******************************************************************************** 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/401/401.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10298 1.0000 500 1585 1.0000 500 15887 1.0000 500 18348 1.0000 500 18662 1.0000 500 21328 1.0000 500 2206 1.0000 500 22592 1.0000 500 22601 1.0000 500 22752 1.0000 500 23704 1.0000 500 23820 1.0000 500 24628 1.0000 500 25078 1.0000 500 25111 1.0000 500 25212 1.0000 500 25261 1.0000 500 261430 1.0000 500 261689 1.0000 500 263685 1.0000 500 264670 1.0000 500 270271 1.0000 500 2731 1.0000 500 27688 1.0000 500 29950 1.0000 500 30887 1.0000 500 31193 1.0000 500 31226 1.0000 500 3348 1.0000 500 34227 1.0000 500 35360 1.0000 500 36735 1.0000 500 37258 1.0000 500 38723 1.0000 500 4898 1.0000 500 5913 1.0000 500 7135 1.0000 500 8812 1.0000 500 bd1938 1.0000 500 bd937 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/401/401.seqs.fa -oc motifs/401 -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= 40 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= 20000 N= 40 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.240 G 0.240 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.240 G 0.240 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 34 llr = 369 E-value = 3.5e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22:532:3:243142561321 pos.-specific C :1115::::3111:1:1::2: probability G 619416919516428418548 matrix T 26:::216::4:44:12122: bits 2.1 1.9 1.6 * * 1.4 * * * Relative 1.2 * * * * Entropy 1.0 * * * * * * (15.6 bits) 0.8 * * * * * * * 0.6 * ******** * ** * * 0.4 * ******** ******** * 0.2 ******************* * 0.0 --------------------- Multilevel GTGACGGTGGTGGAGAAGGGG consensus AA GAA A CAATT G AA sequence T T G TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25111 96 4.47e-09 CAGGTGAAGA GTGACGGTGGTGAAGAAGGTG CACCACCTAG 18348 23 4.47e-09 GGTACAAGTG GTGGCTGTGCTGGAGGAGAAG CCAGATCCGG bd1938 225 1.30e-08 GCAAAACGTA ATGGCGGTGGTGGAAGAGGAG GAACAATCAC 27688 90 3.44e-08 GACGTGAACG AAGACGGTGCCGGTGGAGGGG AACGAGGACA 37258 313 4.66e-08 TGGCGGGAAA GAGACGGTGGAAGGAGAGGGG GTAGAGGGGT 18662 313 4.66e-08 TGGCGGGAAA GAGACGGTGGAAGGAGAGGGG GTAGAGGGGT 10298 180 5.40e-08 GCAAAACGTA ATGGCGGTGGTAGAAGAGGAG GAACAATCAC 3348 342 2.14e-07 TCAGTTTGTG GTGAAGGACCTGGAGGAGGGG AGGTTGGAGG 30887 137 2.76e-07 GATGCTTGTC GAGGCGGAGGTGATGGAGACG CTCACACATA 7135 260 8.95e-07 AATCAACGAG GCGAAGGTGCAGCAGAAGTGA AATCTAGTTG 261689 291 1.53e-06 TTTATCAGTG TGGGCGGTGGTGGGAAGGAGG AGGAGCACAA 36735 437 1.70e-06 CCAACGAAAA GTGAAGGGGCAGCAGACGAAG AAAAACAGCA 2731 22 1.70e-06 CTCTGTGTTT GTGCAGGGGGTGTGGAGGTCG GGGCTCGTGT 22752 89 1.70e-06 GTCGGCGGCT GTGACTGGGGAGGGGTTGTGG TTTGTTTGTG 34227 87 2.31e-06 GTATCTTCAT TTGAGGGAGAACGAGAAGAGG CATCAAAATT 263685 87 2.31e-06 CTCTTCTGAC GTGGATGAGGCGTTGGTGTTG TTCTTGGTTG 24628 474 3.10e-06 GAATGGAAGC GAGGGTGTGAGAGAGAAGGTG TGACGA 25212 231 4.52e-06 GGGCGCGATA ATGAAGGGGGACTTGGGGGCG ACTGTGACTG 8812 304 4.95e-06 GACGAGACAA GAGAGTTGGCAGTAGGAGAGG GTCATTTGGA 270271 39 5.42e-06 GATGGTCTTC TTCGAGGAGGAGGTGGAGGCA CACTAAGTAC 31193 248 7.73e-06 AATTGCCATT GCGGCGTTGCGGCTGAGGAGG GAAGCGGCCA 25078 289 1.18e-05 GTGTGCGGTG ATGAGAGAGCGAGAGAAGGAA GTAGGTTGTC 5913 190 1.28e-05 CGATTTGACG GTGGCGGTTGCGTTGAGAGAG CGAGACGAAT 2206 197 1.28e-05 AGTGTCAGTG TCGCCGTTGGTGTTGATGTCG CGCATGAAAG 38723 231 1.63e-05 CAACACCGAC GGGGAAGTGCAATTGAATTTG TTGTTGTATT 35360 2 2.05e-05 T TCGACGTTGGTGTTGATTGTG AAAATGATGG 31226 279 2.05e-05 AGGTTTTTGT TGGCAGTTGCTGTTGATGGTG TAGAACAAAA 261430 112 2.05e-05 GCTGGCAACA GTGACAGTGGTGTTCATCAAG TAGTGGTGCA 23704 145 2.22e-05 GGTGTGGTGC GTGGCAGTGAGACGGACGTCG CGACAGACTT 22601 95 2.77e-05 GCCATGCATC GTGAGAGAGCCATAGTAAGCG TTGATCAATA 25261 261 3.44e-05 CCTTACTTTC GTCAAAGAGAAATGGAAGAGA AAAGGTCCGT 4898 230 4.24e-05 TTGGGTTTGA AGGACAGAGGTGGAAGAAAGA GGGCCTGGGG 15887 54 4.24e-05 CTGACATGCA TTGGATGTGATGTAGTAGTAC TGCACTTGTT 1585 297 5.20e-05 TAAATTGACG AAGACTGTGAAAGGCAAAGCG AGGACGGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25111 4.5e-09 95_[+1]_384 18348 4.5e-09 22_[+1]_457 bd1938 1.3e-08 224_[+1]_255 27688 3.4e-08 89_[+1]_390 37258 4.7e-08 312_[+1]_167 18662 4.7e-08 312_[+1]_167 10298 5.4e-08 179_[+1]_300 3348 2.1e-07 341_[+1]_138 30887 2.8e-07 136_[+1]_343 7135 9e-07 259_[+1]_220 261689 1.5e-06 290_[+1]_189 36735 1.7e-06 436_[+1]_43 2731 1.7e-06 21_[+1]_458 22752 1.7e-06 88_[+1]_391 34227 2.3e-06 86_[+1]_393 263685 2.3e-06 86_[+1]_393 24628 3.1e-06 473_[+1]_6 25212 4.5e-06 230_[+1]_249 8812 5e-06 303_[+1]_176 270271 5.4e-06 38_[+1]_441 31193 7.7e-06 247_[+1]_232 25078 1.2e-05 288_[+1]_191 5913 1.3e-05 189_[+1]_290 2206 1.3e-05 196_[+1]_283 38723 1.6e-05 230_[+1]_249 35360 2.1e-05 1_[+1]_478 31226 2.1e-05 278_[+1]_201 261430 2.1e-05 111_[+1]_368 23704 2.2e-05 144_[+1]_335 22601 2.8e-05 94_[+1]_385 25261 3.4e-05 260_[+1]_219 4898 4.2e-05 229_[+1]_250 15887 4.2e-05 53_[+1]_426 1585 5.2e-05 296_[+1]_183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=34 25111 ( 96) GTGACGGTGGTGAAGAAGGTG 1 18348 ( 23) GTGGCTGTGCTGGAGGAGAAG 1 bd1938 ( 225) ATGGCGGTGGTGGAAGAGGAG 1 27688 ( 90) AAGACGGTGCCGGTGGAGGGG 1 37258 ( 313) GAGACGGTGGAAGGAGAGGGG 1 18662 ( 313) GAGACGGTGGAAGGAGAGGGG 1 10298 ( 180) ATGGCGGTGGTAGAAGAGGAG 1 3348 ( 342) GTGAAGGACCTGGAGGAGGGG 1 30887 ( 137) GAGGCGGAGGTGATGGAGACG 1 7135 ( 260) GCGAAGGTGCAGCAGAAGTGA 1 261689 ( 291) TGGGCGGTGGTGGGAAGGAGG 1 36735 ( 437) GTGAAGGGGCAGCAGACGAAG 1 2731 ( 22) GTGCAGGGGGTGTGGAGGTCG 1 22752 ( 89) GTGACTGGGGAGGGGTTGTGG 1 34227 ( 87) TTGAGGGAGAACGAGAAGAGG 1 263685 ( 87) GTGGATGAGGCGTTGGTGTTG 1 24628 ( 474) GAGGGTGTGAGAGAGAAGGTG 1 25212 ( 231) ATGAAGGGGGACTTGGGGGCG 1 8812 ( 304) GAGAGTTGGCAGTAGGAGAGG 1 270271 ( 39) TTCGAGGAGGAGGTGGAGGCA 1 31193 ( 248) GCGGCGTTGCGGCTGAGGAGG 1 25078 ( 289) ATGAGAGAGCGAGAGAAGGAA 1 5913 ( 190) GTGGCGGTTGCGTTGAGAGAG 1 2206 ( 197) TCGCCGTTGGTGTTGATGTCG 1 38723 ( 231) GGGGAAGTGCAATTGAATTTG 1 35360 ( 2) TCGACGTTGGTGTTGATTGTG 1 31226 ( 279) TGGCAGTTGCTGTTGATGGTG 1 261430 ( 112) GTGACAGTGGTGTTCATCAAG 1 23704 ( 145) GTGGCAGTGAGACGGACGTCG 1 22601 ( 95) GTGAGAGAGCCATAGTAAGCG 1 25261 ( 261) GTCAAAGAGAAATGGAAGAGA 1 4898 ( 230) AGGACAGAGGTGGAAGAAAGA 1 15887 ( 54) TTGGATGTGATGTAGTAGTAC 1 1585 ( 297) AAGACTGTGAAAGGCAAAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19200 bayes= 9.20846 E= 3.5e-016 -33 -1173 129 -34 -33 -103 -103 110 -1173 -202 197 -1173 103 -144 67 -1173 32 114 -71 -1173 -33 -1173 129 -34 -1173 -1173 183 -83 3 -1173 -71 117 -1173 -302 197 -315 -55 43 106 -1173 45 -103 -103 66 18 -202 143 -1173 -214 -103 88 55 67 -1173 -3 43 -55 -202 167 -1173 103 -1173 67 -157 125 -202 -71 -57 -114 -302 173 -215 18 -1173 97 -15 -14 -3 56 -57 -82 -302 178 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 34 E= 3.5e-016 0.205882 0.000000 0.588235 0.205882 0.205882 0.117647 0.117647 0.558824 0.000000 0.058824 0.941176 0.000000 0.529412 0.088235 0.382353 0.000000 0.323529 0.529412 0.147059 0.000000 0.205882 0.000000 0.588235 0.205882 0.000000 0.000000 0.852941 0.147059 0.264706 0.000000 0.147059 0.588235 0.000000 0.029412 0.941176 0.029412 0.176471 0.323529 0.500000 0.000000 0.352941 0.117647 0.117647 0.411765 0.294118 0.058824 0.647059 0.000000 0.058824 0.117647 0.441176 0.382353 0.411765 0.000000 0.235294 0.352941 0.176471 0.058824 0.764706 0.000000 0.529412 0.000000 0.382353 0.088235 0.617647 0.058824 0.147059 0.176471 0.117647 0.029412 0.794118 0.058824 0.294118 0.000000 0.470588 0.235294 0.235294 0.235294 0.352941 0.176471 0.147059 0.029412 0.823529 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GAT][TA]G[AG][CA][GAT]G[TA]G[GC][TA][GA][GT][ATG]G[AG]AG[GAT][GAC]G -------------------------------------------------------------------------------- Time 12.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 28 llr = 300 E-value = 7.7e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 81a72763488:3516 pos.-specific C 29:28:3651:91383 probability G :::::1::211:4111 matrix T :::::21::1211::: bits 2.1 1.9 * 1.6 ** * 1.4 ** * Relative 1.2 *** * * Entropy 1.0 *** * * * (15.4 bits) 0.8 ****** * *** * 0.6 ****** ***** *** 0.4 ************ *** 0.2 **************** 0.0 ---------------- Multilevel ACAACAACCAACGACA consensus CATCAA AC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 270271 482 9.38e-08 TCTCTCCCGA ACAACTACAAACGCCC TCC 264670 39 9.38e-08 TCTCTCCCGA ACAACTACAAACGCCC TCCACCATGT 2731 481 1.85e-07 GCCTCATATC ACAAAACACAACAACA AACA bd1938 100 2.48e-07 TATCGCATTT ACAACAACCAATGGCA GCCGAGGCGA 10298 55 2.48e-07 TATCGCATTT ACAACAACCAATGGCA GCCGAGGCGA 1585 252 4.10e-07 AAGGAACCTG CCAACTCCCAACAACA AAGGAGTCCC 31226 133 6.54e-07 CAATGGCCGA ACAACAACCTACCCCA CCACCTTCTC 25261 474 7.22e-07 TCAACCGACG ACAGCAACGAACAACA ACAACAGAAC 35360 349 8.06e-07 AAAAAGACCA AAAACAAAGAACAACA AAAGAACAAC 22601 445 1.41e-06 GCAGCGCACC CCAACACCGAACACCC AACCAGCCCC 22752 304 2.13e-06 ATTAGAATAT ACAACTAACAACACGA ATCCATCTCA 5913 397 2.57e-06 GACAGAAGCA ACAACGTCAAACGACG CGACACAGAA 18348 482 3.45e-06 CCTCTACGCA ACAACTAACATCCACC ACC bd937 418 4.14e-06 ATTAATTCCT ACAAAAAAAAACGAGC GTCACTATCT 23820 285 4.14e-06 TCATTCCCTA CCAACACCAATCAACG AAGTTCGTCA 263685 460 4.56e-06 CGTTGCCACA ACATCAAAAATCAACA TACAAAAGAT 24628 145 5.95e-06 TTTCTCTCCC CAACAAACCAACGACA ACATTTCTCT 8812 462 6.53e-06 AAGGCTCTCA ACACAATCAAACTACC TCTGCAGGAC 27688 64 7.12e-06 GTGCGAGAGG ACAACGACGGACGACC GACGTGAACG 15887 470 7.73e-06 GTGGGCGCGC CCACCAAACAACCCCG CATATCGTCT 37258 440 1.17e-05 TATTTACCAA ACAACACCCCTCTGCA GACAGTCGAG 18662 440 1.17e-05 TATTTACCAA ACAACACCCCTCTGCA GACAGTCGAG 261689 387 1.38e-05 CGCTGCCAGA ACACCAACAAGCTAAA CAACCAAGCA 4898 46 2.02e-05 TCTCGAGATA ACAACATCGAGCACAA CACACTCACC 36735 341 2.35e-05 TGTGTCGACG ACAACAGCAAATGCAA CACTTCACCA 29950 38 2.71e-05 GGGCATTCTA ACAAAAAGCGACGACG GCTACACCTC 22592 435 3.59e-05 ATCAGGCATC ACACATCAATACGCCA GTCTCCTCAA 25111 403 4.12e-05 CACCACGAAC AAACGATACAACGACA AAGCTGCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270271 9.4e-08 481_[+2]_3 264670 9.4e-08 38_[+2]_446 2731 1.8e-07 480_[+2]_4 bd1938 2.5e-07 99_[+2]_385 10298 2.5e-07 54_[+2]_430 1585 4.1e-07 251_[+2]_233 31226 6.5e-07 132_[+2]_352 25261 7.2e-07 473_[+2]_11 35360 8.1e-07 348_[+2]_136 22601 1.4e-06 444_[+2]_40 22752 2.1e-06 303_[+2]_181 5913 2.6e-06 396_[+2]_88 18348 3.4e-06 481_[+2]_3 bd937 4.1e-06 417_[+2]_67 23820 4.1e-06 284_[+2]_200 263685 4.6e-06 459_[+2]_25 24628 5.9e-06 144_[+2]_340 8812 6.5e-06 461_[+2]_23 27688 7.1e-06 63_[+2]_421 15887 7.7e-06 469_[+2]_15 37258 1.2e-05 439_[+2]_45 18662 1.2e-05 439_[+2]_45 261689 1.4e-05 386_[+2]_98 4898 2e-05 45_[+2]_439 36735 2.4e-05 340_[+2]_144 29950 2.7e-05 37_[+2]_447 22592 3.6e-05 434_[+2]_50 25111 4.1e-05 402_[+2]_82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=28 270271 ( 482) ACAACTACAAACGCCC 1 264670 ( 39) ACAACTACAAACGCCC 1 2731 ( 481) ACAAAACACAACAACA 1 bd1938 ( 100) ACAACAACCAATGGCA 1 10298 ( 55) ACAACAACCAATGGCA 1 1585 ( 252) CCAACTCCCAACAACA 1 31226 ( 133) ACAACAACCTACCCCA 1 25261 ( 474) ACAGCAACGAACAACA 1 35360 ( 349) AAAACAAAGAACAACA 1 22601 ( 445) CCAACACCGAACACCC 1 22752 ( 304) ACAACTAACAACACGA 1 5913 ( 397) ACAACGTCAAACGACG 1 18348 ( 482) ACAACTAACATCCACC 1 bd937 ( 418) ACAAAAAAAAACGAGC 1 23820 ( 285) CCAACACCAATCAACG 1 263685 ( 460) ACATCAAAAATCAACA 1 24628 ( 145) CAACAAACCAACGACA 1 8812 ( 462) ACACAATCAAACTACC 1 27688 ( 64) ACAACGACGGACGACC 1 15887 ( 470) CCACCAAACAACCCCG 1 37258 ( 440) ACAACACCCCTCTGCA 1 18662 ( 440) ACAACACCCCTCTGCA 1 261689 ( 387) ACACCAACAAGCTAAA 1 4898 ( 46) ACAACATCGAGCACAA 1 36735 ( 341) ACAACAGCAAATGCAA 1 29950 ( 38) ACAAAAAGCGACGACG 1 22592 ( 435) ACACATCAATACGCCA 1 25111 ( 403) AAACGATACAACGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 19400 bayes= 10.0408 E= 7.7e-011 166 -42 -1145 -1145 -127 190 -1145 -1145 195 -1145 -1145 -1145 146 -16 -274 -287 -27 165 -274 -1145 146 -1145 -175 -29 114 6 -274 -87 31 142 -274 -1145 46 95 -43 -1145 160 -174 -175 -187 153 -1145 -175 -55 -1145 190 -1145 -129 31 -116 84 -87 105 42 -75 -1145 -127 178 -175 -1145 123 6 -75 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 28 E= 7.7e-011 0.821429 0.178571 0.000000 0.000000 0.107143 0.892857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.214286 0.035714 0.035714 0.214286 0.750000 0.035714 0.000000 0.714286 0.000000 0.071429 0.214286 0.571429 0.250000 0.035714 0.142857 0.321429 0.642857 0.035714 0.000000 0.357143 0.464286 0.178571 0.000000 0.785714 0.071429 0.071429 0.071429 0.750000 0.000000 0.071429 0.178571 0.000000 0.892857 0.000000 0.107143 0.321429 0.107143 0.428571 0.142857 0.535714 0.321429 0.142857 0.000000 0.107143 0.821429 0.071429 0.000000 0.607143 0.250000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ACA[AC][CA][AT][AC][CA][CA]AAC[GA][AC]C[AC] -------------------------------------------------------------------------------- Time 25.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 27 llr = 302 E-value = 1.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1::::31:3:23312331: pos.-specific C 73a:88266397:5276248 probability G 1::::1::12:11:5:122: matrix T 26:a2153321:62211332 bits 2.1 1.9 ** 1.6 ** 1.4 ** * Relative 1.2 **** * * Entropy 1.0 **** * * (16.2 bits) 0.8 ****** ** * * 0.6 ****** ** *** * * 0.4 ********* ******* * 0.2 ********* ******* ** 0.0 -------------------- Multilevel CTCTCCTCCCCCTCGCCTCC consensus TC T ATTA AACAAATT sequence T CG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 1585 475 3.00e-12 CTCCCACCGT CTCTCCTCCACCTCGCCTCC CCCACA 264670 68 6.42e-08 ACCATGTTCG CCCTCGCTCCCCTCGCCTCC TCCATAGGAA 23704 428 1.12e-07 CTCCAGCCCT CTCTCCTCGTCCTTCCCCGC TATTTTGTTT 37258 1 1.89e-07 . CTCTCCACGACGTTGCCGCC GCCTTGTCAG 18662 1 1.89e-07 . CTCTCCACGACGTTGCCGCC GCCTTGTCAG 27688 368 3.11e-07 CACACATCAA CCCTCCTTCGCCGAGCCCAC CACCACCACC 30887 418 4.44e-07 TCTCTGTCGG TTCTCCTCTCCCTCTCACCT TTCCACTTCC 4898 414 6.25e-07 GTTGGCCAAT CTCTCCTCTCTCGCGACACC GTCTCCCCTG 25111 229 7.81e-07 AAGTAGGACT CCCTTCATTCCCACCCCTGC ATGTGTCCGA 3348 13 9.68e-07 GAGAGTAGTA TTCTCTTCCTCCTCGTCACC GGACTTGTCG 22601 378 9.68e-07 CGAGTAAGTT CTCTTCTTCCCCGCGCTCTC TCTCTCTCTG 34227 471 1.08e-06 CCGTCAGTCT CTCTCCATCACCAAGAGTGC ACAAGAACAA 38723 478 1.32e-06 GAACACCACC CTCTCCTCTTCCAGTCCATC ACG 29950 223 1.32e-06 TTTGAGTAGG CTCTTCAACTCCTTGCCTAC CGACTCCCAA 23820 183 1.47e-06 AACCACCTAC CTTTCCTCCTCAAAGCCTCC CATGCTTTAT 35360 383 1.79e-06 ACTCAGTGAA CCCTCCAACCCAACTCAACC AACGAACACC 24628 109 2.18e-06 GCACACTATC TACTTCTCCCCCTCCCACTC ACACTTTTTC 2731 316 2.40e-06 CACCACCCAC CTCTCCTTCATCTAGACGGT AAATACACAC bd937 198 6.95e-06 GCCTTCATTT GCCTCCTCGTCATAGCACTC ATCAAGTTCG 2206 442 9.59e-06 CGTCACACCC TCCTCCCCCACATAGAGAGC ACTCACGGAA 36735 357 1.30e-05 GCAAATGCAA CACTTCACCACATCACATTC CAATCATTCC 22752 466 1.74e-05 ACTCCGAGCC TCCTCTCTCGCCTTCCCGAC CGCGCGCCAC 25078 354 2.01e-05 GCATGCAGCC TTCTTCTTCGCCACACAGTT TGGCAAACGA 22592 326 2.63e-05 GTACACTCTA CTCTCCACTCTGTACACAGT TCAAGTATTT 25212 444 3.86e-05 CTTCGTTCAA CCCTCCCATCCCAACAGTCT ACACTTCAAT 261689 453 4.36e-05 TTGTCCGACT CTCTCGCCTGCCTCTTTGCC ATCGCTGTGT 270271 453 6.87e-05 AATATCCGTG GCCTCTTTCGCGTCTCAATT CTCTCCCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1585 3e-12 474_[+3]_6 264670 6.4e-08 67_[+3]_413 23704 1.1e-07 427_[+3]_53 37258 1.9e-07 [+3]_480 18662 1.9e-07 [+3]_480 27688 3.1e-07 367_[+3]_113 30887 4.4e-07 417_[+3]_63 4898 6.3e-07 413_[+3]_67 25111 7.8e-07 228_[+3]_252 3348 9.7e-07 12_[+3]_468 22601 9.7e-07 377_[+3]_103 34227 1.1e-06 470_[+3]_10 38723 1.3e-06 477_[+3]_3 29950 1.3e-06 222_[+3]_258 23820 1.5e-06 182_[+3]_298 35360 1.8e-06 382_[+3]_98 24628 2.2e-06 108_[+3]_372 2731 2.4e-06 315_[+3]_165 bd937 7e-06 197_[+3]_283 2206 9.6e-06 441_[+3]_39 36735 1.3e-05 356_[+3]_124 22752 1.7e-05 465_[+3]_15 25078 2e-05 353_[+3]_127 22592 2.6e-05 325_[+3]_155 25212 3.9e-05 443_[+3]_37 261689 4.4e-05 452_[+3]_28 270271 6.9e-05 452_[+3]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=27 1585 ( 475) CTCTCCTCCACCTCGCCTCC 1 264670 ( 68) CCCTCGCTCCCCTCGCCTCC 1 23704 ( 428) CTCTCCTCGTCCTTCCCCGC 1 37258 ( 1) CTCTCCACGACGTTGCCGCC 1 18662 ( 1) CTCTCCACGACGTTGCCGCC 1 27688 ( 368) CCCTCCTTCGCCGAGCCCAC 1 30887 ( 418) TTCTCCTCTCCCTCTCACCT 1 4898 ( 414) CTCTCCTCTCTCGCGACACC 1 25111 ( 229) CCCTTCATTCCCACCCCTGC 1 3348 ( 13) TTCTCTTCCTCCTCGTCACC 1 22601 ( 378) CTCTTCTTCCCCGCGCTCTC 1 34227 ( 471) CTCTCCATCACCAAGAGTGC 1 38723 ( 478) CTCTCCTCTTCCAGTCCATC 1 29950 ( 223) CTCTTCAACTCCTTGCCTAC 1 23820 ( 183) CTTTCCTCCTCAAAGCCTCC 1 35360 ( 383) CCCTCCAACCCAACTCAACC 1 24628 ( 109) TACTTCTCCCCCTCCCACTC 1 2731 ( 316) CTCTCCTTCATCTAGACGGT 1 bd937 ( 198) GCCTCCTCGTCATAGCACTC 1 2206 ( 442) TCCTCCCCCACATAGAGAGC 1 36735 ( 357) CACTTCACCACATCACATTC 1 22752 ( 466) TCCTCTCTCGCCTTCCCGAC 1 25078 ( 354) TTCTTCTTCGCCACACAGTT 1 22592 ( 326) CTCTCCACTCTGTACACAGT 1 25212 ( 444) CCCTCCCATCCCAACAGTCT 1 261689 ( 453) CTCTCGCCTGCCTCTTTGCC 1 270271 ( 453) GCCTCTTTCGCGTCTCAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 19240 bayes= 10.0446 E= 1.2e-008 -1140 155 -169 -23 -181 48 -1140 118 -1140 201 -1140 -282 -1140 -1140 -1140 194 -1140 170 -1140 -23 -1140 177 -169 -123 19 -37 -1140 99 -122 121 -1140 35 -1140 131 -70 -1 0 48 -37 -23 -1140 189 -1140 -123 -48 148 -70 -1140 0 -1140 -111 127 19 101 -269 -50 -181 -11 111 -50 -22 155 -1140 -182 0 121 -111 -182 0 -11 -11 18 -122 77 -11 -1 -1140 170 -1140 -23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 27 E= 1.2e-008 0.000000 0.703704 0.074074 0.222222 0.074074 0.333333 0.000000 0.592593 0.000000 0.962963 0.000000 0.037037 0.000000 0.000000 0.000000 1.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.814815 0.074074 0.111111 0.296296 0.185185 0.000000 0.518519 0.111111 0.555556 0.000000 0.333333 0.000000 0.592593 0.148148 0.259259 0.259259 0.333333 0.185185 0.222222 0.000000 0.888889 0.000000 0.111111 0.185185 0.666667 0.148148 0.000000 0.259259 0.000000 0.111111 0.629630 0.296296 0.481481 0.037037 0.185185 0.074074 0.222222 0.518519 0.185185 0.222222 0.703704 0.000000 0.074074 0.259259 0.555556 0.111111 0.074074 0.259259 0.222222 0.222222 0.296296 0.111111 0.407407 0.222222 0.259259 0.000000 0.777778 0.000000 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][TC]CT[CT]C[TA][CT][CT][CAT]CC[TA][CA][GC][CA][CA][TACG][CTG][CT] -------------------------------------------------------------------------------- Time 37.15 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10298 5.45e-07 54_[+2(2.48e-07)]_109_\ [+1(5.40e-08)]_300 1585 4.00e-12 251_[+2(4.10e-07)]_29_\ [+1(5.20e-05)]_157_[+3(3.00e-12)]_6 15887 4.19e-03 53_[+1(4.24e-05)]_395_\ [+2(7.73e-06)]_15 18348 5.02e-07 22_[+1(4.47e-09)]_388_\ [+2(8.77e-05)]_34_[+2(3.45e-06)]_3 18662 3.96e-09 [+3(1.89e-07)]_292_[+1(4.66e-08)]_\ 106_[+2(1.17e-05)]_45 21328 6.68e-01 500 2206 1.34e-03 196_[+1(1.28e-05)]_224_\ [+3(9.59e-06)]_39 22592 9.12e-03 325_[+3(2.63e-05)]_89_\ [+2(3.59e-05)]_50 22601 8.67e-07 94_[+1(2.77e-05)]_262_\ [+3(9.68e-07)]_47_[+2(1.41e-06)]_40 22752 1.38e-06 88_[+1(1.70e-06)]_194_\ [+2(2.13e-06)]_16_[+2(7.78e-05)]_114_[+3(1.74e-05)]_15 23704 5.55e-05 120_[+1(9.82e-05)]_3_[+1(2.22e-05)]_\ 262_[+3(1.12e-07)]_53 23820 1.03e-04 182_[+3(1.47e-06)]_37_\ [+3(9.86e-05)]_25_[+2(4.14e-06)]_200 24628 9.19e-07 108_[+3(2.18e-06)]_16_\ [+2(5.95e-06)]_313_[+1(3.10e-06)]_6 25078 1.84e-03 288_[+1(1.18e-05)]_44_\ [+3(2.01e-05)]_127 25111 5.34e-09 95_[+1(4.47e-09)]_112_\ [+3(7.81e-07)]_154_[+2(4.12e-05)]_82 25212 1.89e-03 230_[+1(4.52e-06)]_192_\ [+3(3.86e-05)]_37 25261 3.37e-04 260_[+1(3.44e-05)]_192_\ [+2(7.22e-07)]_11 261430 2.67e-02 111_[+1(2.05e-05)]_368 261689 1.49e-05 290_[+1(1.53e-06)]_75_\ [+2(1.38e-05)]_50_[+3(4.36e-05)]_28 263685 1.15e-04 86_[+1(2.31e-06)]_12_[+1(1.18e-05)]_\ 275_[+2(6.47e-05)]_28_[+2(4.56e-06)]_25 264670 3.11e-07 9_[+3(6.87e-05)]_9_[+2(9.38e-08)]_\ 13_[+3(6.42e-08)]_413 270271 8.00e-07 38_[+1(5.42e-06)]_393_\ [+3(6.87e-05)]_9_[+2(9.38e-08)]_3 2731 2.48e-08 21_[+1(1.70e-06)]_273_\ [+3(2.40e-06)]_6_[+2(5.00e-06)]_123_[+2(1.85e-07)]_4 27688 2.99e-09 63_[+2(7.12e-06)]_10_[+1(3.44e-08)]_\ 257_[+3(3.11e-07)]_113 29950 2.34e-04 37_[+2(2.71e-05)]_169_\ [+3(1.32e-06)]_133_[+3(5.50e-05)]_105 30887 1.44e-06 136_[+1(2.76e-07)]_260_\ [+3(4.44e-07)]_63 31193 5.83e-02 247_[+1(7.73e-06)]_232 31226 1.68e-04 132_[+2(6.54e-07)]_130_\ [+1(2.05e-05)]_201 3348 6.76e-06 12_[+3(9.68e-07)]_309_\ [+1(2.14e-07)]_55_[+1(7.67e-05)]_62 34227 5.43e-05 86_[+1(2.31e-06)]_363_\ [+3(1.08e-06)]_10 35360 6.98e-07 1_[+1(2.05e-05)]_326_[+2(8.06e-07)]_\ 18_[+3(1.79e-06)]_98 36735 9.05e-06 340_[+2(2.35e-05)]_[+3(1.30e-05)]_\ 60_[+1(1.70e-06)]_43 37258 3.96e-09 [+3(1.89e-07)]_292_[+1(4.66e-08)]_\ 106_[+2(1.17e-05)]_45 38723 2.20e-04 230_[+1(1.63e-05)]_226_\ [+3(1.32e-06)]_3 4898 9.24e-06 45_[+2(2.02e-05)]_168_\ [+1(4.24e-05)]_163_[+3(6.25e-07)]_67 5913 1.52e-04 189_[+1(1.28e-05)]_186_\ [+2(2.57e-06)]_13_[+2(2.57e-06)]_59 7135 1.16e-02 259_[+1(8.95e-07)]_220 8812 4.35e-04 303_[+1(4.95e-06)]_137_\ [+2(6.53e-06)]_23 bd1938 1.50e-07 99_[+2(2.48e-07)]_109_\ [+1(1.30e-08)]_255 bd937 5.53e-04 197_[+3(6.95e-06)]_200_\ [+2(4.14e-06)]_67 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************