******************************************************************************** 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/171/171.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10123 1.0000 500 10812 1.0000 500 11878 1.0000 500 11998 1.0000 500 1394 1.0000 500 1451 1.0000 500 15593 1.0000 500 22799 1.0000 500 23029 1.0000 500 23169 1.0000 500 23940 1.0000 500 24049 1.0000 500 24779 1.0000 500 2581 1.0000 500 2592 1.0000 500 260890 1.0000 500 261203 1.0000 500 261393 1.0000 500 261400 1.0000 500 262412 1.0000 500 262459 1.0000 500 264129 1.0000 500 264608 1.0000 500 268338 1.0000 500 268863 1.0000 500 270211 1.0000 500 270251 1.0000 500 3093 1.0000 500 3179 1.0000 500 32684 1.0000 500 33766 1.0000 500 34632 1.0000 500 34824 1.0000 500 34876 1.0000 500 37838 1.0000 500 38685 1.0000 500 4452 1.0000 500 4552 1.0000 500 4677 1.0000 500 5117 1.0000 500 5286 1.0000 500 5342 1.0000 500 6223 1.0000 500 6288 1.0000 500 6897 1.0000 500 7945 1.0000 500 8304 1.0000 500 8380 1.0000 500 907 1.0000 500 9166 1.0000 500 9167 1.0000 500 921 1.0000 500 9419 1.0000 500 9568 1.0000 500 9922 1.0000 500 9987 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/171/171.seqs.fa -oc motifs/171 -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= 56 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= 28000 N= 56 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.221 G 0.241 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.221 G 0.241 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 28 llr = 294 E-value = 5.2e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :66:a7:85163 pos.-specific C a13a:2a24927 probability G :3:::1:1::2: matrix T ::2:::::2::: bits 2.2 * * 2.0 * ** * 1.7 * ** * * 1.5 * ** * * Relative 1.3 * ** * * Entropy 1.1 * ** * * * (15.2 bits) 0.9 * ** ** * * 0.7 ******** *** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAACAACAACAC consensus GC C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6223 278 1.99e-07 CAAGAGCAAG CGACAACAACAC ACGATCAACC 6288 488 2.78e-07 CCACCCTCTG CACCAACACCAC G 10123 350 6.96e-07 AAATATGAAC CAACAACAACGC AATTTCAATT 37838 471 8.66e-07 CAGACTAGCG CATCAACACCAC ATAACATCCG 32684 430 8.66e-07 TTCGGACTGA CATCAACACCAC CATTTGTGAT 7945 480 1.28e-06 CGAGGGCACC CGACAACAACAA AGGAACACC 5117 341 1.28e-06 CAGCTTTCAT CGACAACATCAC GATCTGCTGC 11998 107 1.46e-06 AATCAACAAA CACCAACAACCC TCTCCTTCAT 4677 164 2.06e-06 AATGACACGG CAACAACATCAA CGATATCACG 270251 229 2.06e-06 TTTCGTGCTA CACCACCACCAC AACTGCCAAA 270211 104 2.27e-06 CATGAACCGA CACCAACCCCAC AGACAAGTTA 261400 158 2.27e-06 CATGAACCGA CACCAACCCCAC AGACAAGTTA 2592 41 2.78e-06 AAGACAACTC CATCAACATCAC GAGGAACTGA 38685 428 3.18e-06 TTAATCCGAG CAACAACCACAA CAACAGTCGC 2581 74 3.18e-06 ATGCTTGCTT CAACAACACCGA GGAACTATCT 4552 487 4.17e-06 TCACTCCAAA CAACAGCAACAA CA 34632 463 1.17e-05 ATCCATCAGC CATCACCAACGC CCAACCACCC 9419 260 1.28e-05 AAATGGACTA CCACAGCACCAC CTCACCAATC 9987 426 1.46e-05 ACCTGCCATC CGCCACCCACAC CATTTACCGC 4452 178 1.64e-05 ACGCCCTCGT CGACAACGTCAC TGCTTTCATT 260890 458 2.09e-05 CGAACGGTGT CGACAACACACC TCTGCTCCCA 11878 142 2.09e-05 TCACCTGGAC CGACAGCAACGA ACTTCATCTT 33766 468 2.41e-05 ACAAATGATA CAACAACAAACA CAACAATAAC 10812 488 2.41e-05 CAACTCAACA CAACACCGACAA T 261203 429 2.93e-05 TGAAAACAAT CAACACAAACAC AAAAGCTATC 22799 363 2.93e-05 AAAATCATGA CCCCAACATCCC CTCGGTCTCC 9167 455 3.10e-05 TCCTACAGTC CAACAACCCACC ATGCTTTGAG 9568 474 4.25e-05 TCTAGCCTCC CGTCAGCAACGA TGGTAAGAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6223 2e-07 277_[+1]_211 6288 2.8e-07 487_[+1]_1 10123 7e-07 349_[+1]_139 37838 8.7e-07 470_[+1]_18 32684 8.7e-07 429_[+1]_59 7945 1.3e-06 479_[+1]_9 5117 1.3e-06 340_[+1]_148 11998 1.5e-06 106_[+1]_382 4677 2.1e-06 163_[+1]_325 270251 2.1e-06 228_[+1]_260 270211 2.3e-06 103_[+1]_385 261400 2.3e-06 157_[+1]_331 2592 2.8e-06 40_[+1]_448 38685 3.2e-06 427_[+1]_61 2581 3.2e-06 73_[+1]_415 4552 4.2e-06 486_[+1]_2 34632 1.2e-05 462_[+1]_26 9419 1.3e-05 259_[+1]_229 9987 1.5e-05 425_[+1]_63 4452 1.6e-05 177_[+1]_311 260890 2.1e-05 457_[+1]_31 11878 2.1e-05 141_[+1]_347 33766 2.4e-05 467_[+1]_21 10812 2.4e-05 487_[+1]_1 261203 2.9e-05 428_[+1]_60 22799 2.9e-05 362_[+1]_126 9167 3.1e-05 454_[+1]_34 9568 4.2e-05 473_[+1]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=28 6223 ( 278) CGACAACAACAC 1 6288 ( 488) CACCAACACCAC 1 10123 ( 350) CAACAACAACGC 1 37838 ( 471) CATCAACACCAC 1 32684 ( 430) CATCAACACCAC 1 7945 ( 480) CGACAACAACAA 1 5117 ( 341) CGACAACATCAC 1 11998 ( 107) CACCAACAACCC 1 4677 ( 164) CAACAACATCAA 1 270251 ( 229) CACCACCACCAC 1 270211 ( 104) CACCAACCCCAC 1 261400 ( 158) CACCAACCCCAC 1 2592 ( 41) CATCAACATCAC 1 38685 ( 428) CAACAACCACAA 1 2581 ( 74) CAACAACACCGA 1 4552 ( 487) CAACAGCAACAA 1 34632 ( 463) CATCACCAACGC 1 9419 ( 260) CCACAGCACCAC 1 9987 ( 426) CGCCACCCACAC 1 4452 ( 178) CGACAACGTCAC 1 260890 ( 458) CGACAACACACC 1 11878 ( 142) CGACAGCAACGA 1 33766 ( 468) CAACAACAAACA 1 10812 ( 488) CAACACCGACAA 1 261203 ( 429) CAACACAAACAC 1 22799 ( 363) CCCCAACATCCC 1 9167 ( 455) CAACAACCCACC 1 9568 ( 474) CGTCAGCAACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 27384 bayes= 11.6031 E= 5.2e-012 -1145 218 -1145 -1145 125 -163 25 -1145 108 18 -1145 -58 -1145 218 -1145 -1145 189 -1145 -1145 -1145 133 -31 -75 -1145 -292 212 -1145 -1145 147 -31 -175 -1145 78 69 -1145 -58 -134 201 -1145 -1145 125 -31 -43 -1145 25 162 -1145 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 28 E= 5.2e-012 0.000000 1.000000 0.000000 0.000000 0.642857 0.071429 0.285714 0.000000 0.571429 0.250000 0.000000 0.178571 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.678571 0.178571 0.142857 0.000000 0.035714 0.964286 0.000000 0.000000 0.750000 0.178571 0.071429 0.000000 0.464286 0.357143 0.000000 0.178571 0.107143 0.892857 0.000000 0.000000 0.642857 0.178571 0.178571 0.000000 0.321429 0.678571 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AG][AC]CAACA[AC]CA[CA] -------------------------------------------------------------------------------- Time 30.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 33 llr = 346 E-value = 5.6e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :62286167:63:415 pos.-specific C :1:11::1::::12:2 probability G 917814912a14818: matrix T 131::::2::2323:3 bits 2.2 2.0 * 1.7 * * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * ** * * * * (15.1 bits) 0.9 * ***** ** * * 0.7 * ***** *** * * 0.4 ************* ** 0.2 ************* ** 0.0 ---------------- Multilevel GAGGAAGAAGAGGAGA consensus T G TG TA T T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8304 239 1.35e-08 TATCGTCAAT GAGGAAGAAGTAGAGA ACCTCTTTGG 270211 324 1.35e-08 AGAGATTTAG GAGGAAGAAGATGTGT GAGGTGAAGC 261400 378 1.35e-08 AGAGATTTAG GAGGAAGAAGATGTGT GAGGTGAAGC 8380 219 1.10e-07 ACTTTTCGAG GAGGAGGAGGAGGAGC AGAGCACCAG 1394 90 2.25e-07 TGTTTGTATT GTGAAAGAAGAAGAGA ACGATTCAAC 1451 464 4.25e-07 GCTTGTGTCC GTGGAGGTGGATGAGA GATGATGTGT 24049 7 4.95e-07 CGTCTC GAGGGAGAAGAAGAGC AACTACTTTT 6223 86 7.10e-07 GGAGGTGATA GAGGAGGGGGAAGAGA CTGTCAACCA 261393 312 1.01e-06 GTAGAGAGGA GGGGAGGAGGAGGCGA GGTAGTGCAT 268863 212 1.27e-06 GTACTTTAAG GAGGAAGAGGATGCAA AGAAGAAGAT 6288 73 1.58e-06 TTTGAGGTGG GAAGAAGTAGAGTTGA CATTCGATCG 9419 14 2.41e-06 CTGATTTGGA GAGGAAGAAGGTGCAA GTGTACACGT 22799 135 2.97e-06 ATTATCGGTG GATGAAGAAGTAGCGT CTTCAGTGTA 23169 376 3.98e-06 GAGAAGCAAG GAGGAGGAGGGGTTGT AGTTGTAGCA 4552 160 4.83e-06 TGAGTAGTGA GAAGAAGGAGAGGGGT GGTTGGAAGA 262459 284 4.83e-06 GGCTATGGCG GTGGCGGAAGAGTTGA GAATGAGGGT 3179 166 6.40e-06 GGGTTCGTGT GCAGAAGAAGAGCAGA GTGGTGTATG 5342 165 6.97e-06 GTTGGCGGAG TTGGAAGTAGTTGAGA GAGAGGTTTG 2581 216 6.97e-06 CGTCGAAGAG GCAGGAGAAGAAGTGA TTGGAACGCA 34824 224 7.65e-06 TGTGTGTTTA GAGCAAGTAGTTGGGA AGAAGCAAGA 260890 201 7.65e-06 GGCTGCCATT GTGGAGGAAGTATGGC TGGCTGTTTT 11878 253 1.29e-05 TGCTGTAACT GCGGCAGTAGAGGTGC TGGTACAAAG 7945 277 1.40e-05 GTCGATATTT GTGAAGAAAGAAGAGT TTCCCGAGCG 9568 222 1.52e-05 CACGAGCGAG GTAGAGGCAGTTGAGT GTATTGACGC 6897 297 1.52e-05 GTAGGACGTA GGGAGGGAAGAGGTGA GGGGGCTTTT 33766 309 1.79e-05 TCGAGCTGTA GATGAAGATGAAGTGT ATCGCTCAAA 15593 191 2.46e-05 AGGATCTTCA GTAGAGGCAGAGTTGT CGACGATCGT 264129 182 2.65e-05 TCGTCGTCTA TTGGAGGTGGTGGCGA TGGTGCTATG 5286 235 2.86e-05 CCGTTGCGCA GAGGAGGAAGGAGGCC TGAAGGGTGA 23940 142 3.32e-05 TAGAACAAGT GAGCAAGAGGTGCAGT ATGGTAGAGA 9166 19 3.84e-05 CCGAAGAGAT GAGAACGAAGATGCAA ATAGATCGTT 270251 319 3.84e-05 CATGCAATCG GAGGAAGTAGGTTATA ATACCCTGCT 4452 336 9.26e-05 CAAAAATGAA GACAAAATAGAAGAGA AAAATAAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8304 1.3e-08 238_[+2]_246 270211 1.3e-08 323_[+2]_161 261400 1.3e-08 377_[+2]_107 8380 1.1e-07 218_[+2]_266 1394 2.2e-07 89_[+2]_395 1451 4.2e-07 463_[+2]_21 24049 4.9e-07 6_[+2]_478 6223 7.1e-07 85_[+2]_399 261393 1e-06 311_[+2]_173 268863 1.3e-06 211_[+2]_273 6288 1.6e-06 72_[+2]_412 9419 2.4e-06 13_[+2]_471 22799 3e-06 134_[+2]_350 23169 4e-06 375_[+2]_109 4552 4.8e-06 159_[+2]_325 262459 4.8e-06 283_[+2]_201 3179 6.4e-06 165_[+2]_319 5342 7e-06 164_[+2]_320 2581 7e-06 215_[+2]_269 34824 7.7e-06 223_[+2]_261 260890 7.7e-06 200_[+2]_284 11878 1.3e-05 252_[+2]_232 7945 1.4e-05 276_[+2]_208 9568 1.5e-05 221_[+2]_263 6897 1.5e-05 296_[+2]_188 33766 1.8e-05 308_[+2]_176 15593 2.5e-05 190_[+2]_294 264129 2.7e-05 181_[+2]_303 5286 2.9e-05 234_[+2]_250 23940 3.3e-05 141_[+2]_343 9166 3.8e-05 18_[+2]_466 270251 3.8e-05 318_[+2]_166 4452 9.3e-05 335_[+2]_149 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=33 8304 ( 239) GAGGAAGAAGTAGAGA 1 270211 ( 324) GAGGAAGAAGATGTGT 1 261400 ( 378) GAGGAAGAAGATGTGT 1 8380 ( 219) GAGGAGGAGGAGGAGC 1 1394 ( 90) GTGAAAGAAGAAGAGA 1 1451 ( 464) GTGGAGGTGGATGAGA 1 24049 ( 7) GAGGGAGAAGAAGAGC 1 6223 ( 86) GAGGAGGGGGAAGAGA 1 261393 ( 312) GGGGAGGAGGAGGCGA 1 268863 ( 212) GAGGAAGAGGATGCAA 1 6288 ( 73) GAAGAAGTAGAGTTGA 1 9419 ( 14) GAGGAAGAAGGTGCAA 1 22799 ( 135) GATGAAGAAGTAGCGT 1 23169 ( 376) GAGGAGGAGGGGTTGT 1 4552 ( 160) GAAGAAGGAGAGGGGT 1 262459 ( 284) GTGGCGGAAGAGTTGA 1 3179 ( 166) GCAGAAGAAGAGCAGA 1 5342 ( 165) TTGGAAGTAGTTGAGA 1 2581 ( 216) GCAGGAGAAGAAGTGA 1 34824 ( 224) GAGCAAGTAGTTGGGA 1 260890 ( 201) GTGGAGGAAGTATGGC 1 11878 ( 253) GCGGCAGTAGAGGTGC 1 7945 ( 277) GTGAAGAAAGAAGAGT 1 9568 ( 222) GTAGAGGCAGTTGAGT 1 6897 ( 297) GGGAGGGAAGAGGTGA 1 33766 ( 309) GATGAAGATGAAGTGT 1 15593 ( 191) GTAGAGGCAGAGTTGT 1 264129 ( 182) TTGGAGGTGGTGGCGA 1 5286 ( 235) GAGGAGGAAGGAGGCC 1 23940 ( 142) GAGCAAGAGGTGCAGT 1 9166 ( 19) GAGAACGAAGATGCAA 1 270251 ( 319) GAGGAAGTAGGTTATA 1 4452 ( 336) GACAAAATAGAAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 27160 bayes= 9.7185 E= 5.6e-011 -1169 -1169 196 -214 109 -128 -199 3 -57 -287 159 -214 -84 -187 171 -1169 165 -187 -141 -1169 109 -287 71 -1169 -216 -1169 196 -1169 123 -187 -199 -14 143 -1169 1 -314 -1169 -1169 205 -1169 123 -1169 -99 -14 30 -1169 59 18 -1169 -187 165 -55 54 -28 -99 18 -157 -287 182 -314 101 -55 -1169 18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 33 E= 5.6e-011 0.000000 0.000000 0.939394 0.060606 0.575758 0.090909 0.060606 0.272727 0.181818 0.030303 0.727273 0.060606 0.151515 0.060606 0.787879 0.000000 0.848485 0.060606 0.090909 0.000000 0.575758 0.030303 0.393939 0.000000 0.060606 0.000000 0.939394 0.000000 0.636364 0.060606 0.060606 0.242424 0.727273 0.000000 0.242424 0.030303 0.000000 0.000000 1.000000 0.000000 0.636364 0.000000 0.121212 0.242424 0.333333 0.000000 0.363636 0.303030 0.000000 0.060606 0.757576 0.181818 0.393939 0.181818 0.121212 0.303030 0.090909 0.030303 0.848485 0.030303 0.545455 0.151515 0.000000 0.303030 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AT]GGA[AG]G[AT][AG]G[AT][GAT]G[AT]G[AT] -------------------------------------------------------------------------------- Time 54.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 22 llr = 287 E-value = 8.3e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 311:12::12:3:53::13: pos.-specific C :::::1112::12:11:613 probability G :7::91:9418:152:5::6 matrix T 729a:58:37267:49536: bits 2.2 2.0 1.7 * 1.5 *** * Relative 1.3 *** * * * Entropy 1.1 * *** ** * * ** (18.8 bits) 0.9 ***** ** ** ** ** 0.7 ***** ** ***** ***** 0.4 ***** ** ***** ***** 0.2 ************** ***** 0.0 -------------------- Multilevel TGTTGTTGGTGTTGTTGCTG consensus A T TA AA TTAC sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 921 123 1.34e-10 GAGCCGTGGT TGTTGTTGTTGTTGTTGTTG TTGTTGTTGT 38685 255 1.34e-10 GGGGGTGCGT TGTTGTTGTTGTTGTTGTTG TTGTTGTTGT 260890 130 3.90e-10 GGCCCGCCAT TGTTGTTGTTGTTAATGTTG GGGTTGCGAG 907 135 1.70e-09 ATCTGCGAGG TGTTGCTGGTGTTGCTGCTG CGTGGACGTT 8380 88 5.47e-08 CTCATTGTAA TGTTATTGGTGTCGATTCAG GCAGGATGAG 23940 342 5.47e-08 TTTAATGTAA AGTTGATGTTGATAGTTCTC AGCAGTTGGT 3179 294 8.58e-08 TACTCGCGAG AGTGGTTGTTGTTAGTTCTG TGGCTGTTCT 261393 161 1.07e-07 CCAGATGCTT TGTTGTTGCTGTTGGTTATA TGAGCTTGTC 5286 13 1.32e-07 TAAGATTCCA TTTTGATGCAGTTGATGTTG CCAGCACTTT 9166 183 1.62e-07 GTCTGCGTTG AGTTGCTGCAGATGATGCAG TAGCAGATGA 7945 105 2.19e-07 CAGCGTCAGC TGATGATGGTGATAGTTCAG AACAGATTAA 9987 148 1.01e-06 ACTTTAAAGT AGTTGGTGTTTCTATTTCAC GATTGTTTAG 4552 338 1.09e-06 ACCGTCTTAA TTTTGTTCGGTTTGATTCTC ACAACGATGT 11998 29 1.28e-06 GCAATCAGCT TTTTGATCGTGTGATTGCAC AGAATTTTGG 270251 394 1.38e-06 TCTCATCAAC TGTTGTCGTTGCCATTGCTT TCTCTCACAC 22799 459 1.49e-06 ATATTTGCAG TGTTGTTGATGATAACGACG TTGTATTTGT 33766 240 2.89e-06 CGTCGCGTTG TGTTGTGGCATATATTGTAG GAAACATTGC 24779 275 3.31e-06 GTTGGGTGAT TATTGGCGGTGTCGTCGTTG TCGTGTTTCT 1394 137 3.55e-06 GGAGAAGCCA TATTGGTGGTGACGACGATG ACGTTCGTTT 15593 232 4.92e-06 AGAACTGTAT AGATATTGATGTTAGTTCAC GTGTTAGAGC 10123 61 5.24e-06 GACCGACCGT TGTTGTTGCGTTGGCTTCCC TCGTCACTCG 32684 277 1.01e-05 ATTCTAGACG ATTTGCCCGATTTGTTTCTC ATGCCGACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 921 1.3e-10 122_[+3]_358 38685 1.3e-10 254_[+3]_226 260890 3.9e-10 129_[+3]_351 907 1.7e-09 134_[+3]_346 8380 5.5e-08 87_[+3]_393 23940 5.5e-08 341_[+3]_139 3179 8.6e-08 293_[+3]_187 261393 1.1e-07 160_[+3]_320 5286 1.3e-07 12_[+3]_468 9166 1.6e-07 182_[+3]_298 7945 2.2e-07 104_[+3]_376 9987 1e-06 147_[+3]_333 4552 1.1e-06 337_[+3]_143 11998 1.3e-06 28_[+3]_452 270251 1.4e-06 393_[+3]_87 22799 1.5e-06 458_[+3]_22 33766 2.9e-06 239_[+3]_241 24779 3.3e-06 274_[+3]_206 1394 3.5e-06 136_[+3]_344 15593 4.9e-06 231_[+3]_249 10123 5.2e-06 60_[+3]_420 32684 1e-05 276_[+3]_204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=22 921 ( 123) TGTTGTTGTTGTTGTTGTTG 1 38685 ( 255) TGTTGTTGTTGTTGTTGTTG 1 260890 ( 130) TGTTGTTGTTGTTAATGTTG 1 907 ( 135) TGTTGCTGGTGTTGCTGCTG 1 8380 ( 88) TGTTATTGGTGTCGATTCAG 1 23940 ( 342) AGTTGATGTTGATAGTTCTC 1 3179 ( 294) AGTGGTTGTTGTTAGTTCTG 1 261393 ( 161) TGTTGTTGCTGTTGGTTATA 1 5286 ( 13) TTTTGATGCAGTTGATGTTG 1 9166 ( 183) AGTTGCTGCAGATGATGCAG 1 7945 ( 105) TGATGATGGTGATAGTTCAG 1 9987 ( 148) AGTTGGTGTTTCTATTTCAC 1 4552 ( 338) TTTTGTTCGGTTTGATTCTC 1 11998 ( 29) TTTTGATCGTGTGATTGCAC 1 270251 ( 394) TGTTGTCGTTGCCATTGCTT 1 22799 ( 459) TGTTGTTGATGATAACGACG 1 33766 ( 240) TGTTGTGGCATATATTGTAG 1 24779 ( 275) TATTGGCGGTGTCGTCGTTG 1 1394 ( 137) TATTGGTGGTGACGACGATG 1 15593 ( 232) AGATATTGATGTTAGTTCAC 1 10123 ( 61) TGTTGTTGCGTTGGCTTCCC 1 32684 ( 277) ATTTGCCCGATTTGTTTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 26936 bayes= 11.7908 E= 8.3e-011 1 -1110 -1110 144 -157 -1110 159 -55 -157 -1110 -1110 177 -1110 -1110 -240 184 -157 -1110 192 -1110 -57 -70 -82 103 -1110 -70 -240 161 -1110 -70 184 -1110 -157 4 59 25 -57 -1110 -141 144 -1110 -1110 168 -23 1 -128 -1110 125 -1110 -28 -141 144 75 -1110 118 -1110 23 -128 -8 44 -1110 -70 -1110 169 -1110 -1110 118 77 -99 142 -1110 3 23 -128 -1110 114 -257 52 129 -255 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 22 E= 8.3e-011 0.272727 0.000000 0.000000 0.727273 0.090909 0.000000 0.727273 0.181818 0.090909 0.000000 0.000000 0.909091 0.000000 0.000000 0.045455 0.954545 0.090909 0.000000 0.909091 0.000000 0.181818 0.136364 0.136364 0.545455 0.000000 0.136364 0.045455 0.818182 0.000000 0.136364 0.863636 0.000000 0.090909 0.227273 0.363636 0.318182 0.181818 0.000000 0.090909 0.727273 0.000000 0.000000 0.772727 0.227273 0.272727 0.090909 0.000000 0.636364 0.000000 0.181818 0.090909 0.727273 0.454545 0.000000 0.545455 0.000000 0.318182 0.090909 0.227273 0.363636 0.000000 0.136364 0.000000 0.863636 0.000000 0.000000 0.545455 0.454545 0.136364 0.590909 0.000000 0.272727 0.318182 0.090909 0.000000 0.590909 0.045455 0.318182 0.590909 0.045455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]GTTGTTG[GTC]T[GT][TA]T[GA][TAG]T[GT][CT][TA][GC] -------------------------------------------------------------------------------- Time 77.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10123 1.91e-05 60_[+3(5.24e-06)]_269_\ [+1(6.96e-07)]_139 10812 1.05e-01 487_[+1(2.41e-05)]_1 11878 3.56e-03 141_[+1(2.09e-05)]_99_\ [+2(1.29e-05)]_232 11998 4.92e-05 28_[+3(1.28e-06)]_58_[+1(1.46e-06)]_\ 382 1394 1.23e-05 89_[+2(2.25e-07)]_31_[+3(3.55e-06)]_\ 185_[+2(7.64e-05)]_143 1451 2.30e-03 463_[+2(4.25e-07)]_21 15593 5.13e-04 190_[+2(2.46e-05)]_25_\ [+3(4.92e-06)]_249 22799 2.67e-06 134_[+2(2.97e-06)]_212_\ [+1(2.93e-05)]_29_[+1(5.95e-05)]_43_[+3(1.49e-06)]_22 23029 4.06e-01 500 23169 3.89e-03 375_[+2(3.98e-06)]_109 23940 1.04e-05 103_[+2(9.85e-05)]_22_\ [+2(3.32e-05)]_184_[+3(5.47e-08)]_139 24049 4.73e-03 6_[+2(4.95e-07)]_478 24779 4.14e-02 274_[+3(3.31e-06)]_206 2581 2.43e-04 73_[+1(3.18e-06)]_130_\ [+2(6.97e-06)]_269 2592 4.97e-03 40_[+1(2.78e-06)]_448 260890 2.52e-09 129_[+3(3.90e-10)]_51_\ [+2(7.65e-06)]_241_[+1(2.09e-05)]_7_[+1(6.99e-05)]_12 261203 3.25e-02 428_[+1(2.93e-05)]_60 261393 3.59e-06 160_[+3(1.07e-07)]_131_\ [+2(1.01e-06)]_173 261400 6.15e-07 157_[+1(2.27e-06)]_155_\ [+2(4.44e-05)]_37_[+2(1.35e-08)]_107 262412 1.74e-01 500 262459 1.92e-02 283_[+2(4.83e-06)]_201 264129 4.87e-02 181_[+2(2.65e-05)]_84_\ [+2(9.26e-05)]_203 264608 6.40e-01 500 268338 5.15e-01 500 268863 3.38e-03 211_[+2(1.27e-06)]_273 270211 6.15e-07 103_[+1(2.27e-06)]_155_\ [+2(4.44e-05)]_37_[+2(1.35e-08)]_161 270251 2.29e-06 228_[+1(2.06e-06)]_78_\ [+2(3.84e-05)]_59_[+3(1.38e-06)]_87 3093 6.84e-01 500 3179 5.93e-06 165_[+2(6.40e-06)]_112_\ [+3(8.58e-08)]_187 32684 1.39e-04 276_[+3(1.01e-05)]_133_\ [+1(8.66e-07)]_59 33766 1.98e-05 239_[+3(2.89e-06)]_49_\ [+2(1.79e-05)]_143_[+1(2.41e-05)]_21 34632 3.47e-02 462_[+1(1.17e-05)]_26 34824 2.75e-03 20_[+3(5.29e-05)]_183_\ [+2(7.65e-06)]_261 34876 4.09e-01 500 37838 3.99e-04 470_[+1(8.66e-07)]_18 38685 1.20e-08 254_[+3(1.34e-10)]_1_[+3(3.86e-05)]_\ 132_[+1(3.18e-06)]_61 4452 4.58e-03 177_[+1(1.64e-05)]_146_\ [+2(9.26e-05)]_149 4552 5.44e-07 159_[+2(4.83e-06)]_162_\ [+3(1.09e-06)]_129_[+1(4.17e-06)]_2 4677 3.93e-03 163_[+1(2.06e-06)]_325 5117 1.49e-03 340_[+1(1.28e-06)]_148 5286 4.58e-05 12_[+3(1.32e-07)]_202_\ [+2(2.86e-05)]_250 5342 1.09e-02 164_[+2(6.97e-06)]_320 6223 3.24e-06 85_[+2(7.10e-07)]_176_\ [+1(1.99e-07)]_211 6288 3.30e-06 72_[+2(1.58e-06)]_399_\ [+1(2.78e-07)]_1 6897 1.42e-02 296_[+2(1.52e-05)]_188 7945 1.14e-07 104_[+3(2.19e-07)]_10_\ [+3(9.33e-05)]_34_[+3(4.02e-05)]_68_[+2(1.40e-05)]_187_[+1(1.28e-06)]_9 8304 5.89e-05 238_[+2(1.35e-08)]_246 8380 9.79e-08 19_[+3(9.33e-05)]_48_[+3(5.47e-08)]_\ 111_[+2(1.10e-07)]_266 907 6.24e-06 134_[+3(1.70e-09)]_94_\ [+3(7.35e-05)]_232 9166 4.09e-05 18_[+2(3.84e-05)]_148_\ [+3(1.62e-07)]_298 9167 8.75e-02 454_[+1(3.10e-05)]_34 921 1.09e-06 81_[+3(6.61e-05)]_21_[+3(1.34e-10)]_\ 1_[+3(1.34e-10)]_337 9419 1.75e-04 13_[+2(2.41e-06)]_230_\ [+1(1.28e-05)]_229 9568 6.42e-03 221_[+2(1.52e-05)]_236_\ [+1(4.25e-05)]_15 9922 8.45e-01 500 9987 2.74e-04 147_[+3(1.01e-06)]_84_\ [+1(3.79e-05)]_162_[+1(1.46e-05)]_63 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************