******************************************************************************** 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/366/366.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11180 1.0000 500 17585 1.0000 500 20662 1.0000 500 20726 1.0000 500 21530 1.0000 500 21901 1.0000 500 22316 1.0000 500 22764 1.0000 500 24053 1.0000 500 24060 1.0000 500 24171 1.0000 500 24255 1.0000 500 25308 1.0000 500 25342 1.0000 500 25444 1.0000 90 264786 1.0000 500 264937 1.0000 500 269718 1.0000 500 27686 1.0000 500 36213 1.0000 500 36971 1.0000 500 38011 1.0000 500 406 1.0000 500 41754 1.0000 500 4267 1.0000 500 4510 1.0000 500 5036 1.0000 500 5185 1.0000 500 6086 1.0000 500 8586 1.0000 500 bd460 1.0000 500 bd686 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/366/366.seqs.fa -oc motifs/366 -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= 32 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= 15590 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.239 G 0.229 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.239 G 0.229 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 28 llr = 271 E-value = 1.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4::4:292264:464: pos.-specific C ::112::1:1:2::2: probability G 388158:58348441a matrix T 42:33::2::212:3: bits 2.1 * 1.9 * 1.7 * 1.5 * * * Relative 1.3 ** ** * * Entropy 1.1 ** ** * * * * (14.0 bits) 0.9 ** ** ** * * * 0.6 ** *** ** * * * 0.4 *** ******** * * 0.2 *** ********** * 0.0 ---------------- Multilevel TGGAGGAGGAAGGAAG consensus A TT AGG AGT sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 27686 56 4.20e-08 GGTGGCTCTT TGGTGGAGGGGGAGAG CAGAGCGCAC 25308 180 5.12e-08 GTCGAGTAAG AGGGGGAGGAAGAAAG AAAAAATCTC 41754 16 6.36e-08 TTGGCACTTC GGGAGGAGGAGGAACG ACCAGCCGGT 36213 16 6.36e-08 TTGGCACTTC GGGAGGAGGAGGAACG ACCAGCCGGT 20726 33 2.32e-06 GCTCATGGAA AGGGTGATGAGGGATG ATGGTTGACT 8586 271 2.96e-06 GGAATGCTGT AGGTGGAGGGATGGAG GTGTACCGTT 269718 29 3.34e-06 GACGATGTTC TGGTGGACGAACGATG TTGTGCAAGG 6086 328 3.75e-06 GACTTGGACA TGGTCGAAGAGGTGTG AGGTGTGTGA 17585 237 5.28e-06 TTGAAGGAGA TGGCCGAGAAAGGACG GTTGAGAGAG 4510 246 8.94e-06 AATGCCGACG TGGCGGAGGGATGGTG GATGCACTAT 20662 351 9.89e-06 GAACTAAAGA GGGAGGAAAAAGTAGG AAAAACAAAG 38011 308 1.09e-05 CAGATGCCAC AGCAGAAGGAAGAAGG AACCTCCTCC 21530 25 1.32e-05 TGACACGCGC GGCGGGAGGGAGAGGG CAGTCCAGAT 264786 275 1.46e-05 TTATTGATTG AGGTTGAGGAGCCAAG TGAATACGCA 36971 225 1.60e-05 GACATGGTTG ATGTTGATGATGGATG GCAGGCCGTT 5036 439 1.75e-05 GAGAGGTCGG GGGATCAGGAGGAACG AGTGGAGCCA 24171 157 1.91e-05 GTACGCGTTC TGACGGATGAAGGAAG ATACAAAGCA 4267 270 2.28e-05 GCAGTTGGCT TTGACGAAGGAGTGAG AGTATCACTA 406 424 2.70e-05 AATTAGAAGC AGGAGAAGAGGCAGAG CTCTCCCGTA 11180 277 2.70e-05 TCTTGTGGAA AGGATGATGCTGTGAG GAATTCATCG 264937 105 2.94e-05 TTGGTGTTAC TGGTCGTTGAGGGGAG GGCATTCAAA 21901 73 3.74e-05 CGCCGGATAA TGCAGAAGGCTGGAAG TTCCCAGATG 5185 101 4.72e-05 ATATCACCAC GGGTTAAAAAGGTGAG TTTTGTTTGA bd686 269 5.47e-05 TGCTATCTTT TTGTGAACGAACGAAG TAAACCAACT 24053 391 5.47e-05 GGCGTGTTGG TTGGTGAGAGTGGGTG AGATTCATGT 22764 437 5.47e-05 GGCGATGGAG AGGCCGACGGTGTACG CTGCACCCTG 24255 215 7.28e-05 TGCACAGCAT GTCATGAGGAACAGTG TATGTTAACA bd460 103 1.30e-04 TGCTATGACG AGGAGGCAAATGAAGG CGAAATGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27686 4.2e-08 55_[+1]_429 25308 5.1e-08 179_[+1]_305 41754 6.4e-08 15_[+1]_469 36213 6.4e-08 15_[+1]_469 20726 2.3e-06 32_[+1]_452 8586 3e-06 270_[+1]_214 269718 3.3e-06 28_[+1]_456 6086 3.7e-06 327_[+1]_157 17585 5.3e-06 236_[+1]_248 4510 8.9e-06 245_[+1]_239 20662 9.9e-06 350_[+1]_134 38011 1.1e-05 307_[+1]_177 21530 1.3e-05 24_[+1]_460 264786 1.5e-05 274_[+1]_210 36971 1.6e-05 224_[+1]_260 5036 1.7e-05 438_[+1]_46 24171 1.9e-05 156_[+1]_328 4267 2.3e-05 269_[+1]_215 406 2.7e-05 423_[+1]_61 11180 2.7e-05 276_[+1]_208 264937 2.9e-05 104_[+1]_380 21901 3.7e-05 72_[+1]_412 5185 4.7e-05 100_[+1]_384 bd686 5.5e-05 268_[+1]_216 24053 5.5e-05 390_[+1]_94 22764 5.5e-05 436_[+1]_48 24255 7.3e-05 214_[+1]_270 bd460 0.00013 102_[+1]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=28 27686 ( 56) TGGTGGAGGGGGAGAG 1 25308 ( 180) AGGGGGAGGAAGAAAG 1 41754 ( 16) GGGAGGAGGAGGAACG 1 36213 ( 16) GGGAGGAGGAGGAACG 1 20726 ( 33) AGGGTGATGAGGGATG 1 8586 ( 271) AGGTGGAGGGATGGAG 1 269718 ( 29) TGGTGGACGAACGATG 1 6086 ( 328) TGGTCGAAGAGGTGTG 1 17585 ( 237) TGGCCGAGAAAGGACG 1 4510 ( 246) TGGCGGAGGGATGGTG 1 20662 ( 351) GGGAGGAAAAAGTAGG 1 38011 ( 308) AGCAGAAGGAAGAAGG 1 21530 ( 25) GGCGGGAGGGAGAGGG 1 264786 ( 275) AGGTTGAGGAGCCAAG 1 36971 ( 225) ATGTTGATGATGGATG 1 5036 ( 439) GGGATCAGGAGGAACG 1 24171 ( 157) TGACGGATGAAGGAAG 1 4267 ( 270) TTGACGAAGGAGTGAG 1 406 ( 424) AGGAGAAGAGGCAGAG 1 11180 ( 277) AGGATGATGCTGTGAG 1 264937 ( 105) TGGTCGTTGAGGGGAG 1 21901 ( 73) TGCAGAAGGCTGGAAG 1 5185 ( 101) GGGTTAAAAAGGTGAG 1 bd686 ( 269) TTGTGAACGAACGAAG 1 24053 ( 391) TTGGTGAGAGTGGGTG 1 22764 ( 437) AGGCCGACGGTGTACG 1 24255 ( 215) GTCATGAGGAACAGTG 1 bd460 ( 103) AGGAGGCAAATGAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15110 bayes= 9.67982 E= 1.1e-005 41 -1145 13 57 -1145 -1145 184 -56 -291 -74 184 -1145 55 -74 -68 29 -1145 -42 123 12 -59 -274 178 -1145 179 -274 -1145 -288 -59 -116 123 -56 -33 -1145 178 -1145 126 -174 32 -1145 67 -1145 64 -30 -1145 -42 171 -188 41 -274 78 -30 109 -1145 90 -1145 67 -42 -68 -8 -1145 -1145 213 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 28 E= 1.1e-005 0.357143 0.000000 0.250000 0.392857 0.000000 0.000000 0.821429 0.178571 0.035714 0.142857 0.821429 0.000000 0.392857 0.142857 0.142857 0.321429 0.000000 0.178571 0.535714 0.285714 0.178571 0.035714 0.785714 0.000000 0.928571 0.035714 0.000000 0.035714 0.178571 0.107143 0.535714 0.178571 0.214286 0.000000 0.785714 0.000000 0.642857 0.071429 0.285714 0.000000 0.428571 0.000000 0.357143 0.214286 0.000000 0.178571 0.750000 0.071429 0.357143 0.035714 0.392857 0.214286 0.571429 0.000000 0.428571 0.000000 0.428571 0.178571 0.142857 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TAG]GG[AT][GT]GAG[GA][AG][AGT]G[GAT][AG][AT]G -------------------------------------------------------------------------------- Time 7.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 20 llr = 239 E-value = 5.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3a3368:79747377:9329 pos.-specific C 65:462:7314413:38:192 probability G 22:22:111::234212:1:: matrix T 3112:223:1:1:12::26:: bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 * ** ** Entropy 1.1 * * ** ** ** (17.2 bits) 0.9 * ***** * **** ** 0.6 * * ******* * **** ** 0.4 * * ******* * ******* 0.2 *** ***************** 0.0 --------------------- Multilevel CCACCAACAAAAAGAACATCA consensus TA AAC TC CCGC CG A sequence G TGT G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24053 296 5.61e-10 AAATTCCAAA CGAGCAACAAAGAGAACATCA CACACAAGAA 20726 480 1.47e-09 ACACAGCCAC CAATCAACAACAACAACAACA 264937 9 7.87e-09 ACACACCA GAACAAACAACAACAACATCA ACGCATTCAA 24060 478 1.46e-07 ACCCCCCCCC CCACACACACACACACCATCA TA 8586 352 1.64e-07 AGTGTACTAG CAAAATATCAAAAGAACAACA GGGATAATAG 21901 454 2.05e-07 TCCCCTGTTC CGACCAATAAATCGAACATCA ATTGGCGCCG 4267 448 2.84e-07 CACCAAATTT TCAGCCACCACCACAACTTCA CATTAGATGC 21530 108 3.50e-07 CTGTTTATTC TAAAGAACAAACACGACATCC AAAGTTGTTC 6086 185 7.76e-07 CAGCCTCAGC CAACGTGTCAACAGAACAACA ATTCGCGACG bd686 424 1.47e-06 GAAACACCCC CCATAAATAAAGGAACCAACC CCCCAATCAT 25342 292 1.91e-06 TATGAGGACA CGATCCACCAAAAGACGAAAA ACGCCTCCTC 17585 329 2.66e-06 TCCACGGTTA CCACGTACAACCAGTACTACC ACTGGCAAAA 36971 66 3.66e-06 TCCAACGGCA GCACCATCAACAGCAGCAGCA GCAGATGGCT 41754 236 5.35e-06 TGAGCCCACT TCAACATCATCGAATCCATCA TAACGTGTGG 36213 236 5.35e-06 TGAGCCCACT TCAACATCATCGAATCCATCA TAACGTGTGG 22316 213 5.76e-06 CCGTACCTAC TCAAATGCGAAAGAAACATCA ACTGAGCTCC 5185 227 9.43e-06 ATTCTTTAGA CGATCCATCAATATGAGATCA AGATCTGATC 20662 2 1.01e-05 T GCAGCAACAAACATGCCACAA GGATGAAGAT 27686 315 1.15e-05 AGGTCGAGAG CTACGAAGAAAAGGAAGATAA TATTACACGT 11180 36 1.31e-05 CAAGTTTGGG CATCCAACCAACGAAAGTGCA CGTGTATTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24053 5.6e-10 295_[+2]_184 20726 1.5e-09 479_[+2] 264937 7.9e-09 8_[+2]_471 24060 1.5e-07 477_[+2]_2 8586 1.6e-07 351_[+2]_128 21901 2e-07 453_[+2]_26 4267 2.8e-07 447_[+2]_32 21530 3.5e-07 107_[+2]_372 6086 7.8e-07 184_[+2]_295 bd686 1.5e-06 423_[+2]_56 25342 1.9e-06 291_[+2]_188 17585 2.7e-06 328_[+2]_151 36971 3.7e-06 65_[+2]_414 41754 5.4e-06 235_[+2]_244 36213 5.4e-06 235_[+2]_244 22316 5.8e-06 212_[+2]_267 5185 9.4e-06 226_[+2]_253 20662 1e-05 1_[+2]_478 27686 1.2e-05 314_[+2]_165 11180 1.3e-05 35_[+2]_444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=20 24053 ( 296) CGAGCAACAAAGAGAACATCA 1 20726 ( 480) CAATCAACAACAACAACAACA 1 264937 ( 9) GAACAAACAACAACAACATCA 1 24060 ( 478) CCACACACACACACACCATCA 1 8586 ( 352) CAAAATATCAAAAGAACAACA 1 21901 ( 454) CGACCAATAAATCGAACATCA 1 4267 ( 448) TCAGCCACCACCACAACTTCA 1 21530 ( 108) TAAAGAACAAACACGACATCC 1 6086 ( 185) CAACGTGTCAACAGAACAACA 1 bd686 ( 424) CCATAAATAAAGGAACCAACC 1 25342 ( 292) CGATCCACCAAAAGACGAAAA 1 17585 ( 329) CCACGTACAACCAGTACTACC 1 36971 ( 66) GCACCATCAACAGCAGCAGCA 1 41754 ( 236) TCAACATCATCGAATCCATCA 1 36213 ( 236) TCAACATCATCGAATCCATCA 1 22316 ( 213) TCAAATGCGAAAGAAACATCA 1 5185 ( 227) CGATCCATCAATATGAGATCA 1 20662 ( 2) GCAGCAACAAACATGCCACAA 1 27686 ( 315) CTACGAAGAAAAGGAAGATAA 1 11180 ( 36) CATCCAACCAACGAAAGTGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14950 bayes= 9.79585 E= 5.4e-002 -1097 133 -61 -8 16 91 -19 -240 182 -1097 -1097 -240 -10 74 -61 -40 -10 120 -19 -1097 116 -26 -1097 -40 148 -1097 -119 -81 -1097 155 -219 -8 127 33 -219 -1097 166 -225 -1097 -140 127 55 -1097 -1097 38 55 -19 -140 138 -225 13 -1097 -10 33 61 -140 138 -1097 -61 -81 127 33 -219 -1097 -1097 174 -19 -1097 166 -1097 -1097 -81 16 -225 -119 106 -84 183 -1097 -1097 166 -67 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 5.4e-002 0.000000 0.600000 0.150000 0.250000 0.300000 0.450000 0.200000 0.050000 0.950000 0.000000 0.000000 0.050000 0.250000 0.400000 0.150000 0.200000 0.250000 0.550000 0.200000 0.000000 0.600000 0.200000 0.000000 0.200000 0.750000 0.000000 0.100000 0.150000 0.000000 0.700000 0.050000 0.250000 0.650000 0.300000 0.050000 0.000000 0.850000 0.050000 0.000000 0.100000 0.650000 0.350000 0.000000 0.000000 0.350000 0.350000 0.200000 0.100000 0.700000 0.050000 0.250000 0.000000 0.250000 0.300000 0.350000 0.100000 0.700000 0.000000 0.150000 0.150000 0.650000 0.300000 0.050000 0.000000 0.000000 0.800000 0.200000 0.000000 0.850000 0.000000 0.000000 0.150000 0.300000 0.050000 0.100000 0.550000 0.150000 0.850000 0.000000 0.000000 0.850000 0.150000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][CAG]A[CAT][CAG][ACT]A[CT][AC]A[AC][ACG][AG][GCA]A[AC][CG]A[TA]CA -------------------------------------------------------------------------------- Time 15.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 22 llr = 248 E-value = 4.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1::3:235141:3::1:::35 pos.-specific C :1212:4:2:::3:1:4::5: probability G 725255:57::92:842191: matrix T 27453331:5812a1548125 bits 2.1 1.9 * 1.7 * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * ** ** ** (16.3 bits) 0.9 ** * ** ** ** * 0.6 *** * ***** *** ** * 0.4 *** ******** *** ** * 0.2 ************ ******** 0.0 --------------------- Multilevel GTGTGGCAGTTGCTGTCTGCA consensus TATTAG A A GT AT sequence C T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41754 261 1.50e-10 CCATCATAAC GTGTGGCAGATGTTGTCTGCA ACCGGCATGC 36213 261 1.50e-10 CCATCATAAC GTGTGGCAGATGTTGTCTGCA ACCGGCATGC 36971 320 4.70e-08 GGGGGTTGAC GTGAGGCAGTTGGTGGCCGCT GAATGTTGGA 24060 74 1.34e-07 GCAAAAGGTA GCGACGTAGTTGATGTGTGCT GCTGCCGTCG 264937 64 5.93e-07 AATTTCAAAA GGTTTTTAGTTGGTCGCTGCT TTTCTTTCCG 38011 171 8.10e-07 AAAGTAAGGT GTTGCAAGGTTGCTCGTTGAT TACATTACCT 22764 260 1.10e-06 AAGCGTGTTA GTGGGTAGAATGGTGGTTGGT GCGTTTGGAG bd686 236 1.21e-06 AAGTGAAAGT GGGTGGTGGAATCTGTCTGAT GTTGCTATCT 8586 218 2.80e-06 CTGCCATGCT GTTCGTTTGTTGTTGTTTGGA TAGGTTGACT 24053 415 3.06e-06 TGAGATTCAT GTTTTGCAGTTGATGATTCTA TGAGATATGT 11180 381 3.06e-06 TCTGCGTTCG GTCGGTCGGAAGGTGTCGGAA GGTCGGGAAG 20726 190 3.34e-06 GCGTTGGATG TGTACATAGTTGCTGTTTGTT TGTTGCGTAG 5185 156 5.10e-06 GTCGATGCAT TGTTTGAAGATGATTGCTGAT GGGTGCTATT 21901 379 6.51e-06 TACACGAATT GTCTATCGTTTGCTGTCTGTA GTAATAAAAG 24255 100 7.05e-06 GACATGAGTG GCTTTGCGAATGCTGGGGGAA TGCAACTGCA 22316 18 7.05e-06 GCATTAAATG TTGTGATGGTTGGTGTATTCA TATGAAATAT bd460 76 8.25e-06 ACCGCACGAG TTCGCGAACTTGATGAGTGCT ATGACGAGGA 24171 45 1.04e-05 GTGCTGAAGT GTGTTGAGCTCGTTTGGTGCT GTTATGCATC 20662 196 1.04e-05 ACGAGGTGAC GTGACGATGTTTATCGGTGAA GAAGTTGTTA 4510 434 1.20e-05 GTACTAGCCT GTCCGTCGCAATCTGGTTGCA GGTCGGGAAG 264786 103 1.20e-05 CCAACAAGAT ATTATGAACATGATGTTTTCA TGTCTCGGAC 269718 80 1.73e-05 CAGTTTGTAG ATGAGACGGGTGCTGTTGGTT TGGTTTTGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41754 1.5e-10 260_[+3]_219 36213 1.5e-10 260_[+3]_219 36971 4.7e-08 319_[+3]_160 24060 1.3e-07 73_[+3]_406 264937 5.9e-07 63_[+3]_416 38011 8.1e-07 170_[+3]_309 22764 1.1e-06 259_[+3]_220 bd686 1.2e-06 235_[+3]_244 8586 2.8e-06 217_[+3]_262 24053 3.1e-06 414_[+3]_65 11180 3.1e-06 380_[+3]_99 20726 3.3e-06 189_[+3]_290 5185 5.1e-06 155_[+3]_324 21901 6.5e-06 378_[+3]_101 24255 7e-06 99_[+3]_380 22316 7e-06 17_[+3]_462 bd460 8.2e-06 75_[+3]_404 24171 1e-05 44_[+3]_435 20662 1e-05 195_[+3]_284 4510 1.2e-05 433_[+3]_46 264786 1.2e-05 102_[+3]_377 269718 1.7e-05 79_[+3]_400 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=22 41754 ( 261) GTGTGGCAGATGTTGTCTGCA 1 36213 ( 261) GTGTGGCAGATGTTGTCTGCA 1 36971 ( 320) GTGAGGCAGTTGGTGGCCGCT 1 24060 ( 74) GCGACGTAGTTGATGTGTGCT 1 264937 ( 64) GGTTTTTAGTTGGTCGCTGCT 1 38011 ( 171) GTTGCAAGGTTGCTCGTTGAT 1 22764 ( 260) GTGGGTAGAATGGTGGTTGGT 1 bd686 ( 236) GGGTGGTGGAATCTGTCTGAT 1 8586 ( 218) GTTCGTTTGTTGTTGTTTGGA 1 24053 ( 415) GTTTTGCAGTTGATGATTCTA 1 11180 ( 381) GTCGGTCGGAAGGTGTCGGAA 1 20726 ( 190) TGTACATAGTTGCTGTTTGTT 1 5185 ( 156) TGTTTGAAGATGATTGCTGAT 1 21901 ( 379) GTCTATCGTTTGCTGTCTGTA 1 24255 ( 100) GCTTTGCGAATGCTGGGGGAA 1 22316 ( 18) TTGTGATGGTTGGTGTATTCA 1 bd460 ( 76) TTCGCGAACTTGATGAGTGCT 1 24171 ( 45) GTGTTGAGCTCGTTTGGTGCT 1 20662 ( 196) GTGACGATGTTTATCGGTGAA 1 4510 ( 434) GTCCGTCGCAATCTGGTTGCA 1 264786 ( 103) ATTATGAACATGATGTTTTCA 1 269718 ( 80) ATGAGACGGGTGCTGTTGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14950 bayes= 9.76186 E= 4.7e-001 -156 -1110 167 -54 -1110 -139 -33 146 -1110 -39 99 46 2 -139 -33 78 -256 -7 99 5 -56 -1110 125 5 24 78 -1110 5 76 -1110 99 -154 -156 -39 157 -253 61 -1110 -233 105 -98 -239 -1110 163 -1110 -1110 192 -95 2 41 -1 -54 -1110 -1110 -1110 192 -1110 -81 175 -154 -156 -1110 84 92 -256 61 -1 46 -1110 -239 -75 163 -1110 -239 192 -154 2 93 -133 -54 90 -1110 -1110 92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 4.7e-001 0.090909 0.000000 0.727273 0.181818 0.000000 0.090909 0.181818 0.727273 0.000000 0.181818 0.454545 0.363636 0.272727 0.090909 0.181818 0.454545 0.045455 0.227273 0.454545 0.272727 0.181818 0.000000 0.545455 0.272727 0.318182 0.409091 0.000000 0.272727 0.454545 0.000000 0.454545 0.090909 0.090909 0.181818 0.681818 0.045455 0.409091 0.000000 0.045455 0.545455 0.136364 0.045455 0.000000 0.818182 0.000000 0.000000 0.863636 0.136364 0.272727 0.318182 0.227273 0.181818 0.000000 0.000000 0.000000 1.000000 0.000000 0.136364 0.772727 0.090909 0.090909 0.000000 0.409091 0.500000 0.045455 0.363636 0.227273 0.363636 0.000000 0.045455 0.136364 0.818182 0.000000 0.045455 0.863636 0.090909 0.272727 0.454545 0.090909 0.181818 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GT[GT][TA][GTC][GT][CAT][AG]G[TA]TG[CAG]TG[TG][CTG]TG[CA][AT] -------------------------------------------------------------------------------- Time 22.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11180 1.73e-05 35_[+2(1.31e-05)]_220_\ [+1(2.70e-05)]_88_[+3(3.06e-06)]_99 17585 2.66e-04 236_[+1(5.28e-06)]_76_\ [+2(2.66e-06)]_151 20662 1.66e-05 1_[+2(1.01e-05)]_173_[+3(1.04e-05)]_\ 134_[+1(9.89e-06)]_134 20726 5.13e-10 32_[+1(2.32e-06)]_141_\ [+3(3.34e-06)]_269_[+2(1.47e-09)] 21530 7.39e-05 24_[+1(1.32e-05)]_67_[+2(3.50e-07)]_\ 151_[+2(3.96e-06)]_200 21901 1.11e-06 72_[+1(3.74e-05)]_290_\ [+3(6.51e-06)]_54_[+2(2.05e-07)]_26 22316 3.70e-04 17_[+3(7.05e-06)]_174_\ [+2(5.76e-06)]_267 22764 2.44e-04 259_[+3(1.10e-06)]_156_\ [+1(5.47e-05)]_48 24053 3.58e-09 295_[+2(5.61e-10)]_74_\ [+1(5.47e-05)]_8_[+3(3.06e-06)]_65 24060 8.22e-07 73_[+3(1.34e-07)]_247_\ [+2(8.22e-06)]_55_[+2(1.49e-05)]_39_[+2(1.46e-07)]_2 24171 1.04e-03 44_[+3(1.04e-05)]_91_[+1(1.91e-05)]_\ 328 24255 5.15e-03 99_[+3(7.05e-06)]_94_[+1(7.28e-05)]_\ 270 25308 1.52e-04 179_[+1(5.12e-08)]_305 25342 1.19e-02 291_[+2(1.91e-06)]_188 25444 8.52e-01 90 264786 1.47e-03 102_[+3(1.20e-05)]_151_\ [+1(1.46e-05)]_210 264937 5.11e-09 8_[+2(7.87e-09)]_34_[+3(5.93e-07)]_\ 20_[+1(2.94e-05)]_380 269718 1.03e-04 28_[+1(3.34e-06)]_35_[+3(1.73e-05)]_\ 400 27686 1.12e-05 55_[+1(4.20e-08)]_243_\ [+2(1.15e-05)]_165 36213 3.26e-12 15_[+1(6.36e-08)]_166_\ [+3(3.36e-05)]_17_[+2(5.35e-06)]_4_[+3(1.50e-10)]_219 36971 8.03e-08 65_[+2(3.66e-06)]_138_\ [+1(1.60e-05)]_79_[+3(4.70e-08)]_160 38011 1.37e-04 170_[+3(8.10e-07)]_116_\ [+1(1.09e-05)]_177 406 1.04e-01 423_[+1(2.70e-05)]_61 41754 3.26e-12 15_[+1(6.36e-08)]_166_\ [+3(3.36e-05)]_17_[+2(5.35e-06)]_4_[+3(1.50e-10)]_219 4267 9.55e-05 269_[+1(2.28e-05)]_162_\ [+2(2.84e-07)]_32 4510 7.43e-04 245_[+1(8.94e-06)]_172_\ [+3(1.20e-05)]_46 5036 2.88e-02 438_[+1(1.75e-05)]_46 5185 3.29e-05 100_[+1(4.72e-05)]_39_\ [+3(5.10e-06)]_50_[+2(9.43e-06)]_10_[+3(6.48e-05)]_222 6086 5.79e-05 184_[+2(7.76e-07)]_122_\ [+1(3.75e-06)]_157 8586 4.23e-08 57_[+2(2.27e-05)]_139_\ [+3(2.80e-06)]_32_[+1(2.96e-06)]_65_[+2(1.64e-07)]_128 bd460 7.35e-03 75_[+3(8.25e-06)]_404 bd686 2.02e-06 235_[+3(1.21e-06)]_12_\ [+1(5.47e-05)]_139_[+2(1.47e-06)]_56 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************