******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/366/366.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31665 1.0000 500 53980 1.0000 500 8706 1.0000 500 54569 1.0000 500 46593 1.0000 500 46747 1.0000 500 47622 1.0000 500 14177 1.0000 500 47847 1.0000 500 48017 1.0000 500 38668 1.0000 500 48482 1.0000 500 15929 1.0000 500 50059 1.0000 500 50172 1.0000 500 1534 1.0000 500 44359 1.0000 500 44656 1.0000 500 11154 1.0000 500 11271 1.0000 500 11901 1.0000 500 45538 1.0000 500 45940 1.0000 500 33436 1.0000 500 46852 1.0000 500 50194 1.0000 500 39615 1.0000 500 43874 1.0000 500 45615 1.0000 500 43777 1.0000 500 49414 1.0000 500 49877 1.0000 500 44800 1.0000 500 49646 1.0000 500 47876 1.0000 500 45617 1.0000 500 46265 1.0000 500 47747 1.0000 500 16471 1.0000 500 45109 1.0000 500 49757 1.0000 500 44294 1.0000 500 50011 1.0000 500 44570 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/366/366.seqs.fa -oc motifs/366 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 44 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= 22000 N= 44 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.240 G 0.227 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.240 G 0.227 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 26 llr = 273 E-value = 1.7e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:1:a:41::a4 pos.-specific C :7:6:a:::5:1 probability G 21:4:::9:5:4 matrix T 429:::6:a::: 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 ACTCACTGTCAA consensus T G A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 31665 374 1.19e-07 GGACAATTAA TCTCACTGTCAG TCAGCGATTT 38668 400 7.43e-07 GGTTGAACAA TCTCACAGTCAG CGACGGAGAT 46747 195 7.43e-07 CGGCAGTTAT TCTCACAGTCAG TTTCACTTGG 11901 159 9.65e-07 TGTAAAATTG ACTGACTGTGAG TTCAATTTCC 46593 459 9.65e-07 ATCGCCTGCT ACTGACTGTGAG AATCGTCTTC 47876 54 1.25e-06 ACCGGTACTG TCTCACAGTCAA TTGCAAATAG 50172 384 1.25e-06 AACCGAAATG TCTCACAGTCAA CGTGTCTTTT 45615 440 1.51e-06 ATTACAGCAT ACTGACTGTGAA GATAATTTGA 54569 382 1.79e-06 CCGCTCCATG GCTCACTGTCAG GGACTTTCAC 49414 154 1.98e-06 CAGGGTAGTC GCTCACTGTGAG TCCAAAAGGA 43777 420 2.42e-06 AAGTATTCTC GCTGACTGTGAG AGAACCCAAC 43874 356 3.67e-06 TCGATTCGCA ACTCACAGTCAC GGTAAGTCAC 8706 39 4.22e-06 CGTTGATCCA ATTCACTGTCAA TAGTCGCCGT 45617 344 5.47e-06 AATTACCCCG ATTGACTGTGAG ACCGCATGCG 49646 12 5.47e-06 TGTTACAGTT AGTCACAGTCAG CTTTTGCAAG 50194 395 6.16e-06 AGGCAAGGGC TTTCACAGTCAA TACTGTTGAT 45109 340 9.50e-06 TACACTCTCT TCTCACGGTCAA CAATTCTCCA 49877 459 1.34e-05 GACCATGACG ACACACAGTCAA TCGTTGCCGT 47622 262 2.00e-05 TAAACGTACT ACTGACAATGAG TAAAAACATC 49757 419 2.12e-05 GTCCCAGCAG TGTGACTGTGAC CAGTACACGA 45538 271 2.33e-05 GACCGATCTG GCTCACAGTCAT GCAGTGACTC 1534 95 2.33e-05 CCTCCTATTT TCTGCCTGTGAA GTACGCACCA 48017 82 2.61e-05 GATCGGTCAT TCTGAATGTGAA GACTAAAGGT 46852 486 3.16e-05 TATGAAAAAG ACGCACTGTCAC ATC 46265 451 3.50e-05 ACAAACACAC TGACACTGTGAA TCAGCGAGTA 50011 269 4.71e-05 TGTGGGATCG ATTGACTATGAA CCAATATCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31665 1.2e-07 373_[+1]_115 38668 7.4e-07 399_[+1]_89 46747 7.4e-07 194_[+1]_294 11901 9.7e-07 158_[+1]_330 46593 9.7e-07 458_[+1]_30 47876 1.2e-06 53_[+1]_435 50172 1.2e-06 383_[+1]_105 45615 1.5e-06 439_[+1]_49 54569 1.8e-06 381_[+1]_107 49414 2e-06 153_[+1]_335 43777 2.4e-06 419_[+1]_69 43874 3.7e-06 355_[+1]_133 8706 4.2e-06 38_[+1]_450 45617 5.5e-06 343_[+1]_145 49646 5.5e-06 11_[+1]_477 50194 6.2e-06 394_[+1]_94 45109 9.5e-06 339_[+1]_149 49877 1.3e-05 458_[+1]_30 47622 2e-05 261_[+1]_227 49757 2.1e-05 418_[+1]_70 45538 2.3e-05 270_[+1]_218 1534 2.3e-05 94_[+1]_394 48017 2.6e-05 81_[+1]_407 46852 3.2e-05 485_[+1]_3 46265 3.5e-05 450_[+1]_38 50011 4.7e-05 268_[+1]_220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=26 31665 ( 374) TCTCACTGTCAG 1 38668 ( 400) TCTCACAGTCAG 1 46747 ( 195) TCTCACAGTCAG 1 11901 ( 159) ACTGACTGTGAG 1 46593 ( 459) ACTGACTGTGAG 1 47876 ( 54) TCTCACAGTCAA 1 50172 ( 384) TCTCACAGTCAA 1 45615 ( 440) ACTGACTGTGAA 1 54569 ( 382) GCTCACTGTCAG 1 49414 ( 154) GCTCACTGTGAG 1 43777 ( 420) GCTGACTGTGAG 1 43874 ( 356) ACTCACAGTCAC 1 8706 ( 39) ATTCACTGTCAA 1 45617 ( 344) ATTGACTGTGAG 1 49646 ( 12) AGTCACAGTCAG 1 50194 ( 395) TTTCACAGTCAA 1 45109 ( 340) TCTCACGGTCAA 1 49877 ( 459) ACACACAGTCAA 1 47622 ( 262) ACTGACAATGAG 1 49757 ( 419) TGTGACTGTGAC 1 45538 ( 271) GCTCACAGTCAT 1 1534 ( 95) TCTGCCTGTGAA 1 48017 ( 82) TCTGAATGTGAA 1 46852 ( 486) ACGCACTGTCAC 1 46265 ( 451) TGACACTGTGAA 1 50011 ( 269) ATTGACTATGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 21516 bayes= 10.8563 E= 1.7e-012 64 -1134 -56 69 -1134 161 -98 -76 -182 -1134 -256 176 -1134 136 76 -1134 183 -264 -1134 -1134 -281 200 -1134 -1134 50 -1134 -256 114 -182 -1134 202 -1134 -1134 -1134 -1134 193 -1134 116 102 -1134 188 -1134 -1134 -1134 64 -106 90 -276 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 26 E= 1.7e-012 0.423077 0.000000 0.153846 0.423077 0.000000 0.730769 0.115385 0.153846 0.076923 0.000000 0.038462 0.884615 0.000000 0.615385 0.384615 0.000000 0.961538 0.038462 0.000000 0.000000 0.038462 0.961538 0.000000 0.000000 0.384615 0.000000 0.038462 0.576923 0.076923 0.000000 0.923077 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.538462 0.461538 0.000000 1.000000 0.000000 0.000000 0.000000 0.423077 0.115385 0.423077 0.038462 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]CT[CG]AC[TA]GT[CG]A[AG] -------------------------------------------------------------------------------- Time 15.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 39 llr = 355 E-value = 6.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 336442522:775186871 pos.-specific C 6:13524146:25122:26 probability G 171215172411:7:22:3 matrix T ::21:1::2:11:11::2: bits 2.1 1.9 1.7 1.5 Relative 1.3 Entropy 1.1 * * * * * (13.1 bits) 0.9 ** * * * * * * 0.6 ** ** ** ******* 0.4 *** * ** ********** 0.2 ******** ********** 0.0 ------------------- Multilevel CGAACGAGCCAACGAAAAC consensus AA CAAC AG A G G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 45615 329 2.32e-11 TACCATACCG CGAACGCGCGAACGAAAAC AAGTGCACTC 15929 156 6.18e-08 CAATCGCAAC CGACCGGGACAACGACAAC CCCCCGCAGC 48017 147 3.95e-07 AAACTTCTTC CAAAAGCGTCATAGAAAAG GACATAGTGA 11154 370 4.55e-07 AAATCGTTCC CGATGGCGGCAACGAGAAC ACGGTTTTTC 14177 353 2.20e-06 AAGTGGAACT CGTCCCCGCCAACGAAGCC GTTGTTGATA 44800 466 4.45e-06 TTCACAGCAA AGCACAACACAAAGAAAAC AACACAATCA 1534 344 4.45e-06 CCAACGATGC CGAAAGCGCCTACGACGTC GGTGATGACC 45109 52 4.99e-06 GTCGGACGGA CGAGAGAGCGTCAGAAAAA TGAGTCGCTC 11901 326 4.99e-06 CTGCAAGACT CAACCGAGGCAAAAAGGAC GAGGGCAGTC 8706 265 4.99e-06 CCGGATCCAG CGAACTCGCGACCGAAACA CCCGTCACGG 47876 135 5.58e-06 CTGCTCATGG AAAAAACGCGTAAGCAAAC CGCTATAGTC 44656 37 9.59e-06 CGCGCTACAC CGCACCCGCCCACGAAAAG ATTCTGTACG 50172 10 9.59e-06 TGACGAAGC CACGACGGCGAACGAGAAC TTCCGCAACA 54569 306 9.59e-06 TCTCGAGTTC GAACGGCGAGAACGCAAAC CGGTTCCGTT 43777 267 1.18e-05 ATGTAACACA CGTACAAGGCAACGTAACC TGCAGAACCC 44359 420 1.18e-05 CGTGACTTTG CATGCGAGAGAAAGAGGAG AGTTCGACAT 47622 420 1.18e-05 TCAGAAGACG CGAGCGGGCGGAAGCCAAG CCATTGTTAC 45617 177 1.45e-05 TCTAACAAAA CAGCATCGACAAAGAAATC AAGACATGTC 49414 232 1.45e-05 TCAACACGTC CAAAAACCGGAACGAGATC ACCTCTCGGA 50011 477 1.77e-05 CTAATGGTTT CGATCTGGGGAACAAAAAG GAACC 45940 349 1.95e-05 TCAGCAGTAA CGTAACCGTGAAAAAAAAA TAGAACCCTC 44294 456 2.14e-05 CGTTAGCGTA AAATAGAGAGAACGAACAC TGCGCAAGCA 49877 216 2.36e-05 TTAGGCAAAA AGAGTGCGCCATCGAAATC AGGAGATTCT 16471 22 2.59e-05 CTTCCACGCC AGAAGGAGACGACAAAATC GCAGCCTTGC 49646 271 2.85e-05 GCAGAAACCA AGACCGAATCAGACAAAAC TACCACGTTA 43874 394 3.42e-05 CTAGAAAAAA GGAACGGACGAAACACAAC AATGGAGAAC 50194 299 3.42e-05 ACCAACAAAC GGACAGAGTCACACAAGAC GACGGATCAG 46265 349 5.32e-05 TACTCGACCC CGTGCGACTGATAGACAAG GCAATTGCAG 48482 365 5.32e-05 CCAATCAAAT AGACACAATCTACCAAAAC GCAAGGATTA 53980 458 5.32e-05 CCGGTCACAT CGCCAGAATCAAAGTGAAC ATATCCCCTA 45538 36 6.31e-05 AGGATGGGGA CGACAACGCCAGCAAAGTC CATCGTCGTT 46747 318 6.86e-05 GATGTTCTGG AAAACGAGGGGAATAAACG GGATTGCTCG 31665 346 8.08e-05 TATTTGTAAC AGAAACAGTCGCCTAAAAG GACAATTAAT 47847 147 8.76e-05 TTGTCTGTCG CATGCGACACGTCGAAAAG GTTCGCGGTT 11271 266 1.03e-04 CGATTCACGA CGGAAACACGATCGCCAAC CTGTAACCGC 38668 127 1.11e-04 GCGCAACGCA CGAACTACGCACACCGAAC AGTTCACTGC 46852 51 2.00e-04 TAACGGCGGC AAGAAAAGCCACAGCGACC AGTGTACGAA 50059 85 2.00e-04 ACGCTTCCAA CATTCACACGTAAGAAAAA TACGTAAAGA 46593 350 3.43e-04 ACAGACAATC AGACGTAGACAAATCAACG TCAGCATCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45615 2.3e-11 328_[+2]_153 15929 6.2e-08 155_[+2]_326 48017 4e-07 146_[+2]_335 11154 4.5e-07 369_[+2]_112 14177 2.2e-06 352_[+2]_129 44800 4.5e-06 465_[+2]_16 1534 4.5e-06 343_[+2]_138 45109 5e-06 51_[+2]_430 11901 5e-06 325_[+2]_156 8706 5e-06 264_[+2]_217 47876 5.6e-06 134_[+2]_347 44656 9.6e-06 36_[+2]_445 50172 9.6e-06 9_[+2]_472 54569 9.6e-06 305_[+2]_176 43777 1.2e-05 266_[+2]_215 44359 1.2e-05 419_[+2]_62 47622 1.2e-05 419_[+2]_62 45617 1.4e-05 176_[+2]_305 49414 1.4e-05 231_[+2]_250 50011 1.8e-05 476_[+2]_5 45940 1.9e-05 348_[+2]_133 44294 2.1e-05 455_[+2]_26 49877 2.4e-05 215_[+2]_266 16471 2.6e-05 21_[+2]_460 49646 2.8e-05 270_[+2]_211 43874 3.4e-05 393_[+2]_88 50194 3.4e-05 298_[+2]_183 46265 5.3e-05 348_[+2]_133 48482 5.3e-05 364_[+2]_117 53980 5.3e-05 457_[+2]_24 45538 6.3e-05 35_[+2]_446 46747 6.9e-05 317_[+2]_164 31665 8.1e-05 345_[+2]_136 47847 8.8e-05 146_[+2]_335 11271 0.0001 265_[+2]_216 38668 0.00011 126_[+2]_355 46852 0.0002 50_[+2]_431 50059 0.0002 84_[+2]_397 46593 0.00034 349_[+2]_132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=39 45615 ( 329) CGAACGCGCGAACGAAAAC 1 15929 ( 156) CGACCGGGACAACGACAAC 1 48017 ( 147) CAAAAGCGTCATAGAAAAG 1 11154 ( 370) CGATGGCGGCAACGAGAAC 1 14177 ( 353) CGTCCCCGCCAACGAAGCC 1 44800 ( 466) AGCACAACACAAAGAAAAC 1 1534 ( 344) CGAAAGCGCCTACGACGTC 1 45109 ( 52) CGAGAGAGCGTCAGAAAAA 1 11901 ( 326) CAACCGAGGCAAAAAGGAC 1 8706 ( 265) CGAACTCGCGACCGAAACA 1 47876 ( 135) AAAAAACGCGTAAGCAAAC 1 44656 ( 37) CGCACCCGCCCACGAAAAG 1 50172 ( 10) CACGACGGCGAACGAGAAC 1 54569 ( 306) GAACGGCGAGAACGCAAAC 1 43777 ( 267) CGTACAAGGCAACGTAACC 1 44359 ( 420) CATGCGAGAGAAAGAGGAG 1 47622 ( 420) CGAGCGGGCGGAAGCCAAG 1 45617 ( 177) CAGCATCGACAAAGAAATC 1 49414 ( 232) CAAAAACCGGAACGAGATC 1 50011 ( 477) CGATCTGGGGAACAAAAAG 1 45940 ( 349) CGTAACCGTGAAAAAAAAA 1 44294 ( 456) AAATAGAGAGAACGAACAC 1 49877 ( 216) AGAGTGCGCCATCGAAATC 1 16471 ( 22) AGAAGGAGACGACAAAATC 1 49646 ( 271) AGACCGAATCAGACAAAAC 1 43874 ( 394) GGAACGGACGAAACACAAC 1 50194 ( 299) GGACAGAGTCACACAAGAC 1 46265 ( 349) CGTGCGACTGATAGACAAG 1 48482 ( 365) AGACACAATCTACCAAAAC 1 53980 ( 458) CGCCAGAATCAAAGTGAAC 1 45538 ( 36) CGACAACGCCAGCAAAGTC 1 46747 ( 318) AAAACGAGGGGAATAAACG 1 31665 ( 346) AGAAACAGTCGCCTAAAAG 1 47847 ( 147) CATGCGACACGTCGAAAAG 1 11271 ( 266) CGGAAACACGATCGCCAAC 1 38668 ( 127) CGAACTACGCACACCGAAC 1 46852 ( 51) AAGAAAAGCCACAGCGACC 1 50059 ( 85) CATTCACACGTAAGAAAAA 1 46593 ( 350) AGACGTAGACAAATCAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 21208 bayes= 9.30827 E= 6.9e+000 6 142 -156 -1193 30 -1193 155 -1193 124 -123 -156 -54 69 23 -34 -135 60 94 -115 -335 -40 -64 117 -103 77 77 -83 -1193 -82 -91 166 -1193 -23 68 -34 -35 -1193 123 94 -1193 141 -322 -83 -103 130 -64 -215 -103 85 109 -1193 -1193 -108 -91 155 -176 150 -42 -1193 -235 124 -64 -15 -1193 160 -322 -56 -1193 135 -64 -1193 -76 -140 142 17 -1193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 39 E= 6.9e+000 0.282051 0.641026 0.076923 0.000000 0.333333 0.000000 0.666667 0.000000 0.641026 0.102564 0.076923 0.179487 0.435897 0.282051 0.179487 0.102564 0.410256 0.461538 0.102564 0.025641 0.205128 0.153846 0.512821 0.128205 0.461538 0.410256 0.128205 0.000000 0.153846 0.128205 0.717949 0.000000 0.230769 0.384615 0.179487 0.205128 0.000000 0.564103 0.435897 0.000000 0.717949 0.025641 0.128205 0.128205 0.666667 0.153846 0.051282 0.128205 0.487179 0.512821 0.000000 0.000000 0.128205 0.128205 0.666667 0.076923 0.769231 0.179487 0.000000 0.051282 0.641026 0.153846 0.205128 0.000000 0.820513 0.025641 0.153846 0.000000 0.692308 0.153846 0.000000 0.153846 0.102564 0.641026 0.256410 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][GA]A[AC][CA][GA][AC]G[CAT][CG]AA[CA]GA[AG]AA[CG] -------------------------------------------------------------------------------- Time 30.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 11 llr = 142 E-value = 3.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :4:1::::::512:1 pos.-specific C :66:319:12311:: probability G a:3::3::98:44a: matrix T ::19761a::354:9 bits 2.1 * * 1.9 * * * 1.7 * *** * 1.5 * * **** ** Relative 1.3 * * **** ** Entropy 1.1 ** ** **** ** (18.6 bits) 0.9 ********** ** 0.6 ********** ** 0.4 ************ ** 0.2 *************** 0.0 --------------- Multilevel GCCTTTCTGGATGGT consensus AG CG CGT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 44800 302 4.74e-09 CTGCGGCCTG GCCTTTCTGGTTGGT AAATCTTGTA 50011 355 1.94e-08 TTGCCAGCCT GCCTCTCTGGAGGGT CGAGCTCGCC 50194 177 7.05e-08 AAACTGGCAC GCCTCGCTGGATTGT GGTGGCAGTA 38668 178 2.60e-07 TTGATGCATC GACTTTCTGGTAGGT GATCGGCTTC 49646 400 3.29e-07 AACACCCAGT GAGTTGCTGGATAGT TTCTTCTGTG 39615 468 7.29e-07 AGTTTCGGCT GCCTTGCTCGCGTGT GCATATTACA 50059 2 8.63e-07 G GCCTTTTTGGACGGT GACATCGGAC 49877 237 1.20e-06 TCGAAATCAG GAGATTCTGGCTTGT CTGGCCGTGC 47847 290 1.74e-06 CTGGTCCGGC GCTTCTCTGCATTGT CAAGACATAG 47622 18 2.20e-06 AGAGCGGATT GAGTTTCTGCTGCGT AGAGAGAATC 45617 317 3.04e-06 ATGCGTTTTG GCCTTCCTGGCGAGA ACAATTACCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44800 4.7e-09 301_[+3]_184 50011 1.9e-08 354_[+3]_131 50194 7e-08 176_[+3]_309 38668 2.6e-07 177_[+3]_308 49646 3.3e-07 399_[+3]_86 39615 7.3e-07 467_[+3]_18 50059 8.6e-07 1_[+3]_484 49877 1.2e-06 236_[+3]_249 47847 1.7e-06 289_[+3]_196 47622 2.2e-06 17_[+3]_468 45617 3e-06 316_[+3]_169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=11 44800 ( 302) GCCTTTCTGGTTGGT 1 50011 ( 355) GCCTCTCTGGAGGGT 1 50194 ( 177) GCCTCGCTGGATTGT 1 38668 ( 178) GACTTTCTGGTAGGT 1 49646 ( 400) GAGTTGCTGGATAGT 1 39615 ( 468) GCCTTGCTCGCGTGT 1 50059 ( 2) GCCTTTTTGGACGGT 1 49877 ( 237) GAGATTCTGGCTTGT 1 47847 ( 290) GCTTCTCTGCATTGT 1 47622 ( 18) GAGTTTCTGCTGCGT 1 45617 ( 317) GCCTTCCTGGCGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 21384 bayes= 11.9509 E= 3.4e+001 -1010 -1010 214 -1010 42 141 -1010 -1010 -1010 141 26 -152 -157 -1010 -1010 180 -1010 18 -1010 148 -1010 -140 26 128 -1010 192 -1010 -152 -1010 -1010 -1010 193 -1010 -140 200 -1010 -1010 -40 185 -1010 75 18 -1010 6 -157 -140 68 80 -58 -140 68 48 -1010 -1010 214 -1010 -157 -1010 -1010 180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 11 E= 3.4e+001 0.000000 0.000000 1.000000 0.000000 0.363636 0.636364 0.000000 0.000000 0.000000 0.636364 0.272727 0.090909 0.090909 0.000000 0.000000 0.909091 0.000000 0.272727 0.000000 0.727273 0.000000 0.090909 0.272727 0.636364 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.181818 0.818182 0.000000 0.454545 0.272727 0.000000 0.272727 0.090909 0.090909 0.363636 0.454545 0.181818 0.090909 0.363636 0.363636 0.000000 0.000000 1.000000 0.000000 0.090909 0.000000 0.000000 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[CA][CG]T[TC][TG]CTGG[ACT][TG][GT]GT -------------------------------------------------------------------------------- Time 45.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31665 1.14e-04 345_[+2(8.08e-05)]_9_[+1(1.19e-07)]_\ 115 53980 8.92e-02 457_[+2(5.32e-05)]_24 8706 1.13e-04 38_[+1(4.22e-06)]_214_\ [+2(4.99e-06)]_217 54569 1.97e-04 58_[+1(5.47e-06)]_235_\ [+2(9.59e-06)]_57_[+1(1.79e-06)]_92_[+1(4.27e-05)]_3 46593 3.68e-04 339_[+1(8.01e-05)]_107_\ [+1(9.65e-07)]_30 46747 1.45e-04 39_[+1(4.48e-05)]_143_\ [+1(7.43e-07)]_111_[+2(6.86e-05)]_164 47622 9.23e-06 17_[+3(2.20e-06)]_229_\ [+1(2.00e-05)]_146_[+2(1.18e-05)]_62 14177 1.99e-02 352_[+2(2.20e-06)]_129 47847 9.14e-04 146_[+2(8.76e-05)]_124_\ [+3(1.74e-06)]_196 48017 1.92e-04 81_[+1(2.61e-05)]_53_[+2(3.95e-07)]_\ 119_[+2(8.08e-05)]_197 38668 5.21e-07 177_[+3(2.60e-07)]_207_\ [+1(7.43e-07)]_89 48482 1.55e-02 364_[+2(5.32e-05)]_117 15929 1.14e-03 155_[+2(6.18e-08)]_326 50059 4.01e-04 1_[+3(8.63e-07)]_484 50172 1.45e-04 9_[+2(9.59e-06)]_355_[+1(1.25e-06)]_\ 105 1534 1.29e-03 94_[+1(2.33e-05)]_237_\ [+2(4.45e-06)]_138 44359 4.20e-02 419_[+2(1.18e-05)]_62 44656 4.53e-02 36_[+2(9.59e-06)]_445 11154 6.10e-03 369_[+2(4.55e-07)]_112 11271 2.91e-01 500 11901 6.58e-05 84_[+1(2.17e-06)]_62_[+1(9.65e-07)]_\ 155_[+2(4.99e-06)]_156 45538 3.16e-03 35_[+2(6.31e-05)]_216_\ [+1(2.33e-05)]_218 45940 6.68e-02 348_[+2(1.95e-05)]_133 33436 9.63e-01 500 46852 3.76e-02 485_[+1(3.16e-05)]_3 50194 3.80e-07 176_[+3(7.05e-08)]_107_\ [+2(3.42e-05)]_77_[+1(6.16e-06)]_94 39615 3.49e-03 467_[+3(7.29e-07)]_18 43874 7.70e-04 355_[+1(3.67e-06)]_26_\ [+2(3.42e-05)]_88 45615 2.07e-09 112_[+1(1.47e-05)]_204_\ [+2(2.32e-11)]_92_[+1(1.51e-06)]_49 43777 5.20e-04 266_[+2(1.18e-05)]_134_\ [+1(2.42e-06)]_69 49414 2.35e-04 153_[+1(1.98e-06)]_66_\ [+2(1.45e-05)]_250 49877 6.98e-06 215_[+2(2.36e-05)]_2_[+3(1.20e-06)]_\ 207_[+1(1.34e-05)]_30 44800 9.63e-07 301_[+3(4.74e-09)]_149_\ [+2(4.45e-06)]_16 49646 1.16e-06 11_[+1(5.47e-06)]_247_\ [+2(2.85e-05)]_110_[+3(3.29e-07)]_86 47876 6.18e-05 15_[+1(6.77e-06)]_26_[+1(1.25e-06)]_\ 69_[+2(5.58e-06)]_347 45617 4.66e-06 176_[+2(1.45e-05)]_121_\ [+3(3.04e-06)]_12_[+1(5.47e-06)]_145 46265 8.95e-03 348_[+2(5.32e-05)]_83_\ [+1(3.50e-05)]_38 47747 3.67e-01 500 16471 1.35e-01 21_[+2(2.59e-05)]_460 45109 2.56e-05 51_[+2(4.99e-06)]_241_\ [+3(3.51e-05)]_13_[+1(9.50e-06)]_149 49757 1.47e-01 418_[+1(2.12e-05)]_70 44294 2.23e-02 455_[+2(2.14e-05)]_26 50011 4.08e-07 268_[+1(4.71e-05)]_74_\ [+3(1.94e-08)]_107_[+2(1.77e-05)]_5 44570 6.22e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************