******************************************************************************** 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/123/123.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11390 1.0000 500 1288 1.0000 500 1799 1.0000 500 1855 1.0000 500 18665 1.0000 500 1954 1.0000 500 1955 1.0000 500 2215 1.0000 500 2292 1.0000 500 23275 1.0000 500 25001 1.0000 500 262320 1.0000 500 264341 1.0000 500 3146 1.0000 500 31757 1.0000 500 3230 1.0000 500 33019 1.0000 500 3422 1.0000 500 35810 1.0000 500 3725 1.0000 500 4296 1.0000 500 4323 1.0000 500 4894 1.0000 500 5339 1.0000 500 6043 1.0000 500 6996 1.0000 500 7166 1.0000 500 7353 1.0000 500 8487 1.0000 500 8689 1.0000 500 8749 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/123/123.seqs.fa -oc motifs/123 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.215 G 0.262 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.215 G 0.262 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 14 llr = 204 E-value = 7.3e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 511::::1::::14::1:::1 pos.-specific C 21:41181:61:64:5::814 probability G 31641:27:13::2112:14: matrix T :63199:1a36a21947a145 bits 2.2 2.0 * * * 1.8 * * * 1.6 * * * * * Relative 1.3 ** * * * * Entropy 1.1 *** * * * ** (21.1 bits) 0.9 *** * ** * *** 0.7 *********** ***** * 0.4 ************* ******* 0.2 ********************* 0.0 --------------------- Multilevel ATGCTTCGTCTTCATCTTCGT consensus G TG G TG TC TG TC sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8487 7 1.71e-10 GATTGT ATGGTTCGTCTTCTTCTTCGC TGCTGCCGGT 262320 377 2.99e-09 CTACTTCCCG ATACTTCGTCTTTCTTTTCTC GAAACTATCT 6043 113 3.83e-09 GGTGAGGAGG ATGCCTCGTCTTTCTTTTCGT CGGAGCTGTC 5339 224 4.31e-09 GATATCGCTG GCTGTTCGTCTTCATCTTCCT GGTGGGTGGT 1954 358 1.82e-08 CGAAGTTTAA ATGGTTCATTCTCCTTTTCTT TCTTTCTGTG 8749 405 3.65e-08 GAAACTAACA CTGCTTCTTCTTCATTATCTC TATCTTACAC 4296 404 4.41e-08 CCATGGCTTA CTTCTTCGTCTTCATGTTGTT GAAAGCCACG 4894 240 6.95e-08 TTCGAAAGAG GAGGTTGGTGTTCATCTTCTT CAGTGTATGT 25001 230 1.75e-07 GATGGACGCC ATGTTTCGTTGTCGTTGTGGC TGTTGCGAGC 1955 267 1.89e-07 CGTGTTGGTT GTGGTCGGTCGTCGTCGTCGT CGGGGCTGGG 7166 83 2.99e-07 GATTGCGAAG ACGCTTGGTCTTACGCTTCCC AGGGAGGTGG 1288 457 6.06e-07 CTTCACATTG GTGCTTCCTTGTTCTCGTCTA ATAAAGCCGT 6996 377 9.52e-07 TCGTTGTCGT CGTTGTCGTTGTCGTCTTCGC TTTTGTTTGC 1799 453 2.40e-06 AAGTTACTGC AGTGTTCATGTTAATTTTTGT CAGGTTCAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8487 1.7e-10 6_[+1]_473 262320 3e-09 376_[+1]_103 6043 3.8e-09 112_[+1]_367 5339 4.3e-09 223_[+1]_256 1954 1.8e-08 357_[+1]_122 8749 3.6e-08 404_[+1]_75 4296 4.4e-08 403_[+1]_76 4894 7e-08 239_[+1]_240 25001 1.8e-07 229_[+1]_250 1955 1.9e-07 266_[+1]_213 7166 3e-07 82_[+1]_397 1288 6.1e-07 456_[+1]_23 6996 9.5e-07 376_[+1]_103 1799 2.4e-06 452_[+1]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=14 8487 ( 7) ATGGTTCGTCTTCTTCTTCGC 1 262320 ( 377) ATACTTCGTCTTTCTTTTCTC 1 6043 ( 113) ATGCCTCGTCTTTCTTTTCGT 1 5339 ( 224) GCTGTTCGTCTTCATCTTCCT 1 1954 ( 358) ATGGTTCATTCTCCTTTTCTT 1 8749 ( 405) CTGCTTCTTCTTCATTATCTC 1 4296 ( 404) CTTCTTCGTCTTCATGTTGTT 1 4894 ( 240) GAGGTTGGTGTTCATCTTCTT 1 25001 ( 230) ATGTTTCGTTGTCGTTGTGGC 1 1955 ( 267) GTGGTCGGTCGTCGTCGTCGT 1 7166 ( 83) ACGCTTGGTCTTACGCTTCCC 1 1288 ( 457) GTGCTTCCTTGTTCTCGTCTA 1 6996 ( 377) CGTTGTCGTTGTCGTCTTCGC 1 1799 ( 453) AGTGTTCATGTTAATTTTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 10.6586 E= 7.3e-005 95 0 13 -1045 -185 -59 -87 128 -185 -1045 130 11 -1045 100 71 -89 -1045 -158 -187 169 -1045 -158 -1045 181 -1045 187 -29 -1045 -86 -158 145 -189 -1045 -1045 -1045 192 -1045 141 -87 11 -1045 -158 13 128 -1045 -1045 -1045 192 -86 158 -1045 -31 46 73 -29 -189 -1045 -1045 -187 181 -1045 122 -187 69 -185 -1045 -29 143 -1045 -1045 -1045 192 -1045 187 -87 -189 -1045 -59 71 69 -185 100 -1045 92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 14 E= 7.3e-005 0.500000 0.214286 0.285714 0.000000 0.071429 0.142857 0.142857 0.642857 0.071429 0.000000 0.642857 0.285714 0.000000 0.428571 0.428571 0.142857 0.000000 0.071429 0.071429 0.857143 0.000000 0.071429 0.000000 0.928571 0.000000 0.785714 0.214286 0.000000 0.142857 0.071429 0.714286 0.071429 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.142857 0.285714 0.000000 0.071429 0.285714 0.642857 0.000000 0.000000 0.000000 1.000000 0.142857 0.642857 0.000000 0.214286 0.357143 0.357143 0.214286 0.071429 0.000000 0.000000 0.071429 0.928571 0.000000 0.500000 0.071429 0.428571 0.071429 0.000000 0.214286 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.785714 0.142857 0.071429 0.000000 0.142857 0.428571 0.428571 0.071429 0.428571 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AGC]T[GT][CG]TT[CG]GT[CT][TG]T[CT][ACG]T[CT][TG]TC[GT][TC] -------------------------------------------------------------------------------- Time 10.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 16 llr = 210 E-value = 5.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::6:59438538:43773344 pos.-specific C 6837216534618373:85:6 probability G :3131::3:11113::2::3: matrix T 4:::2::::::1111:1:33: bits 2.2 2.0 1.8 1.6 Relative 1.3 * * * * * Entropy 1.1 ** * ** * * ** * * (18.9 bits) 0.9 ** * ** * *** ** * * 0.7 **** ******** ***** * 0.4 **** ******** ******* 0.2 ************* ******* 0.0 --------------------- Multilevel CCACAACCAACACACAACCAC consensus TGCG AACCA CAC AAGA sequence G G TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1954 478 3.62e-12 CGACGACCGA CCACAACCAACACGCAACCAA AG 8749 444 3.38e-10 ACGTTATCAG TCAGAAACAACACGCAACCAC CTGCATCTTC 1955 467 2.79e-08 TCCTCCTCCT CCCCAACCACCCCGCAAAAAC CGACTTCCAT 5339 441 4.50e-08 GTCAGACGAC CGACGACGAACACGAAACCTC CGCTGCCCTC 264341 196 7.91e-08 CAACGAACCA TCACCAACAACACTCATCATC GACTATACAG 3725 449 2.68e-07 GCCCACCGCG TCAGCACAAAACCACAACAAC TCCTCGTTGC 262320 478 3.23e-07 AAAGTCAACC TCACTACAACCGCACAAACGA AG 35810 28 4.23e-07 TTTGCTGGAG CCCGCACCAGCACACCGCTGA GAAAGGTGGG 3230 405 4.62e-07 ACTGCCGTCG CCACAACACCCATCACACCTA CCCCATCTTC 3422 470 5.50e-07 CTGCAACACT TCGCAAACACATCACAACTGC ATACAATACC 4894 109 6.51e-07 GCTACCGCCA CGAGACACCACACCCCACTGA TGCCGTGAGA 3146 136 2.20e-06 AGTGTGCCAA CCCGTAAACGAACCAAACCGC GTCGGATCTT 33019 314 2.52e-06 GACGGAACGA CGACGACGACGAGACAAACAA GCCGCCCACT 23275 479 2.52e-06 GGACACGTTT CCGCAAACCACACATCGACAA C 7166 434 5.03e-06 ACCATAACAA TGACAAAGAAGAGCCATCTTC GTACAACATC 7353 392 7.45e-06 TTTGTTACAA CCCCTCCGACAACTACGCATC CATTCCAGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1954 3.6e-12 477_[+2]_2 8749 3.4e-10 443_[+2]_36 1955 2.8e-08 466_[+2]_13 5339 4.5e-08 440_[+2]_39 264341 7.9e-08 195_[+2]_284 3725 2.7e-07 448_[+2]_31 262320 3.2e-07 477_[+2]_2 35810 4.2e-07 27_[+2]_452 3230 4.6e-07 404_[+2]_75 3422 5.5e-07 469_[+2]_10 4894 6.5e-07 108_[+2]_371 3146 2.2e-06 135_[+2]_344 33019 2.5e-06 313_[+2]_166 23275 2.5e-06 478_[+2]_1 7166 5e-06 433_[+2]_46 7353 7.4e-06 391_[+2]_88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=16 1954 ( 478) CCACAACCAACACGCAACCAA 1 8749 ( 444) TCAGAAACAACACGCAACCAC 1 1955 ( 467) CCCCAACCACCCCGCAAAAAC 1 5339 ( 441) CGACGACGAACACGAAACCTC 1 264341 ( 196) TCACCAACAACACTCATCATC 1 3725 ( 449) TCAGCACAAAACCACAACAAC 1 262320 ( 478) TCACTACAACCGCACAAACGA 1 35810 ( 28) CCCGCACCAGCACACCGCTGA 1 3230 ( 405) CCACAACACCCATCACACCTA 1 3422 ( 470) TCGCAAACACATCACAACTGC 1 4894 ( 109) CGAGACACCACACCCCACTGA 1 3146 ( 136) CCCGTAAACGAACCAAACCGC 1 33019 ( 314) CGACGACGACGAGACAAACAA 1 23275 ( 479) CCGCAAACCACACATCGACAA 1 7166 ( 434) TGACAAAGAAGAGCCATCTTC 1 7353 ( 392) CCCCTCCGACAACTACGCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 11.1824 E= 5.0e-002 -1064 154 -1064 50 -1064 180 -7 -1064 127 22 -106 -1064 -1064 168 26 -1064 95 -19 -106 -50 176 -78 -1064 -1064 76 139 -1064 -1064 -5 122 -7 -1064 153 22 -1064 -1064 95 80 -106 -1064 -5 154 -106 -1064 153 -78 -206 -208 -1064 192 -106 -208 53 22 -7 -108 -5 168 -1064 -208 141 54 -1064 -1064 141 -1064 -48 -108 -5 180 -1064 -1064 -5 122 -1064 -8 53 -1064 26 24 76 139 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 5.0e-002 0.000000 0.625000 0.000000 0.375000 0.000000 0.750000 0.250000 0.000000 0.625000 0.250000 0.125000 0.000000 0.000000 0.687500 0.312500 0.000000 0.500000 0.187500 0.125000 0.187500 0.875000 0.125000 0.000000 0.000000 0.437500 0.562500 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.500000 0.375000 0.125000 0.000000 0.250000 0.625000 0.125000 0.000000 0.750000 0.125000 0.062500 0.062500 0.000000 0.812500 0.125000 0.062500 0.375000 0.250000 0.250000 0.125000 0.250000 0.687500 0.000000 0.062500 0.687500 0.312500 0.000000 0.000000 0.687500 0.000000 0.187500 0.125000 0.250000 0.750000 0.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.375000 0.000000 0.312500 0.312500 0.437500 0.562500 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][CG][AC][CG]AA[CA][CAG][AC][AC][CA]AC[ACG][CA][AC]A[CA][CAT][AGT][CA] -------------------------------------------------------------------------------- Time 20.44 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 28 llr = 242 E-value = 7.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2::3::2::3 pos.-specific C ::3112:::::: probability G 1a:1943a32a4 matrix T 8:58:27:58:3 bits 2.2 2.0 * 1.8 * * * 1.6 * * * * Relative 1.3 * * * * Entropy 1.1 ** ** * ** (12.5 bits) 0.9 ** ** ** ** 0.7 ***** ** ** 0.4 ***** ** *** 0.2 ***** ****** 0.0 ------------ Multilevel TGTTGGTGTTGG consensus C AG GG T sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 8749 261 9.62e-07 ATCGGTAAGT TGTTGGTGGTGG GTGTTCTCGC 23275 220 2.06e-06 GGTTATAGCG TGTTGGTGATGG ATTTGAGCTG 1954 154 2.06e-06 GTTTCAAGCA TGTTGCTGTTGA TATTAATGTT 3146 263 4.53e-06 CCTATCATTG TGCTGGTGATGG TGCGCACAAC 4894 283 9.41e-06 AGTAGTTGCT TGCTGTTGGTGG TCGTGTGATC 264341 306 1.20e-05 AGGAATGCAT TGATGGTGATGG CATTCTGTTT 31757 222 1.49e-05 CAGATTGAGC TGATGTTGTTGT GTGTTGCTCT 25001 283 1.83e-05 TTTCTTTGGT TGCTGTGGTTGT TTCTTACTAA 3422 300 2.02e-05 CTTGAGGATA TGATGATGATGA TACGAATGTT 6996 158 2.68e-05 CGGTGACTGC TGTCGCTGTTGT TGCTGCTCAG 1288 74 2.68e-05 GATGATGGGA GGTTGTTGTTGG AGGACGACGA 8689 385 3.59e-05 ATGAGTTTGG TGTTCATGTTGA ATTGCAACTG 7166 25 3.59e-05 TATGGAGTAT TGTCGATGGTGA GAAAAAGGAG 7353 191 3.89e-05 ACTGTCTCTG TGCTGAGGTGGT TTCGGAACCG 5339 97 3.89e-05 GTGGCCTCAC TGTGGCTGTTGG CAGCTACGAA 11390 221 3.89e-05 GAGCGTATGT TGCTCGTGTTGT TAGAAGAAGG 1799 374 4.23e-05 ACGGTCTGGG TGCTGGGGGGGG GGGGTCGAGA 18665 257 4.66e-05 CATGGTGATG TGTTGAGGAGGG GGGACGAATC 3230 104 5.07e-05 TAGTGAGAGA TGTGGCTGTTGA AGATCCCAAT 35810 437 7.80e-05 CTCTTCGTGG CGTTGGTGGTGT TTCTTACGCT 2292 260 7.80e-05 TGGTAACACG TGTTGAGGCTGT CTGAGCAATA 1855 387 7.80e-05 CCTCTGCTCG GGATGGGGTTGG GAGCCGTCGG 262320 190 9.87e-05 ATGGTTGTTG TGTTGTTGTTCG GCGTCGGTGA 4323 427 1.06e-04 AAGTTTGATC TGTTGATCGTGT GGAGGGAAGC 8487 28 1.31e-04 TCTTCTTCGC TGCTGCCGGTGT TATCGTTGTA 2215 413 1.50e-04 ACGATAGTTA TGTCGAGGTGGA AAATGAAATG 1955 291 2.17e-04 TCGTCGTCGG GGCTGGGGGGGA CTGAGTCACT 6043 99 2.30e-04 ACGAGAGGAA GGATGGTGAGGA GGATGCCTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8749 9.6e-07 260_[+3]_228 23275 2.1e-06 219_[+3]_269 1954 2.1e-06 153_[+3]_335 3146 4.5e-06 262_[+3]_226 4894 9.4e-06 282_[+3]_206 264341 1.2e-05 305_[+3]_183 31757 1.5e-05 221_[+3]_267 25001 1.8e-05 282_[+3]_206 3422 2e-05 299_[+3]_189 6996 2.7e-05 157_[+3]_331 1288 2.7e-05 73_[+3]_415 8689 3.6e-05 384_[+3]_104 7166 3.6e-05 24_[+3]_464 7353 3.9e-05 190_[+3]_298 5339 3.9e-05 96_[+3]_392 11390 3.9e-05 220_[+3]_268 1799 4.2e-05 373_[+3]_115 18665 4.7e-05 256_[+3]_232 3230 5.1e-05 103_[+3]_385 35810 7.8e-05 436_[+3]_52 2292 7.8e-05 259_[+3]_229 1855 7.8e-05 386_[+3]_102 262320 9.9e-05 189_[+3]_299 4323 0.00011 426_[+3]_62 8487 0.00013 27_[+3]_461 2215 0.00015 412_[+3]_76 1955 0.00022 290_[+3]_198 6043 0.00023 98_[+3]_390 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=28 8749 ( 261) TGTTGGTGGTGG 1 23275 ( 220) TGTTGGTGATGG 1 1954 ( 154) TGTTGCTGTTGA 1 3146 ( 263) TGCTGGTGATGG 1 4894 ( 283) TGCTGTTGGTGG 1 264341 ( 306) TGATGGTGATGG 1 31757 ( 222) TGATGTTGTTGT 1 25001 ( 283) TGCTGTGGTTGT 1 3422 ( 300) TGATGATGATGA 1 6996 ( 158) TGTCGCTGTTGT 1 1288 ( 74) GGTTGTTGTTGG 1 8689 ( 385) TGTTCATGTTGA 1 7166 ( 25) TGTCGATGGTGA 1 7353 ( 191) TGCTGAGGTGGT 1 5339 ( 97) TGTGGCTGTTGG 1 11390 ( 221) TGCTCGTGTTGT 1 1799 ( 374) TGCTGGGGGGGG 1 18665 ( 257) TGTTGAGGAGGG 1 3230 ( 104) TGTGGCTGTTGA 1 35810 ( 437) CGTTGGTGGTGT 1 2292 ( 260) TGTTGAGGCTGT 1 1855 ( 387) GGATGGGGTTGG 1 262320 ( 190) TGTTGTTGTTCG 1 4323 ( 427) TGTTGATCGTGT 1 8487 ( 28) TGCTGCCGGTGT 1 2215 ( 413) TGTCGAGGTGGA 1 1955 ( 291) GGCTGGGGGGGA 1 6043 ( 99) GGATGGTGAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15159 bayes= 9.6845 E= 7.6e-002 -1145 -258 -87 163 -1145 -1145 193 -1145 -54 41 -1145 102 -1145 -100 -187 163 -1145 -159 183 -1145 14 -26 45 -57 -1145 -258 13 136 -1145 -258 188 -1145 -27 -258 13 81 -1145 -1145 -29 157 -1145 -258 188 -1145 14 -1145 59 28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 28 E= 7.6e-002 0.000000 0.035714 0.142857 0.821429 0.000000 0.000000 1.000000 0.000000 0.178571 0.285714 0.000000 0.535714 0.000000 0.107143 0.071429 0.821429 0.000000 0.071429 0.928571 0.000000 0.285714 0.178571 0.357143 0.178571 0.000000 0.035714 0.285714 0.678571 0.000000 0.035714 0.964286 0.000000 0.214286 0.035714 0.285714 0.464286 0.000000 0.000000 0.214286 0.785714 0.000000 0.035714 0.964286 0.000000 0.285714 0.000000 0.392857 0.321429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TG[TC]TG[GA][TG]G[TGA][TG]G[GTA] -------------------------------------------------------------------------------- Time 30.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11390 4.63e-02 220_[+3(3.89e-05)]_268 1288 1.58e-04 73_[+3(2.68e-05)]_371_\ [+1(6.06e-07)]_23 1799 6.25e-05 22_[+2(4.66e-05)]_330_\ [+3(4.23e-05)]_67_[+1(2.40e-06)]_27 1855 1.20e-01 386_[+3(7.80e-05)]_102 18665 2.63e-02 256_[+3(4.66e-05)]_232 1954 1.21e-14 5_[+1(9.05e-05)]_2_[+3(1.49e-05)]_\ 113_[+3(2.06e-06)]_192_[+1(1.82e-08)]_99_[+2(3.62e-12)]_2 1955 3.49e-08 238_[+1(7.72e-05)]_7_[+1(1.89e-07)]_\ 179_[+2(2.79e-08)]_13 2215 1.60e-01 500 2292 2.30e-01 259_[+3(7.80e-05)]_229 23275 1.22e-04 219_[+3(2.06e-06)]_247_\ [+2(2.52e-06)]_1 25001 2.38e-05 229_[+1(1.75e-07)]_32_\ [+3(1.83e-05)]_206 262320 3.63e-09 172_[+1(2.86e-05)]_132_\ [+2(5.56e-05)]_3_[+2(1.97e-05)]_6_[+1(2.99e-09)]_80_[+2(3.23e-07)]_2 264341 7.05e-06 195_[+2(7.91e-08)]_89_\ [+3(1.20e-05)]_183 3146 1.43e-04 135_[+2(2.20e-06)]_106_\ [+3(4.53e-06)]_226 31757 2.33e-02 221_[+3(1.49e-05)]_267 3230 3.67e-04 103_[+3(5.07e-05)]_289_\ [+2(4.62e-07)]_75 33019 2.44e-02 313_[+2(2.52e-06)]_166 3422 1.47e-04 299_[+3(2.02e-05)]_158_\ [+2(5.50e-07)]_10 35810 1.17e-04 27_[+2(4.23e-07)]_388_\ [+3(7.80e-05)]_52 3725 3.09e-03 448_[+2(2.68e-07)]_31 4296 6.48e-04 403_[+1(4.41e-08)]_76 4323 5.96e-02 500 4894 1.47e-08 108_[+2(6.51e-07)]_110_\ [+1(6.95e-08)]_22_[+3(9.41e-06)]_206 5339 3.50e-10 30_[+1(3.48e-05)]_45_[+3(3.89e-05)]_\ 115_[+1(4.31e-09)]_196_[+2(4.50e-08)]_39 6043 1.89e-05 112_[+1(3.83e-09)]_367 6996 3.15e-04 157_[+3(2.68e-05)]_207_\ [+1(9.52e-07)]_103 7166 1.20e-06 24_[+3(3.59e-05)]_46_[+1(2.99e-07)]_\ 330_[+2(5.03e-06)]_46 7353 2.83e-03 190_[+3(3.89e-05)]_189_\ [+2(7.45e-06)]_88 8487 5.69e-07 6_[+1(1.71e-10)]_473 8689 1.27e-02 384_[+3(3.59e-05)]_104 8749 8.30e-13 260_[+3(9.62e-07)]_132_\ [+1(3.65e-08)]_18_[+2(3.38e-10)]_36 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************