******************************************************************************** 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/156/156.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10222 1.0000 500 11405 1.0000 500 1653 1.0000 500 19099 1.0000 500 2008 1.0000 500 24066 1.0000 500 2454 1.0000 500 25059 1.0000 500 261058 1.0000 500 264722 1.0000 500 38230 1.0000 500 38514 1.0000 500 41045 1.0000 500 4243 1.0000 500 4957 1.0000 500 6408 1.0000 500 6446 1.0000 500 6535 1.0000 500 6718 1.0000 500 7016 1.0000 500 7059 1.0000 500 7512 1.0000 500 8237 1.0000 500 8431 1.0000 500 8528 1.0000 500 9360 1.0000 500 bd1949 1.0000 500 bd661 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/156/156.seqs.fa -oc motifs/156 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.227 G 0.237 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.227 G 0.237 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 18 llr = 226 E-value = 5.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1a42262637317428:4411 pos.-specific C 8:48718351:8338225238 probability G 1:1::3::214::2:16133: matrix T ::1:21:1:121::1:2::21 bits 2.1 1.9 * 1.7 * 1.5 * * Relative 1.3 ** * * * * Entropy 1.1 ** * * ** ** * (18.1 bits) 0.9 ** ** * ** ** * * 0.6 ** ** **** ** **** * 0.4 ** **************** * 0.2 ********************* 0.0 --------------------- Multilevel CAACCACACAGCAACAGCACC consensus C GACA A CC CAGG sequence G T G T CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1949 407 4.64e-10 GAAAGAGGGA CAACCACAGAGCAGCAGAGCC GTAGAAGCAA 24066 306 4.64e-10 AGAAAGAGGT CAACCACAGAGCAGCAGAGCC GTGAAGCAAG 2454 391 6.68e-08 TGCTGTTACT CACCCGCCCAAACACAGCAAC TCGCCGCCTG 38230 39 1.15e-07 GTGTCAGGGA CAAATGCACATCAACACCAGC GACAAGTGCA 7016 17 1.94e-07 TACTACATTT GAACCAACAAACAACAGAAGC TCAAGCTCAA 19099 191 1.94e-07 CTGTGTGTAG CAACCCCACAGCCACAGGCTC TTCTCTCTAG 6535 376 3.17e-07 TCTCCGACGT CATCCGCCCATCACCATCACT TGAACTCACC 7059 394 5.54e-07 ACAATTCTCT CACCCACCCGTCAAACGCCTC AGCCTCGACC 261058 476 7.24e-07 ACACGCGCCA AACACTCACAACACCATCGGC TAAT 8431 18 7.90e-07 ACACATCACT CACCTGAAGTGCCACAGCGTC GAACCCTTAC 11405 89 9.38e-07 TATTGGGGTA CACCAACAACACACCACAAAC CACAAACCTC 2008 472 1.42e-06 GCCTACTCAT CAACCACCCAACAAACCAAGA CGTGTACC 9360 323 1.54e-06 CTGTGTATGG CAGCCGCTAATCAGCAGAAGT TAGCAATAAC 38514 238 1.67e-06 ACAAGTTAGC CAACAAAACAGCAGTACACCC TCAACAGTAT 6446 353 3.09e-06 TGTTGCAAGT CACCTTCAGAAACCAAGCAGC AAGGGGGTAC 25059 378 3.09e-06 TTGTTGAAGA AATCCACTCAGCCCCCTCCCC TCTGTCCAGT 10222 433 4.13e-06 GCCTCTCCCT CACCAACCATGCCACGTCGTC GTCGTTGCCT bd661 297 1.12e-05 AGCTAAATAT CAGACAAAAGGTACCAGAGCC TGCCCAGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1949 4.6e-10 406_[+1]_73 24066 4.6e-10 305_[+1]_174 2454 6.7e-08 390_[+1]_89 38230 1.2e-07 38_[+1]_441 7016 1.9e-07 16_[+1]_463 19099 1.9e-07 190_[+1]_289 6535 3.2e-07 375_[+1]_104 7059 5.5e-07 393_[+1]_86 261058 7.2e-07 475_[+1]_4 8431 7.9e-07 17_[+1]_462 11405 9.4e-07 88_[+1]_391 2008 1.4e-06 471_[+1]_8 9360 1.5e-06 322_[+1]_157 38514 1.7e-06 237_[+1]_242 6446 3.1e-06 352_[+1]_127 25059 3.1e-06 377_[+1]_102 10222 4.1e-06 432_[+1]_47 bd661 1.1e-05 296_[+1]_183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=18 bd1949 ( 407) CAACCACAGAGCAGCAGAGCC 1 24066 ( 306) CAACCACAGAGCAGCAGAGCC 1 2454 ( 391) CACCCGCCCAAACACAGCAAC 1 38230 ( 39) CAAATGCACATCAACACCAGC 1 7016 ( 17) GAACCAACAAACAACAGAAGC 1 19099 ( 191) CAACCCCACAGCCACAGGCTC 1 6535 ( 376) CATCCGCCCATCACCATCACT 1 7059 ( 394) CACCCACCCGTCAAACGCCTC 1 261058 ( 476) AACACTCACAACACCATCGGC 1 8431 ( 18) CACCTGAAGTGCCACAGCGTC 1 11405 ( 89) CACCAACAACACACCACAAAC 1 2008 ( 472) CAACCACCCAACAAACCAAGA 1 9360 ( 323) CAGCCGCTAATCAGCAGAAGT 1 38514 ( 238) CAACAAAACAGCAGTACACCC 1 6446 ( 353) CACCTTCAGAAACCAAGCAGC 1 25059 ( 378) AATCCACTCAGCCCCCTCCCC 1 10222 ( 433) CACCAACCATGCCACGTCGTC 1 bd661 ( 297) CAGACAAAAGGTACCAGAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 10.3912 E= 5.4e-004 -126 188 -209 -1081 191 -1081 -1081 -1081 55 78 -109 -128 -67 188 -1081 -1081 -67 155 -1081 -69 106 -203 23 -128 -26 178 -1081 -1081 106 55 -1081 -128 6 114 -9 -1081 144 -203 -109 -128 33 -1081 90 -28 -126 188 -1081 -228 133 55 -1081 -1081 74 55 -9 -1081 -67 178 -1081 -228 155 -45 -209 -1081 -1081 -3 123 -28 74 114 -209 -1081 74 -3 49 -1081 -126 55 49 -28 -226 188 -1081 -128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 5.4e-004 0.111111 0.833333 0.055556 0.000000 1.000000 0.000000 0.000000 0.000000 0.388889 0.388889 0.111111 0.111111 0.166667 0.833333 0.000000 0.000000 0.166667 0.666667 0.000000 0.166667 0.555556 0.055556 0.277778 0.111111 0.222222 0.777778 0.000000 0.000000 0.555556 0.333333 0.000000 0.111111 0.277778 0.500000 0.222222 0.000000 0.722222 0.055556 0.111111 0.111111 0.333333 0.000000 0.444444 0.222222 0.111111 0.833333 0.000000 0.055556 0.666667 0.333333 0.000000 0.000000 0.444444 0.333333 0.222222 0.000000 0.166667 0.777778 0.000000 0.055556 0.777778 0.166667 0.055556 0.000000 0.000000 0.222222 0.555556 0.222222 0.444444 0.500000 0.055556 0.000000 0.444444 0.222222 0.333333 0.000000 0.111111 0.333333 0.333333 0.222222 0.055556 0.833333 0.000000 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC]CC[AG][CA][AC][CAG]A[GAT]C[AC][ACG]CA[GCT][CA][AGC][CGT]C -------------------------------------------------------------------------------- Time 8.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 28 llr = 269 E-value = 7.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 21:1:1311:61111:1:: pos.-specific C ::2314:13:21:2:11:: probability G 5253:32149:351:721a matrix T 373493582135469259: bits 2.1 * 1.9 * 1.7 * 1.5 * * * * Relative 1.3 * * * ** Entropy 1.1 * * * ** (13.8 bits) 0.9 * * ** ** 0.6 ** * * ** * ** ** 0.4 *** * ** ** **** ** 0.2 ******************* 0.0 ------------------- Multilevel GTGTTCTTGGATGTTGTTG consensus TGTC GA C TGTC TG sequence A G TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 6446 326 1.84e-09 TTGGTTGAGG TTGCTCATCGATGTTGTTG TTGCAAGTCA 41045 361 9.77e-08 AGTGAAGTGA TTGCTCTTGGTGTTTGGTG CCAAGTGTCG 7059 172 2.96e-07 GCAGAGAGAC ATGGTGTTGGACGTTGCTG TCTGATCGAT 264722 299 2.96e-07 GTTTAGTCGG GTTCTCTTTGATGATGTTG TCCCCTACTA 9360 454 4.59e-07 CATGCGTTGT TGTTTGTTGGCTGTTGTTG AGAAACACTG 2454 4 4.59e-07 AGT GTCTTCGTCGATATTGGTG GCACTGGATG 2008 180 1.04e-06 GCTTGGTGAA GTGGTAATTGTTGTTGGTG CTCGGCCATG bd1949 134 1.52e-06 CTAACTCTTC GAGCTCATCGACGTTTTTG TGTGTTCACG 24066 35 1.52e-06 CTAACTCTTC GAGCTCATCGACGTTTTTG TGTGTTCACG 8431 270 1.73e-06 GTTGCGATCG TGGCTCATGGTGTTTGATG AAGGAACATA 1653 160 1.73e-06 CGGTGGATGA GTGATGGTGGAAGTTGCTG ACGGTGAAGG 4243 152 3.92e-06 TGTGGAGGAG GTGGTTGTAGTTTTTTGTG TCGACGGATT 19099 4 3.92e-06 GTA GTGGTAGTGGTAGCTGTTG TAGAGATGCA 7016 160 1.12e-05 AAGCTAGATA TTTGTTGTGTATTGTGTTG CCGTTGATTG 25059 152 1.23e-05 TAGTAGTAGA GTGTTGAATGCTTTTTTTG AGCTGAATCA 10222 100 1.23e-05 AGATTGTTGC ATTCTCTGCGCTTGTGTTG ATTTTCACAA bd661 141 2.36e-05 TTGGGGAGGC ATTTTCTTCGTTTCAGATG TTCAAGTTCA 38230 102 2.57e-05 CGATTCATCA GGGCTGACCGAGTTTGGGG TGCTGGCGGC 8237 37 3.33e-05 ATTTTGCTTA TGGGTTTTAGATAGTGCTG TGTGTTCACA 6408 394 4.27e-05 TTTGCGGTGA AGCGCGTTGGAGGGTGCTG TGAAACTTTC 6535 28 4.63e-05 TGTTTGCTCC GTCTCCTTCGATGCTGACG ATGACGACGA 4957 191 1.21e-04 GTTAGAGGGA ATGTTTAATTAGGATGTTG GTTTGTAGAT 7512 233 1.29e-04 CGGAGCTGCC GTTTTGTTTTCGGCTCATG TACTCGATCC 8528 49 1.48e-04 GTTTGAGGCA GGCGTCGGCTTGGTTGTGG TTCAGTGATT 38514 136 1.57e-04 AGTAGCAGCT TTCACTTTAGATTCTTTTG TCGAGTCAAT 11405 217 1.57e-04 AGGCTCTCTT GTTTTTTTGGAAACACTTG TATAGGTGCA 261058 356 1.90e-04 TGTCTACTTC GTATTTTGAGAGGTATTTG TATCGAAACG 6718 434 3.40e-04 GAGTGTTCAC AATTTGACGGCGTTTGGGG TACAATTAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6446 1.8e-09 325_[+2]_156 41045 9.8e-08 360_[+2]_121 7059 3e-07 171_[+2]_310 264722 3e-07 298_[+2]_183 9360 4.6e-07 453_[+2]_28 2454 4.6e-07 3_[+2]_478 2008 1e-06 179_[+2]_302 bd1949 1.5e-06 133_[+2]_348 24066 1.5e-06 34_[+2]_447 8431 1.7e-06 269_[+2]_212 1653 1.7e-06 159_[+2]_322 4243 3.9e-06 151_[+2]_330 19099 3.9e-06 3_[+2]_478 7016 1.1e-05 159_[+2]_322 25059 1.2e-05 151_[+2]_330 10222 1.2e-05 99_[+2]_382 bd661 2.4e-05 140_[+2]_341 38230 2.6e-05 101_[+2]_380 8237 3.3e-05 36_[+2]_445 6408 4.3e-05 393_[+2]_88 6535 4.6e-05 27_[+2]_454 4957 0.00012 190_[+2]_291 7512 0.00013 232_[+2]_249 8528 0.00015 48_[+2]_433 38514 0.00016 135_[+2]_346 11405 0.00016 216_[+2]_265 261058 0.00019 355_[+2]_126 6718 0.00034 433_[+2]_48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=28 6446 ( 326) TTGCTCATCGATGTTGTTG 1 41045 ( 361) TTGCTCTTGGTGTTTGGTG 1 7059 ( 172) ATGGTGTTGGACGTTGCTG 1 264722 ( 299) GTTCTCTTTGATGATGTTG 1 9360 ( 454) TGTTTGTTGGCTGTTGTTG 1 2454 ( 4) GTCTTCGTCGATATTGGTG 1 2008 ( 180) GTGGTAATTGTTGTTGGTG 1 bd1949 ( 134) GAGCTCATCGACGTTTTTG 1 24066 ( 35) GAGCTCATCGACGTTTTTG 1 8431 ( 270) TGGCTCATGGTGTTTGATG 1 1653 ( 160) GTGATGGTGGAAGTTGCTG 1 4243 ( 152) GTGGTTGTAGTTTTTTGTG 1 19099 ( 4) GTGGTAGTGGTAGCTGTTG 1 7016 ( 160) TTTGTTGTGTATTGTGTTG 1 25059 ( 152) GTGTTGAATGCTTTTTTTG 1 10222 ( 100) ATTCTCTGCGCTTGTGTTG 1 bd661 ( 141) ATTTTCTTCGTTTCAGATG 1 38230 ( 102) GGGCTGACCGAGTTTGGGG 1 8237 ( 37) TGGGTTTTAGATAGTGCTG 1 6408 ( 394) AGCGCGTTGGAGGGTGCTG 1 6535 ( 28) GTCTCCTTCGATGCTGACG 1 4957 ( 191) ATGTTTAATTAGGATGTTG 1 7512 ( 233) GTTTTGTTTTCGGCTCATG 1 8528 ( 49) GGCGTCGGCTTGGTTGTGG 1 38514 ( 136) TTCACTTTAGATTCTTTTG 1 11405 ( 217) GTTTTTTTGGAAACACTTG 1 261058 ( 356) GTATTTTGAGAGGTATTTG 1 6718 ( 434) AATTTGACGGCGTTTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 13496 bayes= 8.90989 E= 7.1e-004 -31 -1145 117 -11 -131 -1145 -15 133 -289 -35 108 8 -189 33 27 40 -1145 -108 -1145 173 -189 79 27 -11 27 -1145 -15 78 -189 -167 -115 147 -90 50 59 -60 -1145 -1145 185 -92 110 -35 -1145 -11 -131 -108 44 78 -131 -1145 117 40 -189 -8 -73 108 -131 -1145 -1145 173 -1145 -167 159 -33 -90 -67 -15 89 -1145 -267 -115 167 -1145 -1145 207 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 28 E= 7.1e-004 0.214286 0.000000 0.535714 0.250000 0.107143 0.000000 0.214286 0.678571 0.035714 0.178571 0.500000 0.285714 0.071429 0.285714 0.285714 0.357143 0.000000 0.107143 0.000000 0.892857 0.071429 0.392857 0.285714 0.250000 0.321429 0.000000 0.214286 0.464286 0.071429 0.071429 0.107143 0.750000 0.142857 0.321429 0.357143 0.178571 0.000000 0.000000 0.857143 0.142857 0.571429 0.178571 0.000000 0.250000 0.107143 0.107143 0.321429 0.464286 0.107143 0.000000 0.535714 0.357143 0.071429 0.214286 0.142857 0.571429 0.107143 0.000000 0.000000 0.892857 0.000000 0.071429 0.714286 0.214286 0.142857 0.142857 0.214286 0.500000 0.000000 0.035714 0.107143 0.857143 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GTA][TG][GT][TCG]T[CGT][TAG]T[GC]G[AT][TG][GT][TC]T[GT][TG]TG -------------------------------------------------------------------------------- Time 15.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 21 llr = 221 E-value = 1.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 6::431924a3:5:61 pos.-specific C 1:132::3:::2:1:: probability G 3:7329:26:381819 matrix T :a2:2:12::4:4:3: bits 2.1 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 * ** * * * * Entropy 1.1 * ** ** * * * (15.2 bits) 0.9 ** ** ** * * * 0.6 *** ** ** ***** 0.4 **** ** ******** 0.2 **** ** ******** 0.0 ---------------- Multilevel ATGAAGACGATGAGAG consensus G TGC AA GCT T sequence CT T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 4243 60 2.64e-07 CGGTGATAGC GTGATGAGGAGGAGAG CCACGAGGCT 7016 284 5.57e-07 AGATAGCAAG ATGCTGAGAAAGTGAG AACTGATAAT 11405 241 5.57e-07 ACTTGTATAG GTGCAGAAAAGGTGAG TTTGTGTCAA bd661 66 7.33e-07 GTGCCTTTGG GTGGCGACGAGGAGGG GTGATGTCTT 10222 377 7.33e-07 CATGTGTGCA ATGAGGATAATGAGTG GTCAAAATGT 6535 47 1.22e-06 GATGCTGACG ATGACGACGAGGACTG TCATTTGCCT 2008 244 1.39e-06 GCGTTGAGAG ATGGAGATGATGGGTG AATGGAGTTT 9360 302 2.18e-06 TGGATGTTGG ATGCTGACAAGCTGTG TATGGCAGCC 7059 6 2.44e-06 GGAAC ATTGCGTCGATGAGAG AGCTTTCCTT 6446 482 4.06e-06 TTCGAAGATT ATGAAGACGAGCTGAA CAG 8237 283 5.38e-06 CACGGCAATG ATGAAGTGGAGGGGAG AAGGAAGAGC 1653 245 5.38e-06 CTTCATTTTC GTTGGGAAAAAGTGAG ATAGATGTGT 7512 279 5.88e-06 TCCCGAATGG CTTCCGATGAAGAGAG CGACGAGTAT 19099 28 7.03e-06 TGTTGTAGAG ATGCAGTAGATCAGTG AGTACAGAGA 2454 105 9.08e-06 GATCCAAGAG ATGACGACGATCTTAG TCCATGAATT 8528 283 9.87e-06 TGGTGTTGCG ATGAGAAAGAACAGAG TGACATCACA bd1949 390 1.69e-05 AATACTAAAA GTTGGGAGAAAGAGGG ACAACCACAG 41045 280 2.24e-05 GTGGTGGCAG CTGAAGATGATGTCGG ATTGTTTAAG 6718 349 3.11e-05 AATGAACGAA ATCCATACGATGTGTG CAAACAATTC 25059 117 3.11e-05 AACAGAGAAG ATCGTGATAATGTGAA GGAACTTCAT 24066 70 8.24e-05 CACGTGCGGT GTTGTAAAAAAGACAG GGGCATGCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4243 2.6e-07 59_[+3]_425 7016 5.6e-07 283_[+3]_201 11405 5.6e-07 240_[+3]_244 bd661 7.3e-07 65_[+3]_419 10222 7.3e-07 376_[+3]_108 6535 1.2e-06 46_[+3]_438 2008 1.4e-06 243_[+3]_241 9360 2.2e-06 301_[+3]_183 7059 2.4e-06 5_[+3]_479 6446 4.1e-06 481_[+3]_3 8237 5.4e-06 282_[+3]_202 1653 5.4e-06 244_[+3]_240 7512 5.9e-06 278_[+3]_206 19099 7e-06 27_[+3]_457 2454 9.1e-06 104_[+3]_380 8528 9.9e-06 282_[+3]_202 bd1949 1.7e-05 389_[+3]_95 41045 2.2e-05 279_[+3]_205 6718 3.1e-05 348_[+3]_136 25059 3.1e-05 116_[+3]_368 24066 8.2e-05 69_[+3]_415 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=21 4243 ( 60) GTGATGAGGAGGAGAG 1 7016 ( 284) ATGCTGAGAAAGTGAG 1 11405 ( 241) GTGCAGAAAAGGTGAG 1 bd661 ( 66) GTGGCGACGAGGAGGG 1 10222 ( 377) ATGAGGATAATGAGTG 1 6535 ( 47) ATGACGACGAGGACTG 1 2008 ( 244) ATGGAGATGATGGGTG 1 9360 ( 302) ATGCTGACAAGCTGTG 1 7059 ( 6) ATTGCGTCGATGAGAG 1 6446 ( 482) ATGAAGACGAGCTGAA 1 8237 ( 283) ATGAAGTGGAGGGGAG 1 1653 ( 245) GTTGGGAAAAAGTGAG 1 7512 ( 279) CTTCCGATGAAGAGAG 1 19099 ( 28) ATGCAGTAGATCAGTG 1 2454 ( 105) ATGACGACGATCTTAG 1 8528 ( 283) ATGAGAAAGAACAGAG 1 bd1949 ( 390) GTTGGGAGAAAGAGGG 1 41045 ( 280) CTGAAGATGATGTCGG 1 6718 ( 349) ATCCATACGATGTGTG 1 25059 ( 117) ATCGTGATAATGTGAA 1 24066 ( 70) GTTGTAAAAAAGACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 9.63993 E= 1.3e-003 122 -125 27 -1104 -1104 -1104 -1104 189 -1104 -125 149 -18 52 33 49 -1104 33 7 -32 -18 -148 -1104 185 -250 169 -1104 -1104 -92 -16 55 -32 -18 52 -1104 138 -1104 191 -1104 -1104 -1104 10 -1104 49 50 -1104 7 168 -1104 84 -1104 -132 67 -1104 -67 177 -250 110 -1104 -73 8 -148 -1104 193 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 21 E= 1.3e-003 0.619048 0.095238 0.285714 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.095238 0.666667 0.238095 0.380952 0.285714 0.333333 0.000000 0.333333 0.238095 0.190476 0.238095 0.095238 0.000000 0.857143 0.047619 0.857143 0.000000 0.000000 0.142857 0.238095 0.333333 0.190476 0.238095 0.380952 0.000000 0.619048 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.333333 0.380952 0.000000 0.238095 0.761905 0.000000 0.476190 0.000000 0.095238 0.428571 0.000000 0.142857 0.809524 0.047619 0.571429 0.000000 0.142857 0.285714 0.095238 0.000000 0.904762 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG]T[GT][AGC][ACT]GA[CAT][GA]A[TGA][GC][AT]G[AT]G -------------------------------------------------------------------------------- Time 23.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10222 8.60e-07 99_[+2(1.23e-05)]_258_\ [+3(7.33e-07)]_40_[+1(4.13e-06)]_47 11405 1.70e-06 88_[+1(9.38e-07)]_131_\ [+3(5.57e-07)]_244 1653 1.80e-04 159_[+2(1.73e-06)]_66_\ [+3(5.38e-06)]_240 19099 1.48e-07 3_[+2(3.92e-06)]_5_[+3(7.03e-06)]_\ 147_[+1(1.94e-07)]_289 2008 6.21e-08 103_[+2(1.97e-05)]_57_\ [+2(1.04e-06)]_45_[+3(1.39e-06)]_212_[+1(1.42e-06)]_8 24066 2.30e-09 34_[+2(1.52e-06)]_16_[+3(8.24e-05)]_\ 220_[+1(4.64e-10)]_174 2454 9.91e-09 3_[+2(4.59e-07)]_82_[+3(9.08e-06)]_\ 270_[+1(6.68e-08)]_89 25059 1.87e-05 116_[+3(3.11e-05)]_19_\ [+2(1.23e-05)]_207_[+1(3.09e-06)]_102 261058 1.96e-03 475_[+1(7.24e-07)]_4 264722 2.65e-03 269_[+2(1.49e-05)]_10_\ [+2(2.96e-07)]_183 38230 5.27e-05 38_[+1(1.15e-07)]_42_[+2(2.57e-05)]_\ 380 38514 2.19e-03 237_[+1(1.67e-06)]_242 41045 6.12e-05 279_[+3(2.24e-05)]_65_\ [+2(9.77e-08)]_6_[+2(1.23e-05)]_96 4243 2.53e-05 59_[+3(2.64e-07)]_76_[+2(3.92e-06)]_\ 330 4957 3.19e-01 500 6408 9.43e-02 393_[+2(4.27e-05)]_88 6446 9.91e-10 325_[+2(1.84e-09)]_8_[+1(3.09e-06)]_\ 108_[+3(4.06e-06)]_3 6535 4.41e-07 46_[+3(1.22e-06)]_313_\ [+1(3.17e-07)]_104 6718 2.72e-02 348_[+3(3.11e-05)]_136 7016 3.81e-08 16_[+1(1.94e-07)]_122_\ [+2(1.12e-05)]_105_[+3(5.57e-07)]_64_[+3(7.50e-05)]_121 7059 1.38e-08 5_[+3(2.44e-06)]_150_[+2(2.96e-07)]_\ 52_[+3(7.87e-05)]_34_[+2(5.42e-05)]_82_[+1(5.54e-07)]_86 7512 3.00e-03 278_[+3(5.88e-06)]_206 8237 6.18e-04 36_[+2(3.33e-05)]_172_\ [+3(2.74e-05)]_39_[+3(5.38e-06)]_202 8431 3.02e-05 17_[+1(7.90e-07)]_231_\ [+2(1.73e-06)]_212 8528 1.46e-03 282_[+3(9.87e-06)]_202 9360 4.78e-08 301_[+3(2.18e-06)]_5_[+1(1.54e-06)]_\ 66_[+2(3.93e-05)]_25_[+2(4.59e-07)]_28 bd1949 5.37e-10 133_[+2(1.52e-06)]_16_\ [+3(8.24e-05)]_205_[+3(1.69e-05)]_1_[+1(4.64e-10)]_73 bd661 3.74e-06 65_[+3(7.33e-07)]_59_[+2(2.36e-05)]_\ 137_[+1(1.12e-05)]_183 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************