******************************************************************************** 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/294/294.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42587 1.0000 500 31840 1.0000 500 32255 1.0000 500 46448 1.0000 500 36517 1.0000 500 13221 1.0000 500 7072 1.0000 500 47233 1.0000 500 28874 1.0000 500 48086 1.0000 500 38474 1.0000 500 48112 1.0000 500 48237 1.0000 500 48337 1.0000 500 51134 1.0000 500 39066 1.0000 500 9684 1.0000 500 48932 1.0000 500 15536 1.0000 500 49430 1.0000 500 49663 1.0000 500 50362 1.0000 500 54150 1.0000 500 43891 1.0000 500 44027 1.0000 500 31375 1.0000 500 33651 1.0000 500 44545 1.0000 500 44630 1.0000 500 45147 1.0000 500 35460 1.0000 500 12339 1.0000 500 45931 1.0000 500 36016 1.0000 500 46278 1.0000 500 42560 1.0000 500 42653 1.0000 500 42846 1.0000 500 40068 1.0000 500 46602 1.0000 500 35721 1.0000 500 37181 1.0000 500 49357 1.0000 500 43862 1.0000 500 45589 1.0000 500 45297 1.0000 500 49445 1.0000 500 50346 1.0000 500 49866 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/294/294.seqs.fa -oc motifs/294 -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= 49 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= 24500 N= 49 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.242 G 0.219 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.242 G 0.219 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 36 llr = 365 E-value = 2.5e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::913:::a61 pos.-specific C 6:5:9:::5:12 probability G 1:5::19:5:31 matrix T 39:1:71a1::7 bits 2.2 2.0 * 1.8 * ** * 1.5 * ** ** * Relative 1.3 * ** ** * Entropy 1.1 **** ** * (14.6 bits) 0.9 ********* 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTCACTGTCAAT consensus T G A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 50346 378 6.19e-08 GGTTTTTCTG CTGACTGTGAAT ACGACGGTCT 49357 378 6.19e-08 GGTTTTTCTG CTGACTGTGAAT ACGACGGTCT 40068 269 6.19e-08 CGGAAGATTG CTGACTGTGAAT CGTAAAAATA 44027 73 6.19e-08 TTTATTTTGA CTGACTGTGAAT CCGTAGCGAT 39066 202 7.90e-07 TTTGTCCTAG TTCACTGTCAAT TTGTGAGCTG 48112 142 7.90e-07 GAGACATGCC TTCACTGTCAAT TCATTTTGTC 44545 179 1.37e-06 ACCTTCCTGC CTCACAGTCAAT ATTTCCTGGA 36016 369 1.60e-06 TCATTTCTAC CTGACTGTGACT GTGAACAAGT 42587 274 1.91e-06 AGAAGGTGGT CTCACTGTCAAC AAGTTGAGAA 43862 226 2.08e-06 AATCCTCATA CTCACAGTCAGT CGATCATCTT 35721 133 2.61e-06 AATGTTAGGG TTCACAGTCAAT TTTCGATTGT 51134 332 2.61e-06 CCCTATTCTA TTGACTGTGAAC TGCACACGAC 28874 354 2.61e-06 TTCGCAGCAG TTGACTGTGAAC GCTTCACCAC 46602 95 2.92e-06 AACTAGCAGC TTGACTGTGACT GAATGTGAGT 38474 425 3.42e-06 GGTGTTGCCG TTGACTGTCACT GCCAATAACC 31375 159 4.07e-06 TTCTCTGTCT GTGACTGTGAGT TCGAATTTGG 45589 289 4.46e-06 GAACAAGGTA GTGACTGTCAGT GGCTTGTGCT 49430 146 4.46e-06 CACTATCTGA CTGACTGTGAGG AGGAAGCAAT 48237 479 4.93e-06 TCTTTAGCAA CTCACAGTCAAC AAAATTCACC 50362 406 6.42e-06 GGATTTCAAA CTCTCTGTCAAT CAAATATTTT 15536 206 7.06e-06 TACGCGCTCA CTCACTGTGAAA CACAGACACA 48932 175 1.16e-05 AAAGAGGCCT TTCACAGTCAGC ACTTTGAAAA 48086 91 1.28e-05 CGGTCCGCAT CGGACTGTGAAT GACTCTTTCT 45297 14 1.50e-05 TTCCATATGC ATGACTGTGAGT TGGTGACAAT 45931 38 1.50e-05 CAAATTCACA TTGACTTTGAGT ACGTAAAGGT 45147 216 1.65e-05 GTCTCTCTTT CTCACTGTGTAT GCCTTGTACT 42846 199 2.05e-05 TGCCTGTGAG CTCTCAGTCAGT CGCGACGGCA 44630 198 2.78e-05 TCATTAAAAG CTGACGGTGAAG ACTTTTGCGA 32255 403 3.24e-05 GCCTGGAGAT CTCAAAGTCAGT CATTAAGTAA 33651 240 3.75e-05 AGTTAGCGCG CTCACAGTTACT GTAACCAGTA 36517 173 3.96e-05 AAAATTATAT CTCACGGTTAAT CAATCCGATG 7072 199 4.49e-05 ATAACGTCGT CTGTCTGTCACC TGAACGTTCG 49866 342 5.29e-05 GCTTCTCGTT GTCACAGTCAGG TCCGGTCGGT 54150 21 8.33e-05 TCTTTTTTGT TTGACTTTCAAA GCAACTTCCT 48337 426 9.79e-05 GACTAGAGCA TCCACAGTGAAC AAGGGTTTCA 35460 404 1.29e-04 TCCGCGAATA TTCAATTTCAGT AGCTTCATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50346 6.2e-08 377_[+1]_111 49357 6.2e-08 377_[+1]_111 40068 6.2e-08 268_[+1]_220 44027 6.2e-08 72_[+1]_416 39066 7.9e-07 201_[+1]_287 48112 7.9e-07 141_[+1]_347 44545 1.4e-06 178_[+1]_310 36016 1.6e-06 368_[+1]_120 42587 1.9e-06 273_[+1]_215 43862 2.1e-06 225_[+1]_263 35721 2.6e-06 132_[+1]_356 51134 2.6e-06 331_[+1]_157 28874 2.6e-06 353_[+1]_135 46602 2.9e-06 94_[+1]_394 38474 3.4e-06 424_[+1]_64 31375 4.1e-06 158_[+1]_330 45589 4.5e-06 288_[+1]_200 49430 4.5e-06 145_[+1]_343 48237 4.9e-06 478_[+1]_10 50362 6.4e-06 405_[+1]_83 15536 7.1e-06 205_[+1]_283 48932 1.2e-05 174_[+1]_314 48086 1.3e-05 90_[+1]_398 45297 1.5e-05 13_[+1]_475 45931 1.5e-05 37_[+1]_451 45147 1.6e-05 215_[+1]_273 42846 2e-05 198_[+1]_290 44630 2.8e-05 197_[+1]_291 32255 3.2e-05 402_[+1]_86 33651 3.7e-05 239_[+1]_249 36517 4e-05 172_[+1]_316 7072 4.5e-05 198_[+1]_290 49866 5.3e-05 341_[+1]_147 54150 8.3e-05 20_[+1]_468 48337 9.8e-05 425_[+1]_63 35460 0.00013 403_[+1]_85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=36 50346 ( 378) CTGACTGTGAAT 1 49357 ( 378) CTGACTGTGAAT 1 40068 ( 269) CTGACTGTGAAT 1 44027 ( 73) CTGACTGTGAAT 1 39066 ( 202) TTCACTGTCAAT 1 48112 ( 142) TTCACTGTCAAT 1 44545 ( 179) CTCACAGTCAAT 1 36016 ( 369) CTGACTGTGACT 1 42587 ( 274) CTCACTGTCAAC 1 43862 ( 226) CTCACAGTCAGT 1 35721 ( 133) TTCACAGTCAAT 1 51134 ( 332) TTGACTGTGAAC 1 28874 ( 354) TTGACTGTGAAC 1 46602 ( 95) TTGACTGTGACT 1 38474 ( 425) TTGACTGTCACT 1 31375 ( 159) GTGACTGTGAGT 1 45589 ( 289) GTGACTGTCAGT 1 49430 ( 146) CTGACTGTGAGG 1 48237 ( 479) CTCACAGTCAAC 1 50362 ( 406) CTCTCTGTCAAT 1 15536 ( 206) CTCACTGTGAAA 1 48932 ( 175) TTCACAGTCAGC 1 48086 ( 91) CGGACTGTGAAT 1 45297 ( 14) ATGACTGTGAGT 1 45931 ( 38) TTGACTTTGAGT 1 45147 ( 216) CTCACTGTGTAT 1 42846 ( 199) CTCTCAGTCAGT 1 44630 ( 198) CTGACGGTGAAG 1 32255 ( 403) CTCAAAGTCAGT 1 33651 ( 240) CTCACAGTTACT 1 36517 ( 173) CTCACGGTTAAT 1 7072 ( 199) CTGTCTGTCACC 1 49866 ( 342) GTCACAGTCAGG 1 54150 ( 21) TTGACTTTCAAA 1 48337 ( 426) TCCACAGTGAAC 1 35460 ( 404) TTCAATTTCAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 23961 bayes= 10.782 E= 2.5e-024 -331 120 -139 34 -1181 -312 -297 184 -1181 105 119 -1181 173 -1181 -1181 -166 -231 196 -1181 -1181 1 -1181 -198 134 -1181 -1181 207 -166 -1181 -1181 -1181 193 -1181 96 111 -224 182 -1181 -1181 -324 101 -80 48 -1181 -231 -32 -139 134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 36 E= 2.5e-024 0.027778 0.555556 0.083333 0.333333 0.000000 0.027778 0.027778 0.944444 0.000000 0.500000 0.500000 0.000000 0.916667 0.000000 0.000000 0.083333 0.055556 0.944444 0.000000 0.000000 0.277778 0.000000 0.055556 0.666667 0.000000 0.000000 0.916667 0.083333 0.000000 0.000000 0.000000 1.000000 0.000000 0.472222 0.472222 0.055556 0.972222 0.000000 0.000000 0.027778 0.555556 0.138889 0.305556 0.000000 0.055556 0.194444 0.083333 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]T[CG]AC[TA]GT[CG]A[AG]T -------------------------------------------------------------------------------- Time 19.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 10 llr = 168 E-value = 2.3e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::2::::72:2:2::::66 pos.-specific C ::1::1::12729::244:4 probability G aa5579aa243212:2664: matrix T ::433::::2:4:6a6:::: bits 2.2 ** ** 2.0 ** ** * 1.8 ** *** * 1.5 ** *** * * Relative 1.3 ** **** * * * Entropy 1.1 ** **** * * * *** (24.2 bits) 0.9 ** ***** * * * **** 0.7 ********* * ******** 0.4 ********* * ******** 0.2 *********** ******** 0.0 -------------------- Multilevel GGGGGGGGAGCTCTTTGGAA consensus TTT GAGA A CCCGC sequence A C C G G T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 50346 269 3.51e-10 TGGGGGGGGG GGGGGGGGAGCTCTTGCCAC GACCAGAATT 49357 269 3.51e-10 ATATGGGGGG GGGGGGGGAGCTCTTGCCAC GACCAGAATT 38474 143 1.28e-09 TTAGTACTAC GGTGGGGGACCACGTTGGAA TCCCGGGTGT 28874 376 2.91e-09 GCTTCACCAC GGCGGGGGACCTCGTTGGAA TCCCGATTGT 45931 313 7.27e-09 GAAGGCAGTC GGGATGGGATCCCTTTGGGC TGTAATGGCA 46278 101 1.43e-08 GTCACCGCGC GGTGGGGGCACGCTTCGGAA CGACCGGTAT 45147 164 2.53e-08 CCAGCCACAA GGTTGGGGAGGCGTTTGCGA ACCCGCTGTG 50362 241 3.38e-08 TATTATGTGC GGTTTGGGGGGTCATTCGAA AAAGCGCAAT 42587 156 3.61e-08 AGCCTATTTT GGGAGGGGGTCACATTCGGA TGAGCATTCT 49430 366 1.49e-07 CGAAACTCCA GGGTTCGGAAGGCTTCGCGC CCGGGATCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50346 3.5e-10 268_[+2]_212 49357 3.5e-10 268_[+2]_212 38474 1.3e-09 142_[+2]_338 28874 2.9e-09 375_[+2]_105 45931 7.3e-09 312_[+2]_168 46278 1.4e-08 100_[+2]_380 45147 2.5e-08 163_[+2]_317 50362 3.4e-08 240_[+2]_240 42587 3.6e-08 155_[+2]_325 49430 1.5e-07 365_[+2]_115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=10 50346 ( 269) GGGGGGGGAGCTCTTGCCAC 1 49357 ( 269) GGGGGGGGAGCTCTTGCCAC 1 38474 ( 143) GGTGGGGGACCACGTTGGAA 1 28874 ( 376) GGCGGGGGACCTCGTTGGAA 1 45931 ( 313) GGGATGGGATCCCTTTGGGC 1 46278 ( 101) GGTGGGGGCACGCTTCGGAA 1 45147 ( 164) GGTTGGGGAGGCGTTTGCGA 1 50362 ( 241) GGTTTGGGGGGTCATTCGAA 1 42587 ( 156) GGGAGGGGGTCACATTCGGA 1 49430 ( 366) GGGTTCGGAAGGCTTCGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 23569 bayes= 11.4537 E= 2.3e-005 -997 -997 219 -997 -997 -997 219 -997 -997 -127 119 60 -46 -997 119 19 -997 -997 168 19 -997 -127 204 -997 -997 -997 219 -997 -997 -997 219 -997 134 -127 -13 -997 -46 -27 87 -40 -997 153 46 -997 -46 -27 -13 60 -997 189 -113 -997 -46 -997 -13 119 -997 -997 -997 193 -997 -27 -13 119 -997 72 146 -997 -997 72 146 -997 112 -997 87 -997 112 72 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.3e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.100000 0.500000 0.400000 0.200000 0.000000 0.500000 0.300000 0.000000 0.000000 0.700000 0.300000 0.000000 0.100000 0.900000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.700000 0.100000 0.200000 0.000000 0.200000 0.200000 0.400000 0.200000 0.000000 0.700000 0.300000 0.000000 0.200000 0.200000 0.200000 0.400000 0.000000 0.900000 0.100000 0.000000 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.400000 0.600000 0.000000 0.000000 0.400000 0.600000 0.000000 0.600000 0.000000 0.400000 0.000000 0.600000 0.400000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GG[GT][GTA][GT]GGG[AG][GACT][CG][TACG]C[TAG]T[TCG][GC][GC][AG][AC] -------------------------------------------------------------------------------- Time 38.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 14 llr = 197 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 6:13:::11:1:12:3:34:: pos.-specific C 193:a1138:9:4:4:81:42 probability G 1:6::4611::a4:322441: matrix T 1117:624:a1:2835:3368 bits 2.2 * 2.0 * * * 1.8 * * * * 1.5 * * * * Relative 1.3 * * *** * Entropy 1.1 * ** **** * * * (20.3 bits) 0.9 * ** * **** * * * 0.7 ****** **** * * ** 0.4 ******* **** **** *** 0.2 ********************* 0.0 --------------------- Multilevel ACGTCTGTCTCGCTCTCGATT consensus CA GTC GAGAGAGCC sequence T TG TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 48112 290 7.18e-11 TGCAAGCTGT ACCTCTGTCTCGGTCTCTATT TGTGACCTTT 50346 390 4.70e-10 GACTGTGAAT ACGACGGTCTCGCTGTCAGTT TCCTACAGAA 49357 390 4.70e-10 GACTGTGAAT ACGACGGTCTCGCTGTCAGTT TCCTACAGAA 13221 258 9.22e-08 AGTCTCCGCC ACGTCGTTCTCGCAGGCGTTC GAGTCGATTG 31840 444 1.01e-07 AGCTTCGACG ACCTCTGCCTTGGACTCATTT CCCCACGAAC 38474 120 1.22e-07 AAGTTAAGCA TCGTCGGGCTCGGTTAGTACT ACGGTGGGGG 49663 74 2.69e-07 GTTCGAATTA ACGACGGACTCGATCACTATC TGTAATTGTA 12339 17 3.43e-07 CCAAGACTCC CCGTCTGGCTCGTATAGGGCT AGGAAAGGTA 36517 436 3.43e-07 ACTCTCTACG ACTTCTTCGTCGGTTGCTGTT GGTAGTCTGC 33651 83 5.03e-07 TCCCAAGGAC GCGTCTTTGTCGCTCACGACC TTTTGGCTTG 48086 299 5.84e-07 ACCTACGGCC ATCTCTCCCTCGGTCTCGTGT GTTCCCACGG 43862 402 7.75e-07 TGTCTTTTGG ACATCTCTCTCGTTCTGCTTT CGGAGGGCAG 37181 216 9.51e-07 GGTCGCACCC CCGACTGACTAGCTTGCAGCT TGTCGACCCG 15536 276 1.31e-06 CTTGTGGTTC TCCTCCGCATCGTTGTCGACT ACATCGTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48112 7.2e-11 289_[+3]_190 50346 4.7e-10 389_[+3]_90 49357 4.7e-10 389_[+3]_90 13221 9.2e-08 257_[+3]_222 31840 1e-07 443_[+3]_36 38474 1.2e-07 119_[+3]_360 49663 2.7e-07 73_[+3]_406 12339 3.4e-07 16_[+3]_463 36517 3.4e-07 435_[+3]_44 33651 5e-07 82_[+3]_397 48086 5.8e-07 298_[+3]_181 43862 7.8e-07 401_[+3]_78 37181 9.5e-07 215_[+3]_264 15536 1.3e-06 275_[+3]_204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=14 48112 ( 290) ACCTCTGTCTCGGTCTCTATT 1 50346 ( 390) ACGACGGTCTCGCTGTCAGTT 1 49357 ( 390) ACGACGGTCTCGCTGTCAGTT 1 13221 ( 258) ACGTCGTTCTCGCAGGCGTTC 1 31840 ( 444) ACCTCTGCCTTGGACTCATTT 1 38474 ( 120) TCGTCGGGCTCGGTTAGTACT 1 49663 ( 74) ACGACGGACTCGATCACTATC 1 12339 ( 17) CCGTCTGGCTCGTATAGGGCT 1 36517 ( 436) ACTTCTTCGTCGGTTGCTGTT 1 33651 ( 83) GCGTCTTTGTCGCTCACGACC 1 48086 ( 299) ATCTCTCCCTCGGTCTCGTGT 1 43862 ( 402) ACATCTCTCTCGTTCTGCTTT 1 37181 ( 216) CCGACTGACTAGCTTGCAGCT 1 15536 ( 276) TCCTCCGCATCGTTGTCGACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 23520 bayes= 11.3194 E= 1.4e+000 122 -76 -161 -88 -1045 194 -1045 -188 -195 24 138 -188 5 -1045 -1045 144 -1045 205 -1045 -1045 -1045 -176 71 112 -1045 -76 155 -30 -95 24 -61 70 -195 170 -61 -1045 -1045 -1045 -1045 193 -195 182 -1045 -188 -1045 -1045 219 -1045 -195 56 71 -30 -37 -1045 -1045 158 -1045 82 39 12 5 -1045 -3 93 -1045 170 -3 -1045 5 -176 71 12 37 -1045 71 12 -1045 56 -161 112 -1045 -18 -1045 158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 14 E= 1.4e+000 0.642857 0.142857 0.071429 0.142857 0.000000 0.928571 0.000000 0.071429 0.071429 0.285714 0.571429 0.071429 0.285714 0.000000 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.071429 0.357143 0.571429 0.000000 0.142857 0.642857 0.214286 0.142857 0.285714 0.142857 0.428571 0.071429 0.785714 0.142857 0.000000 0.000000 0.000000 0.000000 1.000000 0.071429 0.857143 0.000000 0.071429 0.000000 0.000000 1.000000 0.000000 0.071429 0.357143 0.357143 0.214286 0.214286 0.000000 0.000000 0.785714 0.000000 0.428571 0.285714 0.285714 0.285714 0.000000 0.214286 0.500000 0.000000 0.785714 0.214286 0.000000 0.285714 0.071429 0.357143 0.285714 0.357143 0.000000 0.357143 0.285714 0.000000 0.357143 0.071429 0.571429 0.000000 0.214286 0.000000 0.785714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AC[GC][TA]C[TG][GT][TC]CTCG[CGT][TA][CGT][TAG][CG][GAT][AGT][TC][TC] -------------------------------------------------------------------------------- Time 59.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42587 2.55e-06 155_[+2(3.61e-08)]_98_\ [+1(1.91e-06)]_215 31840 1.24e-03 443_[+3(1.01e-07)]_36 32255 3.35e-03 217_[+2(7.83e-06)]_165_\ [+1(3.24e-05)]_86 46448 7.28e-01 500 36517 1.24e-04 172_[+1(3.96e-05)]_251_\ [+3(3.43e-07)]_44 13221 9.60e-05 257_[+3(9.22e-08)]_70_\ [+2(9.30e-05)]_132 7072 8.29e-02 198_[+1(4.49e-05)]_290 47233 8.42e-01 500 28874 2.58e-07 353_[+1(2.61e-06)]_10_\ [+2(2.91e-09)]_105 48086 1.34e-04 90_[+1(1.28e-05)]_196_\ [+3(5.84e-07)]_181 38474 2.99e-11 119_[+3(1.22e-07)]_2_[+2(1.28e-09)]_\ 262_[+1(3.42e-06)]_64 48112 3.68e-09 141_[+1(7.90e-07)]_13_\ [+1(2.25e-06)]_111_[+3(7.18e-11)]_190 48237 1.08e-03 159_[+1(4.73e-05)]_307_\ [+1(4.93e-06)]_10 48337 1.13e-02 22_[+2(2.87e-05)]_383_\ [+1(9.79e-05)]_63 51134 8.49e-03 157_[+1(3.00e-05)]_162_\ [+1(2.61e-06)]_157 39066 1.69e-03 201_[+1(7.90e-07)]_287 9684 6.35e-01 500 48932 1.67e-02 174_[+1(1.16e-05)]_314 15536 8.02e-05 205_[+1(7.06e-06)]_58_\ [+3(1.31e-06)]_79_[+1(5.66e-05)]_113 49430 5.36e-06 145_[+1(4.46e-06)]_208_\ [+2(1.49e-07)]_115 49663 1.01e-03 73_[+3(2.69e-07)]_406 50362 7.71e-06 240_[+2(3.38e-08)]_145_\ [+1(6.42e-06)]_83 54150 2.08e-01 20_[+1(8.33e-05)]_468 43891 3.39e-01 500 44027 1.23e-04 72_[+1(6.19e-08)]_182_\ [+2(8.98e-05)]_214 31375 9.76e-04 158_[+1(4.07e-06)]_205_\ [+2(4.91e-05)]_105 33651 5.15e-05 82_[+3(5.03e-07)]_136_\ [+1(3.75e-05)]_249 44545 1.40e-02 178_[+1(1.37e-06)]_310 44630 2.75e-02 197_[+1(2.78e-05)]_291 45147 5.40e-06 163_[+2(2.53e-08)]_32_\ [+1(1.65e-05)]_273 35460 3.17e-01 500 12339 1.08e-03 16_[+3(3.43e-07)]_463 45931 6.72e-07 37_[+1(1.50e-05)]_263_\ [+2(7.27e-09)]_168 36016 3.79e-04 368_[+1(1.60e-06)]_120 46278 1.68e-04 100_[+2(1.43e-08)]_380 42560 4.58e-01 500 42653 8.34e-01 500 42846 4.11e-02 198_[+1(2.05e-05)]_290 40068 9.14e-04 268_[+1(6.19e-08)]_204_\ [+1(9.79e-05)]_4 46602 4.51e-04 94_[+1(2.92e-06)]_336_\ [+3(2.21e-05)]_37 35721 2.19e-03 132_[+1(2.61e-06)]_356 37181 5.76e-03 215_[+3(9.51e-07)]_264 49357 1.03e-15 230_[+1(9.79e-05)]_26_\ [+2(3.51e-10)]_89_[+1(6.19e-08)]_[+3(4.70e-10)]_90 43862 1.08e-05 225_[+1(2.08e-06)]_164_\ [+3(7.75e-07)]_78 45589 1.05e-02 288_[+1(4.46e-06)]_200 45297 1.15e-01 13_[+1(1.50e-05)]_475 49445 4.53e-01 500 50346 1.03e-15 227_[+1(9.79e-05)]_29_\ [+2(3.51e-10)]_89_[+1(6.19e-08)]_[+3(4.70e-10)]_90 49866 5.44e-02 341_[+1(5.29e-05)]_147 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************