******************************************************************************** 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/6/6.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10497 1.0000 500 11331 1.0000 500 11418 1.0000 500 1291 1.0000 500 16695 1.0000 500 1936 1.0000 500 1972 1.0000 500 21145 1.0000 500 21282 1.0000 500 21306 1.0000 500 21620 1.0000 500 22074 1.0000 500 22526 1.0000 500 24931 1.0000 500 260841 1.0000 500 261184 1.0000 500 264361 1.0000 500 264773 1.0000 500 264807 1.0000 500 264811 1.0000 500 269017 1.0000 500 269395 1.0000 500 27352 1.0000 500 30178 1.0000 500 31169 1.0000 500 31316 1.0000 500 33685 1.0000 500 36037 1.0000 500 40630 1.0000 500 5807 1.0000 500 8058 1.0000 500 8222 1.0000 500 8514 1.0000 500 8672 1.0000 500 915 1.0000 500 9436 1.0000 500 9483 1.0000 500 9776 1.0000 500 bd1772 1.0000 500 bd1810 1.0000 500 bd2107 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/6/6.seqs.fa -oc motifs/6 -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= 41 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= 20500 N= 41 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.226 G 0.233 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.226 G 0.233 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 26 llr = 312 E-value = 2.5e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 584177:3:7:2:2:2:15:: pos.-specific C 2:3::2:2::::1::1::12: probability G 22172:91916572a238229 matrix T ::22:114123326:57135: bits 2.1 * 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * * * ** * (17.3 bits) 0.9 * ** * * * * * ** * 0.6 * **** *** * * ** ** 0.4 ** **** ******* ** ** 0.2 ********************* 0.0 --------------------- Multilevel AAAGAAGTGAGGGTGTTGATG consensus C C A TTTTG AG TC sequence G A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31316 377 4.06e-10 CTGCAGGCGG AAAGAAGAGAGATTGTTGATG GCAATTGGGT 36037 257 2.68e-09 AGGAAAAAGA AATGAAGAGAGTGTGTTGCTG TTCGGTTGAC 269395 258 2.68e-09 AGGAAAAAGA AATGAAGAGAGTGTGTTGCTG TTCGGTTGAC 21620 131 6.11e-09 CTGGCAGAAG CAGGAAGTGAGAGTGTGGTTG GCTGACAGAT 31169 333 3.01e-08 TGCTGACACC AACGAAGTGAGTTTGAGGGCG TTGAGAGAGG 1936 332 3.01e-08 TGCTGACACC AACGAAGTGAGTTTGAGGGCG TTGAGAGAGG 915 204 3.92e-08 AGAAAACTTC GAAGAAGTGAGAGGGCGGTTG GTATGCGAGA 8058 36 1.67e-07 GGTGTCTCGT CAAAAAGCGTTGGTGATGATG TTCTAGCAGT 5807 8 3.56e-07 GAGTAGT GAAGCAGAGTTGTTGTTGATG GGTGTGGTGG 22074 362 5.34e-07 GTGTTCTCCT AAAGTAGAGTGGGAGATGGTG TTCTCATCTT 269017 156 6.50e-07 AGAGGCTATT CGCGAAGTTAGAGAGTTGACG CAAATGTATT 8672 124 8.67e-07 CTTGGTATCA GATGACGTGTTGCTGCTGATG AAAACATTGT 11418 184 8.67e-07 CACTGTAAAC CACGATGTGATGGGGTGATTG GGATCATCGT 24931 45 1.96e-06 AAGACTTTGT AAATAGGTGGTGGAGATGATG TTGTGCGCGG 11331 82 2.74e-06 GAGATAGTGA AACAAATCGATAGTGGTGACG GGCTGATGCT 30178 340 4.12e-06 AACTCTAAAT AAATATTCGAGAGAGTGGATG CTAACAATGA 21282 35 4.82e-06 ATGGTGTTTC AGGTGAGTGGGTGTGTTGCGG AGAGAGGAGT 1291 359 5.62e-06 CAGGCTGACT CACTGCGCGACGGTGGTGACG ACGGCACCTT 264811 254 7.05e-06 GTTCATCGCG AAGGGAGGTGTGGTGTGGTTG TGTACACAGA 264807 469 7.05e-06 GTACGAGGCC GGCGGCGTGTGGCAGTGGTGG GTATTCGCCT 9483 293 7.59e-06 TTCATGTTGA GGATACGAGAGGGGGTTCTGG GTGTGCCAGG 9776 60 8.16e-06 CCTCTGTATA ATAAACGAGTGGTGGTTGAGG TGAACAGAGA 27352 185 9.43e-06 AGTTGTTTGA AGTGGTGTGATGGTGGTGATC CGTTATGGAT 264361 19 1.09e-05 TGAGAGGTCA AACGAAGGGATTCTGCGTTGG ATGTATCGTC 21306 9 1.09e-05 GATGCAAT CACGAAGAGAGGTGGGTAAGT CGATCCATTT 264773 166 1.53e-05 ACGTTCTGTG GAAGAAGAGAGTGGGATTGCA AAAGAGATTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31316 4.1e-10 376_[+1]_103 36037 2.7e-09 256_[+1]_223 269395 2.7e-09 257_[+1]_222 21620 6.1e-09 130_[+1]_349 31169 3e-08 332_[+1]_147 1936 3e-08 331_[+1]_148 915 3.9e-08 203_[+1]_276 8058 1.7e-07 35_[+1]_444 5807 3.6e-07 7_[+1]_472 22074 5.3e-07 361_[+1]_118 269017 6.5e-07 155_[+1]_324 8672 8.7e-07 123_[+1]_356 11418 8.7e-07 183_[+1]_296 24931 2e-06 44_[+1]_435 11331 2.7e-06 81_[+1]_398 30178 4.1e-06 339_[+1]_140 21282 4.8e-06 34_[+1]_445 1291 5.6e-06 358_[+1]_121 264811 7e-06 253_[+1]_226 264807 7e-06 468_[+1]_11 9483 7.6e-06 292_[+1]_187 9776 8.2e-06 59_[+1]_420 27352 9.4e-06 184_[+1]_295 264361 1.1e-05 18_[+1]_461 21306 1.1e-05 8_[+1]_471 264773 1.5e-05 165_[+1]_314 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=26 31316 ( 377) AAAGAAGAGAGATTGTTGATG 1 36037 ( 257) AATGAAGAGAGTGTGTTGCTG 1 269395 ( 258) AATGAAGAGAGTGTGTTGCTG 1 21620 ( 131) CAGGAAGTGAGAGTGTGGTTG 1 31169 ( 333) AACGAAGTGAGTTTGAGGGCG 1 1936 ( 332) AACGAAGTGAGTTTGAGGGCG 1 915 ( 204) GAAGAAGTGAGAGGGCGGTTG 1 8058 ( 36) CAAAAAGCGTTGGTGATGATG 1 5807 ( 8) GAAGCAGAGTTGTTGTTGATG 1 22074 ( 362) AAAGTAGAGTGGGAGATGGTG 1 269017 ( 156) CGCGAAGTTAGAGAGTTGACG 1 8672 ( 124) GATGACGTGTTGCTGCTGATG 1 11418 ( 184) CACGATGTGATGGGGTGATTG 1 24931 ( 45) AAATAGGTGGTGGAGATGATG 1 11331 ( 82) AACAAATCGATAGTGGTGACG 1 30178 ( 340) AAATATTCGAGAGAGTGGATG 1 21282 ( 35) AGGTGAGTGGGTGTGTTGCGG 1 1291 ( 359) CACTGCGCGACGGTGGTGACG 1 264811 ( 254) AAGGGAGGTGTGGTGTGGTTG 1 264807 ( 469) GGCGGCGTGTGGCAGTGGTGG 1 9483 ( 293) GGATACGAGAGGGGGTTCTGG 1 9776 ( 60) ATAAACGAGTGGTGGTTGAGG 1 27352 ( 185) AGTGGTGTGATGGTGGTGATC 1 264361 ( 19) AACGAAGGGATTCTGCGTTGG 1 21306 ( 9) CACGAAGAGAGGTGGGTAAGT 1 264773 ( 166) GAAGAAGAGAGTGGGATTGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19680 bayes= 10.0932 E= 2.5e-012 99 3 -1 -1134 150 -1134 -28 -281 50 62 -101 -81 -123 -1134 157 -49 143 -255 -28 -281 127 -23 -260 -122 -1134 -1134 198 -181 35 -55 -160 65 -1134 -1134 198 -181 127 -1134 -101 -22 -1134 -255 140 36 -23 -1134 110 0 -1134 -97 149 -22 -50 -1134 -1 110 -1134 -1134 210 -1134 -23 -97 -60 89 -1134 -1134 57 128 -182 -255 179 -181 76 -97 -60 0 -1134 3 -1 100 -282 -255 192 -281 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 2.5e-012 0.538462 0.230769 0.230769 0.000000 0.769231 0.000000 0.192308 0.038462 0.384615 0.346154 0.115385 0.153846 0.115385 0.000000 0.692308 0.192308 0.730769 0.038462 0.192308 0.038462 0.653846 0.192308 0.038462 0.115385 0.000000 0.000000 0.923077 0.076923 0.346154 0.153846 0.076923 0.423077 0.000000 0.000000 0.923077 0.076923 0.653846 0.000000 0.115385 0.230769 0.000000 0.038462 0.615385 0.346154 0.230769 0.000000 0.500000 0.269231 0.000000 0.115385 0.653846 0.230769 0.192308 0.000000 0.230769 0.576923 0.000000 0.000000 1.000000 0.000000 0.230769 0.115385 0.153846 0.500000 0.000000 0.000000 0.346154 0.653846 0.076923 0.038462 0.807692 0.076923 0.461538 0.115385 0.153846 0.269231 0.000000 0.230769 0.230769 0.538462 0.038462 0.038462 0.884615 0.038462 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACG]A[AC]GAAG[TA]G[AT][GT][GTA][GT][TG]G[TA][TG]G[AT][TCG]G -------------------------------------------------------------------------------- Time 12.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 38 llr = 343 E-value = 9.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :6313::53122163: pos.-specific C 64:9238427537139 probability G 2:1:1::11:::::31 matrix T 2:6:472:3235231: bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * ** * * * (13.0 bits) 0.9 ** * ** * * * 0.6 **** *** ** ** * 0.4 **** *** ***** * 0.2 ******** ******* 0.0 ---------------- Multilevel CATCTTCAACCTCAAC consensus GCA AC CTTTC TC sequence C C A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11331 450 1.33e-07 CGTTCGACAA CATCCTCACCTTCAAC TTCCAACGCT 36037 479 4.27e-07 CCAACCGTAA CAACTTCACCCACAGC CTGATC 269395 480 4.27e-07 CCAACCGTAA CAACTTCACCCACAGC CTGAT 22074 387 4.27e-07 ATGGTGTTCT CATCTTCATCAACACC TCCTTTACAC 31169 425 5.15e-07 GCGCCAAACA GCTCTTCAACTTCAGC TCGCCTGTCG 1936 424 5.15e-07 GCGCCAAACA GCTCTTCAACTTCAGC TCGCCTGTCG bd1772 128 1.37e-06 TTGTTGCTTG CCACTTCAGCCTCTCC AACTGATGTG 8222 2 1.60e-06 C GAACTTCAACTTCAAC GTAGAAACGG 10497 101 1.86e-06 CCCGTGTTAC CCTCTTCAGCTCCTCC CTCCCATCTG 22526 303 4.21e-06 ACTTCCTTGT CATCATCAATCTCCCC ACAGAGAAAA bd1810 423 4.80e-06 CCCGCGCGAC CATCTCCGCCATCACC GACACCCAAG 269017 253 5.45e-06 ATTGGTGGTG CAGCTCCCTCTTCTAC CGGTTTAGAC 264361 395 6.17e-06 TCTGACGGTT CATCTTCATCATTTGC ATATCATATC 1972 446 7.83e-06 TTTACCGTCA CCTCTCTCTTCTCACC CGATCAAGAT 260841 331 9.84e-06 TTGAGCTTCA TCTCACCATCTCCAAC TTTGAACAGA 21145 429 9.84e-06 TGATCTTCGT CATCGTCACCCGCACC GCGAAGCGAA 261184 396 1.23e-05 CCGCGCCTGA CCTCTTCCACACAAAC GAAATCCATC 8058 170 2.80e-05 TCTCCCCAAA CCTCTCCAGCTCTTCC AGAACTCACG bd2107 438 3.08e-05 GCTGCCGCTG CCAAATCCTCCTCTGC TGACGGTGCA 9436 189 3.71e-05 TTGAAGCGCC CATCCTCCATATTTCC GGTGTCACGT 33685 243 3.71e-05 GGCATCAGCA GCACATCATCCACCGC ATGAGAAGCC 27352 139 3.71e-05 CTTCTTCTCG CCGCGTCCTCCTTTAC CTTTTCCTGA 264811 453 4.85e-05 TCACCATAGG GAACCTCCTCCTTATC TTTATCTTCG 264807 97 5.29e-05 ATGTACAACA TAGCACCACTCTCAGC CCTCAACATC 21282 256 5.29e-05 AACTATTGTA CAACACCCGCCCAAGC CATCCAGCCA 16695 338 5.76e-05 CGCCTATCCA CAGCACCCGTTCCAAC TGCGCTGCTA 264773 293 7.38e-05 TCGTAAGGGT TCTCATCCTCATCACG AAATCTTCTT 24931 366 1.01e-04 TTTGTCCATA TATATTCCCCTTTAAC ATATAATAGT 8672 224 1.09e-04 AGATAATACA CATCGTCACACACATC AGTGACGAGC 30178 377 1.09e-04 ATGAACTTTC GAGCCTCCTTCCTAGC CGCCTCCGTC 31316 229 1.17e-04 CGAACACTAA CAACGCCGTCCCCCAC AAAATAAAGA 11418 311 1.17e-04 TGTATTTCAC CCTATTTCACCCCATC ACATCGTGTT 9483 438 1.26e-04 TCAAGCACTA TCTCCTTCCTCCCTCC CCTCCGTCGT 915 485 1.36e-04 TTTTCGATCA CATCCCTGACAACAGC 21620 343 1.46e-04 GACAATTAAT GAACATTCATTTCTCC TTCAATGTAT 8514 476 1.67e-04 TTGCCACTCG GCTCATCCAACACCAC CTTGCTATC 1291 239 1.92e-04 ACTTTACAAC TATCCTTAACCAAAAC GAATGTTTTC 9776 306 2.48e-04 TGTGACGAAG CGTCCCCAACTTCAAG ACTAAGCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11331 1.3e-07 449_[+2]_35 36037 4.3e-07 478_[+2]_6 269395 4.3e-07 479_[+2]_5 22074 4.3e-07 386_[+2]_98 31169 5.1e-07 424_[+2]_60 1936 5.1e-07 423_[+2]_61 bd1772 1.4e-06 127_[+2]_357 8222 1.6e-06 1_[+2]_483 10497 1.9e-06 100_[+2]_384 22526 4.2e-06 302_[+2]_182 bd1810 4.8e-06 422_[+2]_62 269017 5.5e-06 252_[+2]_232 264361 6.2e-06 394_[+2]_90 1972 7.8e-06 445_[+2]_39 260841 9.8e-06 330_[+2]_154 21145 9.8e-06 428_[+2]_56 261184 1.2e-05 395_[+2]_89 8058 2.8e-05 169_[+2]_315 bd2107 3.1e-05 437_[+2]_47 9436 3.7e-05 188_[+2]_296 33685 3.7e-05 242_[+2]_242 27352 3.7e-05 138_[+2]_346 264811 4.8e-05 452_[+2]_32 264807 5.3e-05 96_[+2]_388 21282 5.3e-05 255_[+2]_229 16695 5.8e-05 337_[+2]_147 264773 7.4e-05 292_[+2]_192 24931 0.0001 365_[+2]_119 8672 0.00011 223_[+2]_261 30178 0.00011 376_[+2]_108 31316 0.00012 228_[+2]_256 11418 0.00012 310_[+2]_174 9483 0.00013 437_[+2]_47 915 0.00014 484_[+2] 21620 0.00015 342_[+2]_142 8514 0.00017 475_[+2]_9 1291 0.00019 238_[+2]_246 9776 0.00025 305_[+2]_179 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=38 11331 ( 450) CATCCTCACCTTCAAC 1 36037 ( 479) CAACTTCACCCACAGC 1 269395 ( 480) CAACTTCACCCACAGC 1 22074 ( 387) CATCTTCATCAACACC 1 31169 ( 425) GCTCTTCAACTTCAGC 1 1936 ( 424) GCTCTTCAACTTCAGC 1 bd1772 ( 128) CCACTTCAGCCTCTCC 1 8222 ( 2) GAACTTCAACTTCAAC 1 10497 ( 101) CCTCTTCAGCTCCTCC 1 22526 ( 303) CATCATCAATCTCCCC 1 bd1810 ( 423) CATCTCCGCCATCACC 1 269017 ( 253) CAGCTCCCTCTTCTAC 1 264361 ( 395) CATCTTCATCATTTGC 1 1972 ( 446) CCTCTCTCTTCTCACC 1 260841 ( 331) TCTCACCATCTCCAAC 1 21145 ( 429) CATCGTCACCCGCACC 1 261184 ( 396) CCTCTTCCACACAAAC 1 8058 ( 170) CCTCTCCAGCTCTTCC 1 bd2107 ( 438) CCAAATCCTCCTCTGC 1 9436 ( 189) CATCCTCCATATTTCC 1 33685 ( 243) GCACATCATCCACCGC 1 27352 ( 139) CCGCGTCCTCCTTTAC 1 264811 ( 453) GAACCTCCTCCTTATC 1 264807 ( 97) TAGCACCACTCTCAGC 1 21282 ( 256) CAACACCCGCCCAAGC 1 16695 ( 338) CAGCACCCGTTCCAAC 1 264773 ( 293) TCTCATCCTCATCACG 1 24931 ( 366) TATATTCCCCTTTAAC 1 8672 ( 224) CATCGTCACACACATC 1 30178 ( 377) GAGCCTCCTTCCTAGC 1 31316 ( 229) CAACGCCGTCCCCCAC 1 11418 ( 311) CCTATTTCACCCCATC 1 9483 ( 438) TCTCCTTCCTCCCTCC 1 915 ( 485) CATCCCTGACAACAGC 1 21620 ( 343) GAACATTCATTTCTCC 1 8514 ( 476) GCTCATCCAACACCAC 1 1291 ( 239) TATCCTTAACCAAAAC 1 9776 ( 306) CGTCCCCAACTTCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 19885 bayes= 9.22387 E= 9.2e-008 -1189 148 -15 -77 109 81 -314 -1189 -5 -1189 -83 117 -178 203 -1189 -1189 -5 -10 -115 64 -1189 36 -1189 140 -1189 190 -1189 -77 88 90 -156 -1189 22 7 -83 23 -237 171 -1189 -36 -56 115 -1189 23 -37 22 -314 89 -178 171 -1189 -55 122 -110 -1189 -3 22 48 31 -177 -1189 207 -215 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 38 E= 9.2e-008 0.000000 0.631579 0.210526 0.157895 0.578947 0.394737 0.026316 0.000000 0.263158 0.000000 0.131579 0.605263 0.078947 0.921053 0.000000 0.000000 0.263158 0.210526 0.105263 0.421053 0.000000 0.289474 0.000000 0.710526 0.000000 0.842105 0.000000 0.157895 0.500000 0.421053 0.078947 0.000000 0.315789 0.236842 0.131579 0.315789 0.052632 0.736842 0.000000 0.210526 0.184211 0.500000 0.000000 0.315789 0.210526 0.263158 0.026316 0.500000 0.078947 0.736842 0.000000 0.184211 0.631579 0.105263 0.000000 0.263158 0.315789 0.315789 0.289474 0.078947 0.000000 0.947368 0.052632 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG][AC][TA]C[TAC][TC]C[AC][ATC][CT][CT][TCA]C[AT][ACG]C -------------------------------------------------------------------------------- Time 24.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 30 llr = 322 E-value = 8.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3:43:1:::6:::141:42:2 pos.-specific C 273:5:121121:112::215 probability G :22:271:911555:191173 matrix T 51163188:37454651552: bits 2.1 1.9 1.7 * * 1.5 * * Relative 1.3 ** * Entropy 1.1 * *** * * * (15.5 bits) 0.9 * * **** * * * * 0.6 * ****** * * * * ** 0.4 * ************ ** ** 0.2 ********************* 0.0 --------------------- Multilevel TCATCGTTGATGGGTTGTTGC consensus A CAT C T TTTAC AA G sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36037 68 1.59e-08 TCCGTCGTAC TTATCGTTGATGGGATGATGG GAATCTGTCT 269395 69 1.59e-08 TCCGTCGTAC TTATCGTTGATGGGATGATGG GAATCTGTCT 264811 473 1.59e-08 CTTATCTTTA TCTTCGTTGATTGGTAGTAGC TAGCAAC 8514 152 9.65e-08 CGTTTCGGGG ACTTCGTTCATGTTTTGTTGG GAGTGGTTAC 8058 68 4.01e-07 TCTAGCAGTG TCCTCGTTGTTTGGTGGTATA GATTTCCTCC 264773 115 5.73e-07 CTCCAAGAGA ACTTCGTTGTTGGGAAGTTTG ATCCATTCTA 31169 58 9.05e-07 CTGTTCTTGA AGGATGTCGTTTGTTTGTTGC TGTTGTTCCC 1936 57 9.05e-07 CTGTTCTTGA AGGATGTCGTTTGTTTGTTGC TGTTGTTCCC bd1772 350 1.01e-06 TTACTTATGT TCCTGGTCCATTTGTTGTGGC GTTTGATGTT 10497 334 1.01e-06 CAGGTAGTTG TCGACGCTGATCGTATGGTGC ACGTTGATGA 5807 399 1.26e-06 TGGGCTAATG TCCACGTTGACGTCCTGTTGG TGAATTACAT 1972 318 2.13e-06 CCTCTGCCTA CCAACGCTGTTCGGTTGACGG CGTAATCTCT 11331 120 2.13e-06 GCTGATGGAT ACATCAGTGATGTGACGACGC TGAGACGACG 8672 344 3.18e-06 AAATAATGCG CCGTTATTGTTCGGTAGTTGC AACACTAGTG 30178 172 3.86e-06 GTATATTCTT TCCTTGTTGCTGTATCTTTGC TTTGAAGGAG bd1810 35 4.67e-06 GACGTGTTTT TGCACGTCGAGTTGATGATGA ATTCATCTTG 21620 77 7.38e-06 AATATGTCGT CCATGGCTGCTGTGTTGGCGG GTTGTTTGGG 33685 271 8.07e-06 GAGAAGCCTC CCAACGTTGAGTTGTGGGAGA CACTTGCAAC 21145 24 8.07e-06 TGTTCTTCGT CCAATGTTGACTGAATGATTG CCCCTGAATA 24931 429 8.81e-06 CAATTAGTCG ACATGGTTCACGTTTCGTCTC GTGATTTCTC 22074 75 1.05e-05 ACTTCGTGAG TCCACTTTGTCGTATTGTATC CATTCGATAA 22526 210 1.14e-05 GTTACTCACT TGTTCATTGATTTTTCGTTCA TTCCGTAAAG 9483 96 1.46e-05 GTAAAGATAC GCATTGTTGTTGTTTTGGACA GAGGTAGAAC 264807 447 1.87e-05 TAGCTTCCGA TCATTGGCGGTGGTACGAGGC CGGCGGCGTG 8222 334 2.18e-05 GAACCCGAGC TCCTTTTTGGAGTGAGGATGC AATAGATCGG 31316 432 2.36e-05 CACGTAAAAG TGCATCTTGATTGTAAGACGC GAACACAAAC 27352 164 2.36e-05 CCTTTTCCTG ACATGGTTGATAGTTGTTTGA AGTGGTGTGA 260841 273 2.36e-05 GGCTTGAACG ATATGTTTGATGGTACGTTCA TACTTCAAGT 21282 284 2.75e-05 TCCAGCCAAT ACCCCTTCGATTTGCTGAAGC TGTTGCTCTT 9436 211 2.96e-05 TTCCGGTGTC ACGTTGCTGTCTTCTCGAGGC ATCGACGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36037 1.6e-08 67_[+3]_412 269395 1.6e-08 68_[+3]_411 264811 1.6e-08 472_[+3]_7 8514 9.6e-08 151_[+3]_328 8058 4e-07 67_[+3]_412 264773 5.7e-07 114_[+3]_365 31169 9e-07 57_[+3]_422 1936 9e-07 56_[+3]_423 bd1772 1e-06 349_[+3]_130 10497 1e-06 333_[+3]_146 5807 1.3e-06 398_[+3]_81 1972 2.1e-06 317_[+3]_162 11331 2.1e-06 119_[+3]_360 8672 3.2e-06 343_[+3]_136 30178 3.9e-06 171_[+3]_308 bd1810 4.7e-06 34_[+3]_445 21620 7.4e-06 76_[+3]_403 33685 8.1e-06 270_[+3]_209 21145 8.1e-06 23_[+3]_456 24931 8.8e-06 428_[+3]_51 22074 1e-05 74_[+3]_405 22526 1.1e-05 209_[+3]_270 9483 1.5e-05 95_[+3]_384 264807 1.9e-05 446_[+3]_33 8222 2.2e-05 333_[+3]_146 31316 2.4e-05 431_[+3]_48 27352 2.4e-05 163_[+3]_316 260841 2.4e-05 272_[+3]_207 21282 2.7e-05 283_[+3]_196 9436 3e-05 210_[+3]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=30 36037 ( 68) TTATCGTTGATGGGATGATGG 1 269395 ( 69) TTATCGTTGATGGGATGATGG 1 264811 ( 473) TCTTCGTTGATTGGTAGTAGC 1 8514 ( 152) ACTTCGTTCATGTTTTGTTGG 1 8058 ( 68) TCCTCGTTGTTTGGTGGTATA 1 264773 ( 115) ACTTCGTTGTTGGGAAGTTTG 1 31169 ( 58) AGGATGTCGTTTGTTTGTTGC 1 1936 ( 57) AGGATGTCGTTTGTTTGTTGC 1 bd1772 ( 350) TCCTGGTCCATTTGTTGTGGC 1 10497 ( 334) TCGACGCTGATCGTATGGTGC 1 5807 ( 399) TCCACGTTGACGTCCTGTTGG 1 1972 ( 318) CCAACGCTGTTCGGTTGACGG 1 11331 ( 120) ACATCAGTGATGTGACGACGC 1 8672 ( 344) CCGTTATTGTTCGGTAGTTGC 1 30178 ( 172) TCCTTGTTGCTGTATCTTTGC 1 bd1810 ( 35) TGCACGTCGAGTTGATGATGA 1 21620 ( 77) CCATGGCTGCTGTGTTGGCGG 1 33685 ( 271) CCAACGTTGAGTTGTGGGAGA 1 21145 ( 24) CCAATGTTGACTGAATGATTG 1 24931 ( 429) ACATGGTTCACGTTTCGTCTC 1 22074 ( 75) TCCACTTTGTCGTATTGTATC 1 22526 ( 210) TGTTCATTGATTTTTCGTTCA 1 9483 ( 96) GCATTGTTGTTGTTTTGGACA 1 264807 ( 447) TCATTGGCGGTGGTACGAGGC 1 8222 ( 334) TCCTTTTTGGAGTGAGGATGC 1 31316 ( 432) TGCATCTTGATTGTAAGACGC 1 27352 ( 164) ACATGGTTGATAGTTGTTTGA 1 260841 ( 273) ATATGTTTGATGGTACGTTCA 1 21282 ( 284) ACCCCTTCGATTTGCTGAAGC 1 9436 ( 211) ACGTTGCTGTCTTCTCGAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19680 bayes= 10.0304 E= 8.6e-005 30 -44 -280 79 -1155 170 -48 -143 56 41 -48 -102 30 -276 -1155 123 -1155 115 -48 31 -144 -276 165 -102 -1155 -76 -181 157 -1155 -17 -1155 157 -1155 -117 195 -1155 106 -176 -181 15 -302 -44 -181 144 -302 -117 100 57 -1155 -1155 110 89 -144 -176 100 44 43 -176 -1155 107 -103 5 -81 89 -1155 -1155 200 -201 43 -1155 -81 89 -44 -44 -122 98 -1155 -117 165 -69 -22 115 19 -1155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 30 E= 8.6e-005 0.333333 0.166667 0.033333 0.466667 0.000000 0.733333 0.166667 0.100000 0.400000 0.300000 0.166667 0.133333 0.333333 0.033333 0.000000 0.633333 0.000000 0.500000 0.166667 0.333333 0.100000 0.033333 0.733333 0.133333 0.000000 0.133333 0.066667 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.100000 0.900000 0.000000 0.566667 0.066667 0.066667 0.300000 0.033333 0.166667 0.066667 0.733333 0.033333 0.100000 0.466667 0.400000 0.000000 0.000000 0.500000 0.500000 0.100000 0.066667 0.466667 0.366667 0.366667 0.066667 0.000000 0.566667 0.133333 0.233333 0.133333 0.500000 0.000000 0.000000 0.933333 0.066667 0.366667 0.000000 0.133333 0.500000 0.200000 0.166667 0.100000 0.533333 0.000000 0.100000 0.733333 0.166667 0.233333 0.500000 0.266667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]C[AC][TA][CT]GT[TC]G[AT]T[GT][GT][GT][TA][TC]G[TA][TA]G[CGA] -------------------------------------------------------------------------------- Time 35.59 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10497 4.10e-05 100_[+2(1.86e-06)]_217_\ [+3(1.01e-06)]_146 11331 2.53e-08 81_[+1(2.74e-06)]_17_[+3(2.13e-06)]_\ 309_[+2(1.33e-07)]_35 11418 4.71e-04 183_[+1(8.67e-07)]_296 1291 8.11e-03 358_[+1(5.62e-06)]_121 16695 2.68e-01 337_[+2(5.76e-05)]_147 1936 6.23e-10 56_[+3(9.05e-07)]_254_\ [+1(3.01e-08)]_2_[+1(7.22e-05)]_48_[+2(5.15e-07)]_61 1972 2.33e-04 317_[+3(2.13e-06)]_107_\ [+2(7.83e-06)]_39 21145 1.11e-03 23_[+3(8.07e-06)]_384_\ [+2(9.84e-06)]_56 21282 8.76e-05 34_[+1(4.82e-06)]_200_\ [+2(5.29e-05)]_12_[+3(2.75e-05)]_196 21306 4.24e-02 8_[+1(1.09e-05)]_471 21620 1.73e-07 76_[+3(7.38e-06)]_33_[+1(6.11e-09)]_\ 349 22074 7.08e-08 74_[+3(1.05e-05)]_266_\ [+1(5.34e-07)]_4_[+2(4.27e-07)]_98 22526 6.43e-04 209_[+3(1.14e-05)]_72_\ [+2(4.21e-06)]_182 24931 2.58e-05 44_[+1(1.96e-06)]_363_\ [+3(8.81e-06)]_51 260841 1.13e-03 272_[+3(2.36e-05)]_37_\ [+2(9.84e-06)]_154 261184 4.71e-02 395_[+2(1.23e-05)]_89 264361 7.32e-04 18_[+1(1.09e-05)]_355_\ [+2(6.17e-06)]_74_[+2(9.35e-05)] 264773 1.08e-05 114_[+3(5.73e-07)]_30_\ [+1(1.53e-05)]_106_[+2(7.38e-05)]_192 264807 8.71e-05 96_[+2(5.29e-05)]_334_\ [+3(1.87e-05)]_1_[+1(7.05e-06)]_11 264811 1.48e-07 49_[+3(3.44e-05)]_183_\ [+1(7.05e-06)]_178_[+2(4.85e-05)]_4_[+3(1.59e-08)]_7 269017 4.68e-05 155_[+1(6.50e-07)]_76_\ [+2(5.45e-06)]_232 269395 1.23e-12 68_[+3(1.59e-08)]_168_\ [+1(2.68e-09)]_201_[+2(4.27e-07)]_5 27352 1.01e-04 138_[+2(3.71e-05)]_9_[+3(2.36e-05)]_\ [+1(9.43e-06)]_295 30178 2.57e-05 171_[+3(3.86e-06)]_147_\ [+1(4.12e-06)]_140 31169 6.23e-10 57_[+3(9.05e-07)]_254_\ [+1(3.01e-08)]_2_[+1(7.22e-05)]_48_[+2(5.15e-07)]_60 31316 3.45e-08 376_[+1(4.06e-10)]_34_\ [+3(2.36e-05)]_48 33685 1.09e-03 242_[+2(3.71e-05)]_12_\ [+3(8.07e-06)]_209 36037 1.23e-12 67_[+3(1.59e-08)]_168_\ [+1(2.68e-09)]_201_[+2(4.27e-07)]_6 40630 6.99e-01 500 5807 1.32e-05 7_[+1(3.56e-07)]_131_[+1(9.34e-05)]_\ 218_[+3(1.26e-06)]_81 8058 5.66e-08 35_[+1(1.67e-07)]_11_[+3(4.01e-07)]_\ 81_[+2(2.80e-05)]_315 8222 4.95e-04 1_[+2(1.60e-06)]_316_[+3(2.18e-05)]_\ 146 8514 4.31e-05 151_[+3(9.65e-08)]_328 8672 5.45e-06 123_[+1(8.67e-07)]_199_\ [+3(3.18e-06)]_136 915 3.21e-05 203_[+1(3.92e-08)]_9_[+1(4.40e-05)]_\ 25_[+1(9.34e-05)]_200 9436 4.99e-03 188_[+2(3.71e-05)]_6_[+3(2.96e-05)]_\ 269 9483 1.58e-04 95_[+3(1.46e-05)]_176_\ [+1(7.59e-06)]_187 9776 1.67e-02 59_[+1(8.16e-06)]_420 bd1772 2.26e-05 127_[+2(1.37e-06)]_206_\ [+3(1.01e-06)]_130 bd1810 2.03e-04 34_[+3(4.67e-06)]_367_\ [+2(4.80e-06)]_62 bd2107 1.13e-01 437_[+2(3.08e-05)]_47 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************