.9 ** ** *** * 0.6 * ** *** *** *** * 0.4 ***************** * 0.2 ***************** ** 0.0 -------------------- Multilevel TGTGGTTGTGGTGGTGGATG consensus GAG A ATT AA ATGA sequence G C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25748 2 2.99e-08 G TGAGGATGTCTTGGTGGATG TGGATTTACG 37497 313 7.84e-08 GCGTAGTGAC TAGGGATGACGTGATGGCTG CGGCTACAGA 270332 314 7.84e-08 GCGTAGTGAC TAGGGATGACGTGATGGCTG CGGCTACAGA bd923 179 9.11e-08 CTGCTTTCCG TGGCGTTGTGGTGATGGACG TGTAGCGATT 9941 25 1.05e-07 TTGTCATCTT GATGGTTGTTGCGTTGATTG CTGTCATCGT 25267 401 2.11e-07 GTGTGGCTAT GGTGGTTGTTGTGTTGAGGT GGTTTGGAGA 20832 149 3.13e-07 CACGGCCGGG TGTGGTTGTGGTGATCGGAG ATAAAATGTG 8405 307 5.12e-07 CTTGCAGACG TGTGGGTGAGTTGGTGGAAT TCGCCTCGGC 269391 359 1.57e-06 AGGGGTTTAA TGTGTTGGAGTTGGTGGATG TCAATCAAGT 10581 321 1.57e-06 TTTTCATTTG GTTGGGTTTGGTGGTGGAGA CTGGCAGTAT 985 80 2.61e-06 GGATGGAGTT GGTGGATGTGGCGTACGTCG ATGACGGAGG 6726 205 2.88e-06 TGGACAACAG GATGGTTGTGGTGGAAAATA TATTCATCAT 25873 277 3.17e-06 GACTAATGAG TGGGGATTGTGTGTTGACTG TTTGCTATTT 25015 69 3.17e-06 TCTGGCAGTT GATCGTTGACTTGTTGATGA TGATGCACCG 8344 19 3.83e-06 GAGGCTCGTT GGTGGTTGGCGCGAAGATGA GCCATCGCTT 11162 191 6.04e-06 TGATTTGGGC TGTGGGAGATTTGGGGATTG ATCTTTGTGT 10490 206 6.59e-06 AGCCTCTGGC AGAGGTTGAGGTTGTGATGG CAACGTCTTT 21532 409 7.19e-06 AGGCCTCCCC TGAGGACGTCGTGATGTTTG TGTAACTAGA 269520 59 8.54e-06 GAATCACTTC GGAGGATGTTTTGAATGTTG GCTATGCGGT 2628 476 1.29e-05 TAGTGTTCTG TTGGGTTGTTGTGTACTCTG TTATT 1303 305 1.29e-05 CATGATCAGA TTTGGTTTGTGCGTTGGACG GCGGCAAGTT 38171 341 1.51e-05 CGGTGAGGAG GCTGGTTTTCTTTTTGGTTG ACAAGCGCGT 21622 7 1.89e-05 ACGTAC AGGCGGTGAGTTGGAGGAGA ATGGACGACA 6924 86 2.20e-05 AGGCTCTCAA GCAAGTTGTGTTGGAGGAGA GGTTGGAAGG 20609 158 2.73e-05 TTGAAAAGAG GATGGTGGTGGTGAGGAGCT TCATGTTCTC 24150 286 4.13e-05 GGGATTGAGG GAGATGTGAGGTGGTGGGTT AAATCACGCT 3394 98 6.47e-05 CAGATTCCCT TGGGTATGATGCGAGGAGCA CAAATCACTG 12403 205 6.87e-05 GTGATATGAT TTGGGGAGAGTTGTTGTAAA TCAATTATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25748 3e-08 1_[+2]_479 37497 7.8e-08 312_[+2]_168 270332 7.8e-08 313_[+2]_167 bd923 9.1e-08 178_[+2]_302 9941 1.1e-07 24_[+2]_456 25267 2.1e-07 400_[+2]_80 20832 3.1e-07 148_[+2]_332 8405 5.1e-07 306_[+2]_174 269391 1.6e-06 358_[+2]_122 10581 1.6e-06 320_[+2]_160 985 2.6e-06 79_[+2]_401 6726 2.9e-06 204_[+2]_276 25873 3.2e-06 276_[+2]_204 25015 3.2e-06 68_[+2]_412 8344 3.8e-06 18_[+2]_462 11162 6e-06 190_[+2]_290 10490 6.6e-06 205_[+2]_275 21532 7.2e-06 408_[+2]_72 269520 8.5e-06 58_[+2]_422 2628 1.3e-05 475_[+2]_5 1303 1.3e-05 304_[+2]_176 38171 1.5e-05 340_[+2]_140 21622 1.9e-05 6_[+2]_474 6924 2.2e-05 85_[+2]_395 20609 2.7e-05 157_[+2]_323 24150 4.1e-05 285_[+2]_195 3394 6.5e-05 97_[+2]_383 12403 6.9e-05 204_[+2]_276 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=28 25748 ( 2) TGAGGATGTCTTGGTGGATG 1 37497 ( 313) TAGGGATGACGTGATGGCTG 1 270332 ( 314) TAGGGATGACGTGATGGCTG 1 bd923 ( 179) TGGCGTTGTGGTGATGGACG 1 9941 ( 25) GATGGTTGTTGCGTTGATTG 1 25267 ( 401) GGTGGTTGTTGTGTTGAGGT 1 20832 ( 149) TGTGGTTGTGGTGATCGGAG 1 8405 ( 307) TGTGGGTGAGTTGGTGGAAT 1 269391 ( 359) TGTGTTGGAGTTGGTGGATG 1 10581 ( 321) GTTGGGTTTGGTGGTGGAGA 1 985 ( 80) GGTGGATGTGGCGTACGTCG 1 6726 ( 205) GATGGTTGTGGTGGAAAATA 1 25873 ( 277) TGGGGATTGTGTGTTGACTG 1 25015 ( 69) GATCGTTGACTTGTTGATGA 1 8344 ( 19) GGTGGTTGGCGCGAAGATGA 1 11162 ( 191) TGTGGGAGATTTGGGGATTG 1 10490 ( 206) AGAGGTTGAGGTTGTGATGG 1 21532 ( 409) TGAGGACGTCGTGATGTTTG 1 269520 ( 59) GGAGGATGTTTTGAATGTTG 1 2628 ( 476) TTGGGTTGTTGTGTACTCTG 1 1303 ( 305) TTTGGTTTGTGCGTTGGACG 1 38171 ( 341) GCTGGTTTTCTTTTTGGTTG 1 21622 ( 7) AGGCGGTGAGTTGGAGGAGA 1 6924 ( 86) GCAAGTTGTGTTGGAGGAGA 1 20609 ( 158) GATGGTGGTGGTGAGGAGCT 1 24150 ( 286) GAGATGTGAGGTGGTGGGTT 1 3394 ( 98) TGGGTATGATGCGAGGAGCA 1 12403 ( 205) TTGGGGAGAGTTGTTGTAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 16354 bayes= 9.7941 E= 1.0e-006 -184 -1145 76 90 -3 -165 109 -91 -52 -1145 35 90 -184 -107 170 -1145 -1145 -1145 182 -132 16 -1145 -24 90 -184 -265 -182 162 -1145 -1145 176 -91 62 -1145 -123 90 -1145 16 88 9 -1145 -1145 135 41 -1145 -33 -1145 162 -1145 -1145 188 -191 33 -1145 50 26 -3 -1145 -123 126 -284 -107 170 -290 48 -1145 109 -132 48 -65 -50 26 -125 -33 -1 79 16 -1145 118 -91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 28 E= 1.0e-006 0.071429 0.000000 0.428571 0.500000 0.250000 0.071429 0.535714 0.142857 0.178571 0.000000 0.321429 0.500000 0.071429 0.107143 0.821429 0.000000 0.000000 0.000000 0.892857 0.107143 0.285714 0.000000 0.214286 0.500000 0.071429 0.035714 0.071429 0.821429 0.000000 0.000000 0.857143 0.142857 0.392857 0.000000 0.107143 0.500000 0.000000 0.250000 0.464286 0.285714 0.000000 0.000000 0.642857 0.357143 0.000000 0.178571 0.000000 0.821429 0.000000 0.000000 0.928571 0.071429 0.321429 0.000000 0.357143 0.321429 0.250000 0.000000 0.107143 0.642857 0.035714 0.107143 0.821429 0.035714 0.357143 0.000000 0.535714 0.107143 0.357143 0.142857 0.178571 0.321429 0.107143 0.178571 0.250000 0.464286 0.285714 0.000000 0.571429 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GA][TG]GG[TAG]TG[TA][GTC][GT]TG[GAT][TA]G[GA][AT][TG][GA] -------------------------------------------------------------------------------- Time 20.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 9 llr = 130 E-value = 1.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3a:7::8::41:9:: pos.-specific C 6:9:aa:99:7814a probability G ::11::2::422:3: matrix T 1::2:::111:::2: bits 2.2 ** * 1.9 * ** * 1.7 ** ** ** * 1.5 ** ** ** * * Relative 1.3 ** ***** ** * Entropy 1.1 ** ***** ** * (20.8 bits) 0.9 ** ***** *** * 0.6 ************* * 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CACACCACCACCACC consensus A T G GGG G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 9941 454 1.71e-08 TACCCGCAGA CACACCACCGCCCCC TGTTGTGTGG 37497 6 2.06e-08 ACTAG AACACCACCACGACC CTGCCGAGGA 270332 7 2.06e-08 CACTAG AACACCACCACGACC CTGCCGAGGA 8344 80 8.34e-08 CGGCGGCTGA CACACCATCACCATC TGCAACTGCA 24744 461 1.75e-07 CCGTCAATTG CACTCCGCCGGCAGC ATCAAGACGA 6924 393 2.23e-07 TCTTCCTTCT CAGACCACCTCCAGC AAGCTCACAT 1303 461 2.23e-07 AGGACCTGTC AACTCCACTGCCACC CGCTGCCTAC bd923 46 3.18e-07 TCGCAACAAA TACACCGCCAGCAGC CAGCAAACGG 269520 456 3.18e-07 TTCTACACAT CACGCCACCGACATC TACTACTCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9941 1.7e-08 453_[+3]_32 37497 2.1e-08 5_[+3]_480 270332 2.1e-08 6_[+3]_479 8344 8.3e-08 79_[+3]_406 24744 1.7e-07 460_[+3]_25 6924 2.2e-07 392_[+3]_93 1303 2.2e-07 460_[+3]_25 bd923 3.2e-07 45_[+3]_440 269520 3.2e-07 455_[+3]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=9 9941 ( 454) CACACCACCGCCCCC 1 37497 ( 6) AACACCACCACGACC 1 270332 ( 7) AACACCACCACGACC 1 8344 ( 80) CACACCATCACCATC 1 24744 ( 461) CACTCCGCCGGCAGC 1 6924 ( 393) CAGACCACCTCCAGC 1 1303 ( 461) AACTCCACTGCCACC 1 bd923 ( 46) TACACCGCCAGCAGC 1 269520 ( 456) CACGCCACCGACATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 16524 bayes= 10.9759 E= 1.9e-002 38 131 -982 -127 197 -982 -982 -982 -982 198 -118 -982 138 -982 -118 -27 -982 215 -982 -982 -982 215 -982 -982 161 -982 -18 -982 -982 198 -982 -127 -982 198 -982 -127 80 -982 82 -127 -120 157 -18 -982 -982 179 -18 -982 180 -101 -982 -982 -982 99 40 -27 -982 215 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.9e-002 0.333333 0.555556 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.666667 0.000000 0.111111 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.444444 0.000000 0.444444 0.111111 0.111111 0.666667 0.222222 0.000000 0.000000 0.777778 0.222222 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.444444 0.333333 0.222222 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA]AC[AT]CC[AG]CC[AG][CG][CG]A[CGT]C -------------------------------------------------------------------------------- Time 29.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10490 3.98e-05 165_[+1(4.24e-07)]_19_\ [+2(6.59e-06)]_275 10581 2.75e-04 217_[+1(7.83e-05)]_82_\ [+2(1.57e-06)]_160 11162 6.82e-04 190_[+2(6.04e-06)]_260_\ [+1(9.52e-06)]_9 12403 3.34e-03 204_[+2(6.87e-05)]_60_\ [+1(6.72e-05)]_195 1303 3.86e-07 304_[+2(1.29e-05)]_81_\ [+1(5.34e-06)]_34_[+3(2.23e-07)]_25 14225 1.50e-02 29_[+1(1.37e-06)]_37_[+1(6.50e-06)]_\ 392 20609 2.97e-03 157_[+2(2.73e-05)]_202_\ [+1(2.77e-05)]_100 20832 1.17e-05 148_[+2(3.13e-07)]_202_\ [+1(3.57e-06)]_109 21532 5.25e-05 195_[+1(8.66e-06)]_192_\ [+2(7.19e-06)]_72 21622 1.46e-04 6_[+2(1.89e-05)]_408_[+1(7.88e-06)]_\ 45 24150 3.65e-02 285_[+2(4.13e-05)]_195 24515 3.06e-03 450_[+1(4.38e-06)]_29 24744 5.62e-05 256_[+1(5.75e-05)]_183_\ [+3(1.75e-07)]_25 24919 8.92e-03 318_[+1(1.37e-06)]_161 25015 1.02e-03 68_[+2(3.17e-06)]_116_\ [+1(2.54e-05)]_275 25267 1.52e-04 54_[+1(4.19e-05)]_144_\ [+2(3.61e-05)]_161_[+2(2.11e-07)]_80 25748 8.94e-06 1_[+2(2.99e-08)]_237_[+2(1.89e-05)]_\ 104_[+1(1.96e-05)]_97 25873 5.78e-04 121_[+1(4.54e-05)]_134_\ [+2(3.17e-06)]_204 2628 2.95e-03 78_[+1(6.72e-05)]_376_\ [+2(1.29e-05)]_5 269391 3.68e-06 70_[+3(3.37e-05)]_9_[+1(3.57e-06)]_\ 243_[+2(1.57e-06)]_122 269520 1.18e-06 58_[+2(8.54e-06)]_101_\ [+1(1.96e-05)]_255_[+3(3.18e-07)]_30 270332 2.48e-10 6_[+3(2.06e-08)]_292_[+2(7.84e-08)]_\ 111_[+1(3.22e-06)]_35 3394 2.88e-03 97_[+2(6.47e-05)]_341_\ [+1(3.96e-06)]_21 37497 2.48e-10 5_[+3(2.06e-08)]_292_[+2(7.84e-08)]_\ 111_[+1(3.22e-06)]_36 37758 9.31e-04 348_[+1(3.31e-07)]_131 38171 2.95e-04 212_[+1(1.26e-05)]_107_\ [+2(1.51e-05)]_140 6726 7.31e-05 204_[+2(2.88e-06)]_167_\ [+1(1.70e-06)]_88 6924 1.82e-07 85_[+2(2.20e-05)]_245_\ [+1(1.37e-06)]_21_[+3(2.23e-07)]_93 8344 2.24e-08 18_[+2(3.83e-06)]_41_[+3(8.34e-08)]_\ 289_[+1(2.11e-06)]_96 8405 1.30e-04 306_[+2(5.12e-07)]_106_\ [+1(1.65e-05)]_47 985 4.34e-07 79_[+2(2.61e-06)]_329_\ [+1(4.44e-09)]_51 9941 3.18e-12 24_[+2(1.05e-07)]_369_\ [+1(2.74e-08)]_19_[+3(1.71e-08)]_32 bd1935 6.84e-02 322_[+1(2.33e-05)]_157 bd923 3.71e-11 8_[+1(2.34e-08)]_16_[+3(3.18e-07)]_\ 118_[+2(9.11e-08)]_302 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************