******************************************************************************** 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/388/388.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31764 1.0000 500 8737 1.0000 500 46405 1.0000 500 46694 1.0000 500 47242 1.0000 500 28689 1.0000 500 47759 1.0000 500 5060 1.0000 500 48135 1.0000 500 15031 1.0000 500 3182 1.0000 500 48473 1.0000 500 15229 1.0000 500 48720 1.0000 500 15699 1.0000 500 49419 1.0000 500 16155 1.0000 500 49801 1.0000 500 16509 1.0000 500 40930 1.0000 500 16560 1.0000 500 41094 1.0000 500 10293 1.0000 500 50613 1.0000 500 44502 1.0000 500 6032 1.0000 500 44977 1.0000 500 54343 1.0000 500 19659 1.0000 500 35473 1.0000 500 12510 1.0000 500 31658 1.0000 500 31819 1.0000 500 39646 1.0000 500 33598 1.0000 500 46398 1.0000 500 46457 1.0000 500 45475 1.0000 500 48427 1.0000 500 49889 1.0000 500 47217 1.0000 500 49475 1.0000 500 49213 1.0000 500 39883 1.0000 500 48255 1.0000 500 49682 1.0000 500 47647 1.0000 500 48149 1.0000 500 48055 1.0000 500 45827 1.0000 500 35839 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/388/388.seqs.fa -oc motifs/388 -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= 51 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= 25500 N= 51 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.253 C 0.253 G 0.236 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.253 G 0.236 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 34 llr = 317 E-value = 3.8e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 46:::9:4:::a pos.-specific C 123:4:91::4: probability G 32314:11a:5: matrix T 314921:5:a1: bits 2.1 * * 1.9 ** * 1.7 * * ** * 1.5 * ** ** * Relative 1.2 * ** ** * Entropy 1.0 * ** ** * (13.5 bits) 0.8 * ** ** * 0.6 * ** **** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel AATTGACTGTGA consensus T C C A C sequence G G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 49475 18 1.18e-07 AGATAAGCAG AATTGACAGTGA CTGTCAATGA 48720 139 1.18e-07 TACCCAGTGC AATTGACAGTGA GTAGCCTGAT 35473 60 1.37e-06 AGTCCAAATC GACTGACTGTGA TCGTGAGTAA 16560 157 1.37e-06 TTATACAACG AACTCACAGTGA CAGCCCGTAC 47242 40 1.37e-06 AGTCCAAATC GACTGACTGTGA TCGCGAGTAA 47217 426 3.17e-06 CCGTACCGGC AACTCACTGTCA CTTTCACCGT 44977 197 3.17e-06 ACAGGTAAGA TATTCACTGTCA GTTGGTTTTT 35839 113 3.80e-06 CGGGAGATTG AAGTCACTGTCA ATCACCGGGT 40930 142 3.80e-06 GGGTTGACCA AACTCACAGTCA ACTTCAACTT 45475 342 5.67e-06 TATCATACCT AGCTGACTGTGA CAGTAACTAA 50613 284 5.67e-06 TCTTTGATCC AATTTACAGTCA CAGTCAGTCA 19659 145 6.48e-06 CACGATTCGT GCTTGACTGTGA GGAGTAGGTG 16509 280 6.48e-06 TCGTATGGAC TCTTGACTGTGA GAGTGACAGA 49419 338 6.48e-06 ATCGTGTCTT GCTTGACTGTGA GTTTCTGCCA 16155 298 1.38e-05 AAGTGTTTCG TCGTCACTGTGA AACCATGCCC 46694 18 1.55e-05 AGAACAAAGC TTTTGACTGTGA ATATTAAAGC 15031 439 1.94e-05 CTAGAACTTA GAGTGACAGTTA AAACTGTCAA 54343 278 2.34e-05 TCCAGCTCTA TGGTCACAGTCA GAATGTCGCG 31658 331 2.56e-05 AAGTGACTGA TATTTACTGTTA GGAACGCGAT 48055 403 2.80e-05 GTATTCGCCG TAGTGACGGTGA GGGTCCACGC 48135 149 2.80e-05 AGCGCAAATC TGTTTACAGTCA ACGTTAACAT 31819 353 3.24e-05 GGACGGGGGA CACTCACAGTCA CATCACGGAC 44502 255 4.84e-05 TGGCCAGAAA AAGTCTCTGTGA CAGGCAGTTT 48427 187 5.18e-05 TCGTAGATCG AGTTTACAGTTA CCTCGTCGAG 15699 178 5.18e-05 GAAGGGACGA GAGTGTCTGTGA GGCGACCTTT 39883 269 5.94e-05 CAAATGATGC TACTTAGAGTGA ACACGTTCTG 46398 240 5.94e-05 TCCCCACTAC GGCTGACCGTGA AAGCGCGCAC 10293 279 6.87e-05 AAAAATCGGC AACTTAGAGTCA GATCTCGCCT 48255 295 7.31e-05 TGAAATGAAC ACGTCAGTGTGA CATACATCGA 45827 73 8.43e-05 AAGGTAACCG AGGGGACTGTGA CGCGGGAAGA 49682 129 1.07e-04 CTTCGTGTCA GTTTTACAGTTA GTACCGGTAC 47759 453 1.07e-04 AGCATAGAGT CATTCACCGTCA ATCGTATAAG 49889 432 1.27e-04 ACAAGAAGTA TTTTCACGGTCA GGTAATGTAA 47647 183 1.57e-04 GAACGCCGGT GCCGCACAGTCA AGCCAGCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49475 1.2e-07 17_[+1]_471 48720 1.2e-07 138_[+1]_350 35473 1.4e-06 59_[+1]_429 16560 1.4e-06 156_[+1]_332 47242 1.4e-06 39_[+1]_449 47217 3.2e-06 425_[+1]_63 44977 3.2e-06 196_[+1]_292 35839 3.8e-06 112_[+1]_376 40930 3.8e-06 141_[+1]_347 45475 5.7e-06 341_[+1]_147 50613 5.7e-06 283_[+1]_205 19659 6.5e-06 144_[+1]_344 16509 6.5e-06 279_[+1]_209 49419 6.5e-06 337_[+1]_151 16155 1.4e-05 297_[+1]_191 46694 1.5e-05 17_[+1]_471 15031 1.9e-05 438_[+1]_50 54343 2.3e-05 277_[+1]_211 31658 2.6e-05 330_[+1]_158 48055 2.8e-05 402_[+1]_86 48135 2.8e-05 148_[+1]_340 31819 3.2e-05 352_[+1]_136 44502 4.8e-05 254_[+1]_234 48427 5.2e-05 186_[+1]_302 15699 5.2e-05 177_[+1]_311 39883 5.9e-05 268_[+1]_220 46398 5.9e-05 239_[+1]_249 10293 6.9e-05 278_[+1]_210 48255 7.3e-05 294_[+1]_194 45827 8.4e-05 72_[+1]_416 49682 0.00011 128_[+1]_360 47759 0.00011 452_[+1]_36 49889 0.00013 431_[+1]_57 47647 0.00016 182_[+1]_306 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=34 49475 ( 18) AATTGACAGTGA 1 48720 ( 139) AATTGACAGTGA 1 35473 ( 60) GACTGACTGTGA 1 16560 ( 157) AACTCACAGTGA 1 47242 ( 40) GACTGACTGTGA 1 47217 ( 426) AACTCACTGTCA 1 44977 ( 197) TATTCACTGTCA 1 35839 ( 113) AAGTCACTGTCA 1 40930 ( 142) AACTCACAGTCA 1 45475 ( 342) AGCTGACTGTGA 1 50613 ( 284) AATTTACAGTCA 1 19659 ( 145) GCTTGACTGTGA 1 16509 ( 280) TCTTGACTGTGA 1 49419 ( 338) GCTTGACTGTGA 1 16155 ( 298) TCGTCACTGTGA 1 46694 ( 18) TTTTGACTGTGA 1 15031 ( 439) GAGTGACAGTTA 1 54343 ( 278) TGGTCACAGTCA 1 31658 ( 331) TATTTACTGTTA 1 48055 ( 403) TAGTGACGGTGA 1 48135 ( 149) TGTTTACAGTCA 1 31819 ( 353) CACTCACAGTCA 1 44502 ( 255) AAGTCTCTGTGA 1 48427 ( 187) AGTTTACAGTTA 1 15699 ( 178) GAGTGTCTGTGA 1 39883 ( 269) TACTTAGAGTGA 1 46398 ( 240) GGCTGACCGTGA 1 10293 ( 279) AACTTAGAGTCA 1 48255 ( 295) ACGTCAGTGTGA 1 45827 ( 73) AGGGGACTGTGA 1 49682 ( 129) GTTTTACAGTTA 1 47759 ( 453) CATTCACCGTCA 1 49889 ( 432) TTTTCACGGTCA 1 47647 ( 183) GCCGCACAGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 24939 bayes= 10.3122 E= 3.8e-008 59 -211 16 19 114 -52 -42 -154 -1173 35 16 68 -1173 -1173 -200 187 -1173 59 80 -32 189 -1173 -1173 -213 -1173 185 -142 -1173 70 -211 -200 87 -1173 -1173 208 -1173 -1173 -1173 -1173 196 -1173 48 116 -113 198 -1173 -1173 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 34 E= 3.8e-008 0.382353 0.058824 0.264706 0.294118 0.558824 0.176471 0.176471 0.088235 0.000000 0.323529 0.264706 0.411765 0.000000 0.000000 0.058824 0.941176 0.000000 0.382353 0.411765 0.205882 0.941176 0.000000 0.000000 0.058824 0.000000 0.911765 0.088235 0.000000 0.411765 0.058824 0.058824 0.470588 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.352941 0.529412 0.117647 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ATG]A[TCG]T[GCT]AC[TA]GT[GC]A -------------------------------------------------------------------------------- Time 19.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 27 llr = 278 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::1:::31::::23 pos.-specific C :22::4:::8:::314 probability G 2:8114613164317: matrix T 77:97139414677:3 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 TTGTTGGTTCGTTTGC consensus GC CT G TGGC A sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 48720 308 3.45e-09 GTTTGTTTGT TTGTTCGTTCGGTTGC CAGAGAAGCA 15699 83 4.00e-08 CTTTCTGAGA TTGTTGTTGCTGTTGC TGCTGATACC 46405 165 3.35e-07 GTTTGTGGAG TTGTTCGTTCTTGCGA ACGTCCTTTT 31819 88 6.32e-07 CTGCCTGCCG TCGTTGGTTCGGTTCC GTTGCTCTAC 47759 184 6.32e-07 TCGAATGGTT TTGTTGGGTCGGTTGT GGAGCTTTCT 40930 294 1.01e-06 AGTACCGACA GTGTTTGTTCGTTCGT CCCCACCACG 49801 417 1.28e-06 GACACACGGT TCGTTGGTACGGTTCC GGTCACTCTT 45827 98 1.43e-06 GGGAAGACCA GTGTTCGTTCGTTGGA ACGAACCTTG 44502 180 1.98e-06 CTCGGTGAGC TTGTTTGTACTTTTCT AGAACTGTAA 39883 212 3.32e-06 CGTTAAAATT TTGTTGTTTAGTTTAA ATAGTTTGAA 48255 219 4.92e-06 TCCTATCGTT TTCTTCATGCTTTTGC TTCTTTCTTA 35839 432 5.41e-06 ACTTGTGTGT GTGTTGGTGTGTGTGA GTGAGTGTGT 45475 169 5.41e-06 TTTGGCAGTG TTGTTGGTTCGGGCTC TCTCGGATAG 41094 43 5.41e-06 CAATTATGAT TCGTGGTTGCGTGTGT GTTTGTCGAT 47242 250 5.92e-06 GCCAGTGAAA TTGTGCTTTGGTTTGA TGCAACTGAC 49682 254 6.51e-06 CGAGACGGTG GTGTGCGTACGGTCGT GATGTGTCTC 48055 104 1.20e-05 ACGGTTAGTA TGGTAGGTGCGTGTGC CTCTCCCATG 47217 222 1.31e-05 TTCGTGAGCG TCCGTCGTGCGTTTGT CAACCGTTGC 16155 434 1.54e-05 TACATTAGTT TTCTTCGTTCTGTGAT AGAGTGTGCA 48427 152 2.11e-05 GTAATTGCTA ATGTAGGTACTTGTGC TGCGTTGAGT 44977 385 2.11e-05 AGAGTGGGTT TTTTTGGTACTGTTGG AGCGAACGTC 15229 96 2.65e-05 GGCGTGATCG GTGTTGTTAGGTGTAC ACATGTGTTC 49475 214 3.08e-05 AGTCTACATC TCGTGTTTACTGTTAC AGCTAGGTAG 46457 196 3.08e-05 TTCGTGTCCA TCCTTCGTGATTTCGA AACCGTACGG 39646 93 3.08e-05 GGCTGGCTGG TTGTTATGGCTTTCGC AACATCGTCA 15031 223 4.38e-05 ACGCTGTCGA TTCGACTTTCTTTTGA AAGAGCATCT 49213 101 5.02e-05 TAATAGGAGC GTGTTTTTTTTTTCAC ACACCCAACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48720 3.5e-09 307_[+2]_177 15699 4e-08 82_[+2]_402 46405 3.4e-07 164_[+2]_320 31819 6.3e-07 87_[+2]_397 47759 6.3e-07 183_[+2]_301 40930 1e-06 293_[+2]_191 49801 1.3e-06 416_[+2]_68 45827 1.4e-06 97_[+2]_387 44502 2e-06 179_[+2]_305 39883 3.3e-06 211_[+2]_273 48255 4.9e-06 218_[+2]_266 35839 5.4e-06 431_[+2]_53 45475 5.4e-06 168_[+2]_316 41094 5.4e-06 42_[+2]_442 47242 5.9e-06 249_[+2]_235 49682 6.5e-06 253_[+2]_231 48055 1.2e-05 103_[+2]_381 47217 1.3e-05 221_[+2]_263 16155 1.5e-05 433_[+2]_51 48427 2.1e-05 151_[+2]_333 44977 2.1e-05 384_[+2]_100 15229 2.7e-05 95_[+2]_389 49475 3.1e-05 213_[+2]_271 46457 3.1e-05 195_[+2]_289 39646 3.1e-05 92_[+2]_392 15031 4.4e-05 222_[+2]_262 49213 5e-05 100_[+2]_384 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=27 48720 ( 308) TTGTTCGTTCGGTTGC 1 15699 ( 83) TTGTTGTTGCTGTTGC 1 46405 ( 165) TTGTTCGTTCTTGCGA 1 31819 ( 88) TCGTTGGTTCGGTTCC 1 47759 ( 184) TTGTTGGGTCGGTTGT 1 40930 ( 294) GTGTTTGTTCGTTCGT 1 49801 ( 417) TCGTTGGTACGGTTCC 1 45827 ( 98) GTGTTCGTTCGTTGGA 1 44502 ( 180) TTGTTTGTACTTTTCT 1 39883 ( 212) TTGTTGTTTAGTTTAA 1 48255 ( 219) TTCTTCATGCTTTTGC 1 35839 ( 432) GTGTTGGTGTGTGTGA 1 45475 ( 169) TTGTTGGTTCGGGCTC 1 41094 ( 43) TCGTGGTTGCGTGTGT 1 47242 ( 250) TTGTGCTTTGGTTTGA 1 49682 ( 254) GTGTGCGTACGGTCGT 1 48055 ( 104) TGGTAGGTGCGTGTGC 1 47217 ( 222) TCCGTCGTGCGTTTGT 1 16155 ( 434) TTCTTCGTTCTGTGAT 1 48427 ( 152) ATGTAGGTACTTGTGC 1 44977 ( 385) TTTTTGGTACTGTTGG 1 15229 ( 96) GTGTTGTTAGGTGTAC 1 49475 ( 214) TCGTGTTTACTGTTAC 1 46457 ( 196) TCCTTCGTGATTTCGA 1 39646 ( 93) TTGTTATGGCTTTCGC 1 15031 ( 223) TTCGACTTTCTTTTGA 1 49213 ( 101) GTGTTTTTTTTTTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 24735 bayes= 10.4073 E= 1.2e+001 -277 -1140 -9 153 -1140 -19 -267 153 -1140 -45 172 -279 -1140 -1140 -167 185 -119 -1140 -67 153 -277 55 91 -80 -277 -1140 141 37 -1140 -1140 -167 185 3 -1140 33 79 -177 162 -167 -179 -1140 -1140 123 79 -1140 -1140 65 129 -1140 -1140 13 153 -1140 3 -167 137 -45 -119 150 -279 3 81 -267 1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 27 E= 1.2e+001 0.037037 0.000000 0.222222 0.740741 0.000000 0.222222 0.037037 0.740741 0.000000 0.185185 0.777778 0.037037 0.000000 0.000000 0.074074 0.925926 0.111111 0.000000 0.148148 0.740741 0.037037 0.370370 0.444444 0.148148 0.037037 0.000000 0.629630 0.333333 0.000000 0.000000 0.074074 0.925926 0.259259 0.000000 0.296296 0.444444 0.074074 0.777778 0.074074 0.074074 0.000000 0.000000 0.555556 0.444444 0.000000 0.000000 0.370370 0.629630 0.000000 0.000000 0.259259 0.740741 0.000000 0.259259 0.074074 0.666667 0.185185 0.111111 0.666667 0.037037 0.259259 0.444444 0.037037 0.259259 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][TC]GTT[GC][GT]T[TGA]C[GT][TG][TG][TC]G[CAT] -------------------------------------------------------------------------------- Time 42.79 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 93 E-value = 5.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::a:::::5::55:::8a pos.-specific C a:5:a:a8:8:5:3:3a3a:: probability G :a:a::::a3a:a::::8:3: matrix T ::5::::3:::::853::::: bits 2.1 ** **** * * * * * * 1.9 ** **** * * * * * * 1.7 ** **** * * * * * * 1.5 ** **** * * * * * * Relative 1.2 ** ******** ** ***** Entropy 1.0 *************** ***** (33.6 bits) 0.8 *************** ***** 0.6 *************** ***** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGCGCACCGCGAGTAACGCAA consensus T T G C CTC C G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35473 109 1.59e-12 ACACATTCTA CGTGCACCGCGAGTAACGCAA ATACCTAGCT 47242 89 1.59e-12 ACACATTCTA CGTGCACCGCGAGTAACGCAA ATACCTGGCT 47217 107 2.50e-11 ACCGGATGTG CGCGCACCGCGCGCTCCGCAA TCGAAGTGAC 8737 278 1.37e-10 GGAAGCCGTA CGCGCACTGGGCGTTTCCCGA CGACGATTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35473 1.6e-12 108_[+3]_371 47242 1.6e-12 88_[+3]_391 47217 2.5e-11 106_[+3]_373 8737 1.4e-10 277_[+3]_202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 35473 ( 109) CGTGCACCGCGAGTAACGCAA 1 47242 ( 89) CGTGCACCGCGAGTAACGCAA 1 47217 ( 107) CGCGCACCGCGCGCTCCGCAA 1 8737 ( 278) CGCGCACTGGGCGTTTCCCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24480 bayes= 12.5791 E= 5.3e+002 -865 198 -865 -865 -865 -865 208 -865 -865 98 -865 96 -865 -865 208 -865 -865 198 -865 -865 198 -865 -865 -865 -865 198 -865 -865 -865 156 -865 -4 -865 -865 208 -865 -865 156 8 -865 -865 -865 208 -865 98 98 -865 -865 -865 -865 208 -865 -865 -2 -865 154 98 -865 -865 96 98 -2 -865 -4 -865 198 -865 -865 -865 -2 166 -865 -865 198 -865 -865 156 -865 8 -865 198 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 5.3e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.500000 0.000000 0.000000 0.500000 0.500000 0.250000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CG[CT]GCAC[CT]G[CG]G[AC]G[TC][AT][ACT]C[GC]C[AG]A -------------------------------------------------------------------------------- Time 64.33 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31764 8.01e-01 500 8737 7.98e-06 277_[+3(1.37e-10)]_202 46405 6.25e-03 164_[+2(3.35e-07)]_320 46694 9.38e-02 17_[+1(1.55e-05)]_471 47242 9.04e-13 39_[+1(1.37e-06)]_37_[+3(1.59e-12)]_\ 140_[+2(5.92e-06)]_235 28689 9.07e-01 500 47759 9.51e-04 183_[+2(6.32e-07)]_301 5060 2.28e-01 432_[+3(5.28e-05)]_47 48135 6.05e-02 148_[+1(2.80e-05)]_340 15031 1.22e-03 222_[+2(4.38e-05)]_200_\ [+1(1.94e-05)]_50 3182 5.81e-01 500 48473 4.09e-01 500 15229 4.41e-02 95_[+2(2.65e-05)]_389 48720 2.57e-08 138_[+1(1.18e-07)]_76_\ [+1(4.45e-06)]_53_[+2(1.28e-06)]_[+2(3.45e-09)]_177 15699 4.24e-05 82_[+2(4.00e-08)]_79_[+1(5.18e-05)]_\ 88_[+2(2.86e-05)]_207 49419 2.85e-02 337_[+1(6.48e-06)]_151 16155 2.97e-03 297_[+1(1.38e-05)]_124_\ [+2(1.54e-05)]_51 49801 4.34e-04 416_[+2(1.28e-06)]_68 16509 3.92e-02 279_[+1(6.48e-06)]_209 40930 1.06e-05 141_[+1(3.80e-06)]_140_\ [+2(1.01e-06)]_145_[+2(2.71e-06)]_30 16560 8.70e-04 114_[+1(3.56e-05)]_30_\ [+1(1.37e-06)]_29_[+1(8.43e-05)]_264_[+3(5.28e-05)]_6 41094 2.49e-02 42_[+2(5.41e-06)]_442 10293 1.87e-01 278_[+1(6.87e-05)]_210 50613 2.34e-02 283_[+1(5.67e-06)]_205 44502 7.21e-04 179_[+2(1.98e-06)]_59_\ [+1(4.84e-05)]_234 6032 5.74e-01 500 44977 1.09e-03 87_[+1(5.67e-06)]_97_[+1(3.17e-06)]_\ 176_[+2(2.11e-05)]_100 54343 1.03e-02 277_[+1(2.34e-05)]_211 19659 4.95e-02 144_[+1(6.48e-06)]_14_\ [+1(1.55e-05)]_318 35473 2.01e-11 59_[+1(1.37e-06)]_37_[+3(1.59e-12)]_\ 371 12510 2.61e-01 500 31658 1.31e-01 330_[+1(2.56e-05)]_158 31819 1.74e-04 87_[+2(6.32e-07)]_249_\ [+1(3.24e-05)]_136 39646 1.05e-01 92_[+2(3.08e-05)]_392 33598 4.60e-01 500 46398 6.31e-02 239_[+1(5.94e-05)]_249 46457 8.31e-02 195_[+2(3.08e-05)]_289 45475 5.20e-04 168_[+2(5.41e-06)]_157_\ [+1(5.67e-06)]_147 48427 1.06e-02 151_[+2(2.11e-05)]_19_\ [+1(5.18e-05)]_302 49889 2.19e-01 500 47217 5.57e-11 106_[+3(2.50e-11)]_94_\ [+2(1.31e-05)]_50_[+1(4.94e-06)]_126_[+1(3.17e-06)]_63 49475 8.48e-05 17_[+1(1.18e-07)]_83_[+1(5.67e-06)]_\ 89_[+2(3.08e-05)]_7_[+1(3.56e-05)]_252 49213 1.50e-01 100_[+2(5.02e-05)]_384 39883 2.29e-03 211_[+2(3.32e-06)]_41_\ [+1(5.94e-05)]_220 48255 4.39e-03 218_[+2(4.92e-06)]_60_\ [+1(7.31e-05)]_194 49682 1.67e-03 253_[+2(6.51e-06)]_231 47647 2.01e-01 500 48149 3.12e-01 500 48055 3.98e-03 103_[+2(1.20e-05)]_283_\ [+1(2.80e-05)]_86 45827 1.32e-03 72_[+1(8.43e-05)]_13_[+2(1.43e-06)]_\ 387 35839 1.96e-04 112_[+1(3.80e-06)]_307_\ [+2(5.41e-06)]_4_[+2(5.37e-05)]_33 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************