******************************************************************************** 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/472/472.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10693 1.0000 500 11104 1.0000 500 13335 1.0000 500 2015 1.0000 500 20955 1.0000 500 21465 1.0000 500 22324 1.0000 500 24018 1.0000 500 24195 1.0000 500 24925 1.0000 500 25319 1.0000 500 263622 1.0000 500 264161 1.0000 500 32564 1.0000 500 33728 1.0000 500 4556 1.0000 500 6068 1.0000 500 8190 1.0000 500 9902 1.0000 500 bd1091 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/472/472.seqs.fa -oc motifs/472 -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= 20 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= 10000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.229 G 0.243 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.229 G 0.243 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 20 llr = 230 E-value = 1.1e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 12::412:::421241132: pos.-specific C 31:211164:11:1131::2 probability G 6:18::72482:a3139:34 matrix T 18a:69133248:554:765 bits 2.1 1.9 1.7 * * 1.5 * * Relative 1.3 ** * * * Entropy 1.1 *** * * ** ** (16.6 bits) 0.9 *** ** * ** ** 0.6 ******* * ** *** 0.4 ********** ** * **** 0.2 ******************** 0.0 -------------------- Multilevel GTTGTTGCCGTTGTTTGTTT consensus C CA ATGTA GAC AGG sequence T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- bd1091 44 9.45e-09 TTGCGATGCC ATTGTTGCCGGTGTTTGTTT TGAGACGATC 8190 45 9.45e-09 TTGCGATGCC ATTGTTGCCGGTGTTTGTTT TGAGACGATC 24018 271 2.03e-08 CAGCGCTCGC GTTGTTGCCGTTGGACATTG GACATATCCA 2015 178 4.13e-08 TACGATACAT GTTGATGTTGATGTTTGAGG AGTTACTTGT 24195 460 1.30e-07 TGGATCGGGG CTTCATGCGGTTGAAGGTTG AATGAGGGAG 20955 480 1.47e-07 TCCAGACTCA CTTGATACCTTTGTTCGTTT G 11104 405 1.65e-07 GAAGACAATT GTTCTTGCTGAAGTTTGTTC GACTACATTC 4556 258 8.25e-07 CGGTTGAGCC GTGGATGTGGATGGACGATG CGTTGGGTTG 33728 188 1.10e-06 GTTTATGTAG GCTGTTGTTGTTGGACGAGG AGGAGACTAG 13335 283 1.10e-06 GTTAGCTCAT CTTCTTGCTGACGTATGATT GAGGTGAAAG 24925 18 1.46e-06 CGTTTGACCC CATGATGCGGATGATGGTGC CAACAACGAA 21465 170 1.75e-06 CTGGCTGGTC GTTGATGGTGTTGGCTGATC TGAGAGTTCA 6068 259 3.49e-06 CTAATGTAAC GATGCTATGGGTGTTGGTGT GTAGGTTGTG 22324 178 3.79e-06 GATATATTAT GTTGTTAGGGATGTACCTAG ATACTGCAAT 263622 404 6.12e-06 CGATTGTGTA GTTGTACTCGTTGTGCGTTT GTATTGGCGT 264161 471 8.91e-06 TCAAGGTACC TTTCTTGCCGTAGCTGGTGG CGGAGAGGGC 32564 147 1.37e-05 ACCGAGGTTG CTTGCCTTCGTTGTTTGATT TTGGTTTGTT 25319 126 1.79e-05 AAAGAGGAAG GTTGTCGCGTAAGGAAGTAT TGAACTGATC 9902 67 3.38e-05 GAGAAGGGGA GATGTTGGGTGTAGGTGTTG TGTGGCTGCC 10693 97 1.47e-04 CTGGGGGAAC TTTGATACTTCTGAAGATAT GATTTGTAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1091 9.4e-09 43_[+1]_437 8190 9.4e-09 44_[+1]_436 24018 2e-08 270_[+1]_210 2015 4.1e-08 177_[+1]_303 24195 1.3e-07 459_[+1]_21 20955 1.5e-07 479_[+1]_1 11104 1.7e-07 404_[+1]_76 4556 8.2e-07 257_[+1]_223 33728 1.1e-06 187_[+1]_293 13335 1.1e-06 282_[+1]_198 24925 1.5e-06 17_[+1]_463 21465 1.8e-06 169_[+1]_311 6068 3.5e-06 258_[+1]_222 22324 3.8e-06 177_[+1]_303 263622 6.1e-06 403_[+1]_77 264161 8.9e-06 470_[+1]_10 32564 1.4e-05 146_[+1]_334 25319 1.8e-05 125_[+1]_355 9902 3.4e-05 66_[+1]_414 10693 0.00015 96_[+1]_384 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=20 bd1091 ( 44) ATTGTTGCCGGTGTTTGTTT 1 8190 ( 45) ATTGTTGCCGGTGTTTGTTT 1 24018 ( 271) GTTGTTGCCGTTGGACATTG 1 2015 ( 178) GTTGATGTTGATGTTTGAGG 1 24195 ( 460) CTTCATGCGGTTGAAGGTTG 1 20955 ( 480) CTTGATACCTTTGTTCGTTT 1 11104 ( 405) GTTCTTGCTGAAGTTTGTTC 1 4556 ( 258) GTGGATGTGGATGGACGATG 1 33728 ( 188) GCTGTTGTTGTTGGACGAGG 1 13335 ( 283) CTTCTTGCTGACGTATGATT 1 24925 ( 18) CATGATGCGGATGATGGTGC 1 21465 ( 170) GTTGATGGTGTTGGCTGATC 1 6068 ( 259) GATGCTATGGGTGTTGGTGT 1 22324 ( 178) GTTGTTAGGGATGTACCTAG 1 263622 ( 404) GTTGTACTCGTTGTGCGTTT 1 264161 ( 471) TTTCTTGCCGTAGCTGGTGG 1 32564 ( 147) CTTGCCTTCGTTGTTTGATT 1 25319 ( 126) GTTGTCGCGTAAGGAAGTAT 1 9902 ( 67) GATGTTGGGTGTAGGTGTTG 1 10693 ( 97) TTTGATACTTCTGAAGATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 9620 bayes= 8.90689 E= 1.1e-007 -137 13 118 -143 -78 -219 -1097 156 -1097 -1097 -228 181 -1097 -19 172 -1097 44 -119 -1097 102 -236 -119 -1097 165 -37 -219 153 -243 -1097 126 -69 15 -1097 61 53 15 -1097 -1097 172 -44 44 -219 -28 56 -78 -219 -1097 156 -236 -1097 197 -1097 -78 -219 31 89 63 -219 -128 73 -236 39 4 56 -137 -219 181 -1097 22 -1097 -1097 137 -78 -1097 4 115 -1097 -61 72 73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 20 E= 1.1e-007 0.100000 0.250000 0.550000 0.100000 0.150000 0.050000 0.000000 0.800000 0.000000 0.000000 0.050000 0.950000 0.000000 0.200000 0.800000 0.000000 0.350000 0.100000 0.000000 0.550000 0.050000 0.100000 0.000000 0.850000 0.200000 0.050000 0.700000 0.050000 0.000000 0.550000 0.150000 0.300000 0.000000 0.350000 0.350000 0.300000 0.000000 0.000000 0.800000 0.200000 0.350000 0.050000 0.200000 0.400000 0.150000 0.050000 0.000000 0.800000 0.050000 0.000000 0.950000 0.000000 0.150000 0.050000 0.300000 0.500000 0.400000 0.050000 0.100000 0.450000 0.050000 0.300000 0.250000 0.400000 0.100000 0.050000 0.850000 0.000000 0.300000 0.000000 0.000000 0.700000 0.150000 0.000000 0.250000 0.600000 0.000000 0.150000 0.400000 0.450000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC]TT[GC][TA]T[GA][CT][CGT][GT][TAG]TG[TG][TA][TCG]G[TA][TG][TG] -------------------------------------------------------------------------------- Time 3.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 18 llr = 217 E-value = 1.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :34448124638431747118 pos.-specific C a6226235316227635:791 probability G :112::6:21::::2::1:11 matrix T ::22::13231:4:1:122:1 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * ** * * * ** (17.4 bits) 0.9 ** ** ** * ****** 0.6 ** ** ** * ****** 0.4 ** **** ************ 0.2 ******** ************ 0.0 --------------------- Multilevel CCAACAGCAACAACCACACCA consensus ACTA CTCTACTA CATT sequence T A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1091 442 2.14e-09 GGCGCAACAG CAAGCAGCCAAATCCAAACCA TTCCTTCTCT 8190 441 2.14e-09 GGCGCAACAG CAAGCAGCCAAATCCAAACCA TTCCTTCTCT 32564 428 3.00e-09 CCTCCATACA CCACCAGCAACACCGCCACCA AGCATTAGGG 264161 104 2.42e-08 GACACCCAAC CCAAAACAAACAAAGAAACCA TGAAGCGACG 24925 444 2.64e-07 ACCAGCCAAG CAAAAATTAACACCCACATCA ACAACAACAG 10693 2 3.26e-07 A CCTTCACAAACAAAACAACCA GTGACGGCTA 6068 449 4.87e-07 TATCTACCAT CCAAACCCATAACCCCATCCA AGCACAAACC 22324 477 7.88e-07 CCAATTCCCC CACACCGCATCAACAACACCC AAC 24018 460 1.24e-06 TTAAACTGGC CACAAACACACATCCACATCT GGTGTCACAA 21465 460 1.61e-06 AGCAGCAACT CCCTCAGTGTAACCCACACAA TACATACTCA 33728 105 1.91e-06 AGCTATTAGG CCACAAACGGCATATACACCA CTGCCAACGG 20955 289 2.44e-06 AGAGTTGTTT CCGACAATCGCATCCCCGCCA TAACCACGTT 11104 144 4.21e-06 TTTATCCAAA CGAGAAGTATCATCCATTCCA CATGAACAAC 13335 415 5.65e-06 AGTATCACAT CATAAAGTCTTCACCACTTCA TCAATGCGAA 263622 36 8.02e-06 AGACAACGCT CCTCCCGATCCAAACCATCCA TCTCGGGCCT 24195 401 1.05e-05 TAAGTCCTCG CCGTCACCGACCAAGCAACCG AAGCCACCAC 2015 90 1.05e-05 ATCTTATTCG CCCTCAGCTAACAATACATCC CTCCTCGTCT 9902 447 1.19e-05 TGTAATTTTG CCTACAGCTATCTCCAAAAGA AGTTCACGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1091 2.1e-09 441_[+2]_38 8190 2.1e-09 440_[+2]_39 32564 3e-09 427_[+2]_52 264161 2.4e-08 103_[+2]_376 24925 2.6e-07 443_[+2]_36 10693 3.3e-07 1_[+2]_478 6068 4.9e-07 448_[+2]_31 22324 7.9e-07 476_[+2]_3 24018 1.2e-06 459_[+2]_20 21465 1.6e-06 459_[+2]_20 33728 1.9e-06 104_[+2]_375 20955 2.4e-06 288_[+2]_191 11104 4.2e-06 143_[+2]_336 13335 5.6e-06 414_[+2]_65 263622 8e-06 35_[+2]_444 24195 1e-05 400_[+2]_79 2015 1e-05 89_[+2]_390 9902 1.2e-05 446_[+2]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=18 bd1091 ( 442) CAAGCAGCCAAATCCAAACCA 1 8190 ( 441) CAAGCAGCCAAATCCAAACCA 1 32564 ( 428) CCACCAGCAACACCGCCACCA 1 264161 ( 104) CCAAAACAAACAAAGAAACCA 1 24925 ( 444) CAAAAATTAACACCCACATCA 1 10693 ( 2) CCTTCACAAACAAAACAACCA 1 6068 ( 449) CCAAACCCATAACCCCATCCA 1 22324 ( 477) CACACCGCATCAACAACACCC 1 24018 ( 460) CACAAACACACATCCACATCT 1 21465 ( 460) CCCTCAGTGTAACCCACACAA 1 33728 ( 105) CCACAAACGGCATATACACCA 1 20955 ( 289) CCGACAATCGCATCCCCGCCA 1 11104 ( 144) CGAGAAGTATCATCCATTCCA 1 13335 ( 415) CATAAAGTCTTCACCACTTCA 1 263622 ( 36) CCTCCCGATCCAAACCATCCA 1 24195 ( 401) CCGTCACCGACCAAGCAACCG 1 2015 ( 90) CCCTCAGCTAACAATACATCC 1 9902 ( 447) CCTACAGCTATCTCCAAAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9600 bayes= 9.19073 E= 1.5e-005 -1081 213 -1081 -1081 37 142 -213 -1081 79 -4 -113 -28 79 -46 -54 -28 59 142 -1081 -1081 169 -46 -1081 -1081 -121 28 119 -228 -21 113 -1081 4 59 28 -54 -70 111 -204 -113 4 11 142 -1081 -128 159 -4 -1081 -1081 59 -4 -1081 52 37 154 -1081 -1081 -121 142 -54 -128 137 54 -1081 -1081 79 113 -1081 -228 149 -1081 -213 -28 -221 166 -1081 -28 -221 196 -213 -1081 159 -104 -213 -228 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 1.5e-005 0.000000 1.000000 0.000000 0.000000 0.333333 0.611111 0.055556 0.000000 0.444444 0.222222 0.111111 0.222222 0.444444 0.166667 0.166667 0.222222 0.388889 0.611111 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.111111 0.277778 0.555556 0.055556 0.222222 0.500000 0.000000 0.277778 0.388889 0.277778 0.166667 0.166667 0.555556 0.055556 0.111111 0.277778 0.277778 0.611111 0.000000 0.111111 0.777778 0.222222 0.000000 0.000000 0.388889 0.222222 0.000000 0.388889 0.333333 0.666667 0.000000 0.000000 0.111111 0.611111 0.166667 0.111111 0.666667 0.333333 0.000000 0.000000 0.444444 0.500000 0.000000 0.055556 0.722222 0.000000 0.055556 0.222222 0.055556 0.722222 0.000000 0.222222 0.055556 0.888889 0.055556 0.000000 0.777778 0.111111 0.055556 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[CA][ACT][AT][CA]A[GC][CTA][AC][AT][CA][AC][ATC][CA]C[AC][CA][AT][CT]CA -------------------------------------------------------------------------------- Time 6.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 19 llr = 195 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 44:757:4129:177 pos.-specific C :12:::124::1:1: probability G 528352844815913 matrix T 13:::11:2::4:1: bits 2.1 1.9 1.7 * * 1.5 * ** * Relative 1.3 * * ** * Entropy 1.1 *** * ** * * (14.8 bits) 0.9 ***** ****** 0.6 * ***** ****** 0.4 * ****** ****** 0.2 *************** 0.0 --------------- Multilevel GAGAGAGACGAGGAA consensus AT GAG GG T G sequence G CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 24925 89 2.42e-07 CCAGAAAGGC GAGAGAGCCGAGGAG ACATATCCAT 22324 426 3.68e-07 CGTCCTTCAA GACAGAGAGGAGGAA GAGGAAAACG 4556 206 6.25e-07 GGGTGTGTGG TTGAGAGGCGAGGAA GGCTGGTGGA bd1091 77 7.17e-07 GACGATCTAC GAGAGAGGCGATGCA AGAGAGAGAG 8190 78 7.17e-07 GACGATCTAC GAGAGAGGCGATGCA AGAGAGAGAG 25319 58 2.57e-06 AGGCTCTCAG GAGAAGGAGAAGGAA TCCCAACAAC 21465 259 2.57e-06 GGCTGTCGGG AGGGGAGCCGAGGAG GAGAGAAGCA 32564 37 3.90e-06 ATGGGCTTTT GAGAAAGCTGATGGA TGAACTTGGG 24195 481 4.74e-06 TGAAGGTTGA ATGAGGGAGGAGGGA GGAGA 20955 169 4.74e-06 TCCAGCTGAA AGGAAAGAGGAGGTA GTGTTTTGGT 13335 2 7.52e-06 G GAGAAATGTGATGAA GAGGGTTGCA 264161 330 8.22e-06 ACGTCGGGAT GGGAGGCGCGATGAA GGGGGCGAAG 24018 73 1.15e-05 GTGTTCTTTC ATCAAAGAGGACGAA ATAGTACAAC 6068 211 1.46e-05 GAACCATATA ATGAAACAGAATGAA GTGACTTATC 33728 321 1.58e-05 GAGTTGGCGG GAGGGAGGGGAGAAG TGGAACAGCC 11104 97 2.48e-05 TCATTGACGA AGGAGAGCAAATGAA GTTTGCCTCA 2015 15 3.51e-05 ATATCATTAG ATGGATGGTGAGGAG GTTTTATTGT 10693 37 4.28e-05 CGGCTAAAGC TCCGAAGACGAGGAA ACTTTACGAT 263622 276 9.24e-05 AAAAGATGTA ATGGAGGATGGTGAG ACTGGAGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24925 2.4e-07 88_[+3]_397 22324 3.7e-07 425_[+3]_60 4556 6.2e-07 205_[+3]_280 bd1091 7.2e-07 76_[+3]_409 8190 7.2e-07 77_[+3]_408 25319 2.6e-06 57_[+3]_428 21465 2.6e-06 258_[+3]_227 32564 3.9e-06 36_[+3]_449 24195 4.7e-06 480_[+3]_5 20955 4.7e-06 168_[+3]_317 13335 7.5e-06 1_[+3]_484 264161 8.2e-06 329_[+3]_156 24018 1.1e-05 72_[+3]_413 6068 1.5e-05 210_[+3]_275 33728 1.6e-05 320_[+3]_165 11104 2.5e-05 96_[+3]_389 2015 3.5e-05 14_[+3]_471 10693 4.3e-05 36_[+3]_449 263622 9.2e-05 275_[+3]_210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=19 24925 ( 89) GAGAGAGCCGAGGAG 1 22324 ( 426) GACAGAGAGGAGGAA 1 4556 ( 206) TTGAGAGGCGAGGAA 1 bd1091 ( 77) GAGAGAGGCGATGCA 1 8190 ( 78) GAGAGAGGCGATGCA 1 25319 ( 58) GAGAAGGAGAAGGAA 1 21465 ( 259) AGGGGAGCCGAGGAG 1 32564 ( 37) GAGAAAGCTGATGGA 1 24195 ( 481) ATGAGGGAGGAGGGA 1 20955 ( 169) AGGAAAGAGGAGGTA 1 13335 ( 2) GAGAAATGTGATGAA 1 264161 ( 330) GGGAGGCGCGATGAA 1 24018 ( 73) ATCAAAGAGGACGAA 1 6068 ( 211) ATGAAACAGAATGAA 1 33728 ( 321) GAGGGAGGGGAGAAG 1 11104 ( 97) AGGAGAGCAAATGAA 1 2015 ( 15) ATGGATGGTGAGGAG 1 10693 ( 37) TCCGAAGACGAGGAA 1 263622 ( 276) ATGGAGGATGGTGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 9720 bayes= 9.19116 E= 1.5e-004 71 -1089 96 -136 71 -212 -21 22 -1089 -54 179 -1089 151 -1089 12 -1089 88 -1089 112 -1089 151 -1089 -21 -236 -1089 -112 179 -236 71 -12 60 -1089 -229 69 60 -36 -71 -1089 179 -1089 188 -1089 -220 -1089 -1089 -212 112 64 -229 -1089 196 -1089 151 -112 -120 -236 151 -1089 12 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 19 E= 1.5e-004 0.421053 0.000000 0.473684 0.105263 0.421053 0.052632 0.210526 0.315789 0.000000 0.157895 0.842105 0.000000 0.736842 0.000000 0.263158 0.000000 0.473684 0.000000 0.526316 0.000000 0.736842 0.000000 0.210526 0.052632 0.000000 0.105263 0.842105 0.052632 0.421053 0.210526 0.368421 0.000000 0.052632 0.368421 0.368421 0.210526 0.157895 0.000000 0.842105 0.000000 0.947368 0.000000 0.052632 0.000000 0.000000 0.052632 0.526316 0.421053 0.052632 0.000000 0.947368 0.000000 0.736842 0.105263 0.105263 0.052632 0.736842 0.000000 0.263158 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][ATG]G[AG][GA][AG]G[AGC][CGT]GA[GT]GA[AG] -------------------------------------------------------------------------------- Time 10.00 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10693 2.95e-05 1_[+2(3.26e-07)]_14_[+3(4.28e-05)]_\ 391_[+2(3.56e-05)]_37 11104 4.27e-07 96_[+3(2.48e-05)]_32_[+2(4.21e-06)]_\ 240_[+1(1.65e-07)]_76 13335 1.06e-06 1_[+3(7.52e-06)]_266_[+1(1.10e-06)]_\ 112_[+2(5.65e-06)]_65 2015 3.79e-07 14_[+3(3.51e-05)]_60_[+2(1.05e-05)]_\ 67_[+1(4.13e-08)]_303 20955 5.20e-08 168_[+3(4.74e-06)]_105_\ [+2(2.44e-06)]_170_[+1(1.47e-07)]_1 21465 1.96e-07 169_[+1(1.75e-06)]_69_\ [+3(2.57e-06)]_186_[+2(1.61e-06)]_20 22324 3.50e-08 177_[+1(3.79e-06)]_228_\ [+3(3.68e-07)]_36_[+2(7.88e-07)]_3 24018 1.02e-08 72_[+3(1.15e-05)]_183_\ [+1(2.03e-08)]_169_[+2(1.24e-06)]_20 24195 1.76e-07 230_[+1(1.37e-05)]_150_\ [+2(1.05e-05)]_38_[+1(1.30e-07)]_1_[+3(4.74e-06)]_5 24925 3.62e-09 17_[+1(1.46e-06)]_51_[+3(2.42e-07)]_\ 130_[+1(5.36e-05)]_146_[+2(3.21e-05)]_23_[+2(2.64e-07)]_36 25319 4.65e-04 57_[+3(2.57e-06)]_53_[+1(1.79e-05)]_\ 355 263622 5.99e-05 35_[+2(8.02e-06)]_219_\ [+3(9.24e-05)]_113_[+1(6.12e-06)]_77 264161 5.41e-08 103_[+2(2.42e-08)]_205_\ [+3(8.22e-06)]_126_[+1(8.91e-06)]_10 32564 5.92e-09 36_[+3(3.90e-06)]_95_[+1(1.37e-05)]_\ 215_[+2(7.49e-06)]_25_[+2(3.00e-09)]_21_[+2(1.35e-06)]_10 33728 7.74e-07 104_[+2(1.91e-06)]_62_\ [+1(1.10e-06)]_113_[+3(1.58e-05)]_165 4556 1.66e-05 205_[+3(6.25e-07)]_37_\ [+1(8.25e-07)]_223 6068 5.97e-07 210_[+3(1.46e-05)]_33_\ [+1(3.49e-06)]_32_[+1(5.99e-05)]_118_[+2(4.87e-07)]_31 8190 1.00e-12 44_[+1(9.45e-09)]_13_[+3(7.17e-07)]_\ 348_[+2(2.14e-09)]_39 9902 4.35e-04 66_[+1(3.38e-05)]_360_\ [+2(1.19e-05)]_33 bd1091 1.00e-12 43_[+1(9.45e-09)]_13_[+3(7.17e-07)]_\ 350_[+2(2.14e-09)]_38 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************