******************************************************************************** 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/301/301.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10937 1.0000 500 11360 1.0000 500 11366 1.0000 500 20970 1.0000 500 21085 1.0000 500 21381 1.0000 500 21480 1.0000 500 21558 1.0000 500 21559 1.0000 500 21656 1.0000 500 21707 1.0000 500 22021 1.0000 500 22339 1.0000 500 22953 1.0000 500 23072 1.0000 500 23511 1.0000 500 23576 1.0000 500 23671 1.0000 500 23802 1.0000 500 23982 1.0000 500 23996 1.0000 500 24028 1.0000 500 24039 1.0000 500 24074 1.0000 500 24596 1.0000 500 24684 1.0000 500 24900 1.0000 500 24918 1.0000 500 25236 1.0000 500 25372 1.0000 500 25381 1.0000 500 25432 1.0000 500 25466 1.0000 500 25626 1.0000 500 25783 1.0000 500 268316 1.0000 500 269057 1.0000 500 31984 1.0000 500 37707 1.0000 500 37803 1.0000 500 42258 1.0000 500 5835 1.0000 500 6635 1.0000 500 7550 1.0000 500 7689 1.0000 500 7872 1.0000 500 bd1692 1.0000 500 bd1890 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/301/301.seqs.fa -oc motifs/301 -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= 48 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= 24000 N= 48 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.237 G 0.228 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.237 G 0.228 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 44 llr = 392 E-value = 2.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3715852473846272 pos.-specific C 338::4:23::22:23 probability G 3:152184:71428:4 matrix T 1:::::1:::1:::11 bits 2.1 1.9 1.7 1.5 Relative 1.3 * Entropy 1.1 **** * ** * (12.8 bits) 0.9 **** * *** ** 0.6 **** * **** ** 0.4 ************** 0.2 **************** 0.0 ---------------- Multilevel AACGAAGAAGAGAGAG consensus CC AGC GCA AG CC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 268316 269 1.03e-08 TCTACTCCCA AACAACGAAGAGAGAG ATGCACGTGT 25466 318 1.38e-07 GCGCCAAAAC AACAAAGCAGAGAGAC TGCAAAGTTG 6635 220 6.81e-07 AGTACACAAT CACAAAGAAAAGGGAC TTTAAATTTA 22953 347 1.44e-06 GTGGTGCATA GACAATGGAGAAAGAG AACACACACA 24074 63 1.93e-06 TGTGAGCGTG CACGAGAGAGAAAGAC ACCGTGTTGT 21085 140 1.93e-06 TGTTAGTGTT GAGAACGGAGAGGGAG AGCAGCAAGC bd1692 446 2.22e-06 TGAGTCGAGA GCCGAAGCAGAGCGAC CAGACGGTTG 37707 34 2.56e-06 GGAGGTCGCC AACGACGACGAGAGCT TGGCTCGTTT 25381 457 2.56e-06 CAACACGAGC CACGAGAGCGAGAGAG TAGCACGAAC 24028 89 2.93e-06 ACCTACAGGA AAGAGAGAAGAGAGAG TTGTTGGCAC 25432 227 3.80e-06 TCGGAGACAA AACGGGGACGAAAGAC AATTGTTTTT 22021 75 4.31e-06 CACTGCCGAT GACGGAGAAGAACGCG AACAGAGAAA 31984 461 6.24e-06 CACTCATCCA ACCAAAGGCAAAGGAG TGTCATCAAG 7689 142 7.05e-06 CCATCACGAG CACGACGAAGAAGAAT TCGTATTATT 7872 143 8.91e-06 CTTGACCTCC GAAGGCGACGAGAGAG GTGTTGGTTG 24918 417 8.91e-06 TAAATCACTC AACAAAGCAAACAGAA AACGTGTAAC 21558 311 1.12e-05 TGTACTCCCT TCCGACGGAAACAGAG AAACAATAGT 25372 165 1.25e-05 TCAAATATTT CCCAAAGAAAAGAGCT CTTTTGAAAT 23982 418 1.39e-05 CTCTCCGTCA GACAAAGAAGGAAGCA CCTCCAACGC 21707 217 1.91e-05 GATAGCGACA AACACAGACGAGAGAC ACGGAGGCTT 37803 413 2.35e-05 TGATCAATCA GAAGGAGGCAAGAGAG TGCTGCTTCA bd1890 479 2.60e-05 AGTCAGGTCG GACGACGACGACCAAC AACACA 25236 51 2.60e-05 TATTGCAACG ACAGAAGGAGAAGGCG ACAGCGATGT 21656 235 2.60e-05 ATTTCATCAA CACAAAGGAATCAGAT CTAACTAACG 5835 159 3.15e-05 ATCATCATCA CACGACAGCAACAGCG TAATCTTTCT 269057 10 3.46e-05 ATGATTTAT ACCAATGGAAAAGGAG AGTGAGAGGA 22339 82 3.81e-05 AGCAGTTTGC CACGAAGCCGGAAAAC AGGGGACAAC 21559 293 4.57e-05 GTCGTTTAGT GCCGACGAAGTGGGTG TGAGAGTGTA 21480 46 4.57e-05 GTTCCAAAGG AACAAGGAAGAGGGTT GCCAGTCTCT 11366 376 6.52e-05 TCTTCCATTT CACGAAAAAGAAAATC CTCTTCATTT 24900 452 7.10e-05 AACAAGACCC TCCGAAAGAGGAAGAC AACACGGCAT 23802 370 7.10e-05 TCCGAACAAC CAAGAAGCAGAAGGCT TCCACGTGTA 20970 294 7.10e-05 TCTCGTTGTT CACAAAACAGAACGCA GCCTTCTTGC 23576 480 7.71e-05 AAATCAAGTC GACGACGAAATCTGAG TGCAT 10937 374 7.71e-05 AATCAAAATC TCCGGGGAAGGGAGAG TGTGACGTAG 23671 180 1.07e-04 TGCGGATGCA GACGGCGAAGTGATAG GGCGTGTGGG 25626 202 1.35e-04 CGACGAAACA ACCGACGGAATGCAAC AGCGTAGAGC 23511 136 1.45e-04 GGCATCATGG CAGAGCGCAGAGTGAC GCCGCTGTGG 23072 472 1.45e-04 TTGGACAAGC CACAAATCAGAACAAC GAACAACGGA 24596 438 1.56e-04 ACGAGAATTC ACCGACTACGAGCAAG TCACGTGATC 24039 53 1.56e-04 TCCCGAGACT CCGGAAAGAGTAAGAA CGGATTTGTC 42258 116 1.68e-04 GGGAGGCAGA AACAGGGGACAAAGAA GTAACTTTTT 7550 75 4.21e-04 TCGAGTGCAA GAGAACTGCAAAGGAA GCTAACTGCA 11360 471 4.47e-04 AGAGCAATAC AACAACAGCAGCAGCA TCAAAGCGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268316 1e-08 268_[+1]_216 25466 1.4e-07 317_[+1]_167 6635 6.8e-07 219_[+1]_265 22953 1.4e-06 346_[+1]_138 24074 1.9e-06 62_[+1]_422 21085 1.9e-06 139_[+1]_345 bd1692 2.2e-06 445_[+1]_39 37707 2.6e-06 33_[+1]_451 25381 2.6e-06 456_[+1]_28 24028 2.9e-06 88_[+1]_396 25432 3.8e-06 226_[+1]_258 22021 4.3e-06 74_[+1]_410 31984 6.2e-06 460_[+1]_24 7689 7.1e-06 141_[+1]_343 7872 8.9e-06 142_[+1]_342 24918 8.9e-06 416_[+1]_68 21558 1.1e-05 310_[+1]_174 25372 1.2e-05 164_[+1]_320 23982 1.4e-05 417_[+1]_67 21707 1.9e-05 216_[+1]_268 37803 2.3e-05 412_[+1]_72 bd1890 2.6e-05 478_[+1]_6 25236 2.6e-05 50_[+1]_434 21656 2.6e-05 234_[+1]_250 5835 3.1e-05 158_[+1]_326 269057 3.5e-05 9_[+1]_475 22339 3.8e-05 81_[+1]_403 21559 4.6e-05 292_[+1]_192 21480 4.6e-05 45_[+1]_439 11366 6.5e-05 375_[+1]_109 24900 7.1e-05 451_[+1]_33 23802 7.1e-05 369_[+1]_115 20970 7.1e-05 293_[+1]_191 23576 7.7e-05 479_[+1]_5 10937 7.7e-05 373_[+1]_111 23671 0.00011 179_[+1]_305 25626 0.00013 201_[+1]_283 23511 0.00014 135_[+1]_349 23072 0.00014 471_[+1]_13 24596 0.00016 437_[+1]_47 24039 0.00016 52_[+1]_432 42258 0.00017 115_[+1]_369 7550 0.00042 74_[+1]_410 11360 0.00045 470_[+1]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=44 268316 ( 269) AACAACGAAGAGAGAG 1 25466 ( 318) AACAAAGCAGAGAGAC 1 6635 ( 220) CACAAAGAAAAGGGAC 1 22953 ( 347) GACAATGGAGAAAGAG 1 24074 ( 63) CACGAGAGAGAAAGAC 1 21085 ( 140) GAGAACGGAGAGGGAG 1 bd1692 ( 446) GCCGAAGCAGAGCGAC 1 37707 ( 34) AACGACGACGAGAGCT 1 25381 ( 457) CACGAGAGCGAGAGAG 1 24028 ( 89) AAGAGAGAAGAGAGAG 1 25432 ( 227) AACGGGGACGAAAGAC 1 22021 ( 75) GACGGAGAAGAACGCG 1 31984 ( 461) ACCAAAGGCAAAGGAG 1 7689 ( 142) CACGACGAAGAAGAAT 1 7872 ( 143) GAAGGCGACGAGAGAG 1 24918 ( 417) AACAAAGCAAACAGAA 1 21558 ( 311) TCCGACGGAAACAGAG 1 25372 ( 165) CCCAAAGAAAAGAGCT 1 23982 ( 418) GACAAAGAAGGAAGCA 1 21707 ( 217) AACACAGACGAGAGAC 1 37803 ( 413) GAAGGAGGCAAGAGAG 1 bd1890 ( 479) GACGACGACGACCAAC 1 25236 ( 51) ACAGAAGGAGAAGGCG 1 21656 ( 235) CACAAAGGAATCAGAT 1 5835 ( 159) CACGACAGCAACAGCG 1 269057 ( 10) ACCAATGGAAAAGGAG 1 22339 ( 82) CACGAAGCCGGAAAAC 1 21559 ( 293) GCCGACGAAGTGGGTG 1 21480 ( 46) AACAAGGAAGAGGGTT 1 11366 ( 376) CACGAAAAAGAAAATC 1 24900 ( 452) TCCGAAAGAGGAAGAC 1 23802 ( 370) CAAGAAGCAGAAGGCT 1 20970 ( 294) CACAAAACAGAACGCA 1 23576 ( 480) GACGACGAAATCTGAG 1 10937 ( 374) TCCGGGGAAGGGAGAG 1 23671 ( 180) GACGGCGAAGTGATAG 1 25626 ( 202) ACCGACGGAATGCAAC 1 23511 ( 136) CAGAGCGCAGAGTGAC 1 23072 ( 472) CACAAATCAGAACAAC 1 24596 ( 438) ACCGACTACGAGCAAG 1 24039 ( 53) CCGGAAAGAGTAAGAA 1 42258 ( 116) AACAGGGGACAAAGAA 1 7550 ( 75) GAGAACTGCAAAGGAA 1 11360 ( 471) AACAACAGCAGCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 23280 bayes= 9.40033 E= 2.2e-008 36 42 26 -198 145 20 -1210 -1210 -155 175 -100 -1210 77 -1210 126 -1210 154 -338 -16 -1210 77 62 -74 -256 -55 -1210 172 -198 70 -38 76 -1210 141 32 -1210 -1210 15 -338 158 -1210 150 -1210 -100 -98 62 -58 92 -1210 110 -58 0 -256 -74 -1210 184 -356 145 -21 -1210 -198 -74 32 84 -98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 44 E= 2.2e-008 0.340909 0.318182 0.272727 0.068182 0.727273 0.272727 0.000000 0.000000 0.090909 0.795455 0.113636 0.000000 0.454545 0.000000 0.545455 0.000000 0.772727 0.022727 0.204545 0.000000 0.454545 0.363636 0.136364 0.045455 0.181818 0.000000 0.750000 0.068182 0.431818 0.181818 0.386364 0.000000 0.704545 0.295455 0.000000 0.000000 0.295455 0.022727 0.681818 0.000000 0.750000 0.000000 0.113636 0.136364 0.409091 0.159091 0.431818 0.000000 0.568182 0.159091 0.227273 0.045455 0.159091 0.000000 0.818182 0.022727 0.727273 0.204545 0.000000 0.068182 0.159091 0.295455 0.409091 0.136364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACG][AC]C[GA][AG][AC]G[AG][AC][GA]A[GA][AG]G[AC][GC] -------------------------------------------------------------------------------- Time 18.57 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 35 llr = 303 E-value = 8.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:::::121::: pos.-specific C 112:1:21:32: probability G 3:86:a3194:7 matrix T 59:49:46:373 bits 2.1 * 1.9 * 1.7 * 1.5 * ** * Relative 1.3 ** ** * * Entropy 1.1 ***** * * (12.5 bits) 0.9 ***** * ** 0.6 ***** * ** 0.4 ****** ***** 0.2 ************ 0.0 ------------ Multilevel TTGGTGTTGGTG consensus G T GA CCT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 37803 451 4.93e-07 CATGCTGTGC TTGTTGTTGGTG CGTCTGATGT 21656 67 4.93e-07 ATAGGTGGTC GTGGTGGTGCTG CGAGGAGGCA 25783 141 9.14e-07 GGTATTGTTT TTGTTGTTGCTG GCATCATCGT 24074 85 1.48e-06 AGACACCGTG TTGTTGTTGTTG TTGGCGGCGA 21707 33 1.98e-06 GATTCAAATG GTGGTGGAGGTG CACCAAATCT 10937 33 2.92e-06 CACGGAGACG TTGGTGATGCTG GCCTTGAACG 25381 212 4.04e-06 CTTTCGGTTG GTGGTGTAGCTG GGCGGGCTGA 11366 144 5.48e-06 ACGAATAGTG TTCGTGGTGCTG ATTGATGCGC 25466 207 1.28e-05 TAGCTTCATG GTGTTGATGTTG ACAATCTCTG 25236 169 1.59e-05 ATCTTAATTA CTGGTGCTGGTG GCCATCGGCC 6635 87 1.78e-05 GAGACCTCCG TCGGTGTTGTTG TATGTCTCTC 23996 55 1.98e-05 CGACTCGACT TTGTTGGAGCCG ATTGCAAGAG bd1692 23 2.47e-05 AGATCTCCGT GTGTTGATGGTT GGTCTAAGAC 24900 146 2.74e-05 TGACATGGTT GTGTTGGTAGTG TATTGTAGTG 20970 29 3.04e-05 GTTGTGTATA ATGGTGGCGTTG CGCGCTCACT 22021 300 3.32e-05 CTCCCAAGAC GTCTTGCTGCTG CTGGTCTTGA 23671 132 3.61e-05 AGAGGCTGTC TCGGTGGCGGTG TGGTGGATGA 7872 47 3.97e-05 CATTGACCCG ATGTTGGTGTTT CACGTTACCT 25432 64 4.38e-05 CCCACTTGGG GTGGTGTGGGCG GGGAGTGCAA 21480 284 4.76e-05 GCAACGACCA TTGGCGTAGGTG ACGACCGACG 25372 432 5.19e-05 GACAGAGTCT TCGTTGTTGGTT GGAGCTTTGG 23072 79 5.19e-05 GGCAGTACTA TTGGTGGCGCCT TTCAATCGTC 7550 157 5.67e-05 CTTTCGCATT CTGTTGTTGCCG TCAGAGGCCA 23576 412 6.12e-05 TACCTCGGCT GTCGTGGAGGCG GAAAGGAGAG 21558 231 8.65e-05 GCCATTGTGT TGGGTGTTGGTT TGAAGCTTCT 7689 177 9.27e-05 TGCTTCAAGC TTGTCGGTGCCG AGATGGACGA 42258 302 1.00e-04 GTCTGTGACA GTGGTGCTTGTG CCTGCAAGCA 24596 154 1.09e-04 ACTTCATCTG ATGGTGCTGCCT TCCTGCTTCC 21381 168 1.09e-04 AGGGTGTCTT TTCTTGCCGTTG GGTGGAGAAA 37707 136 1.17e-04 CTTGAGAGGC ATCGTGTTGTTT GCATTACAAT 268316 393 1.56e-04 AAGCCACCAG TTGGTGGAGGGT GTGTGGATGC 5835 96 1.68e-04 TACGACATCC TTGGTGTGATTG ATCAACGGGT 31984 85 1.68e-04 TATGGTTAGT TTGTTGCAATTG AGAAAGCAGT 23511 43 1.92e-04 ATGTGATTGT TTGGTGATGGAT TGGCGACGAA 21559 278 1.92e-04 CGTTACTCCA GTCTTGTCGTTT AGTGCCGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37803 4.9e-07 450_[+2]_38 21656 4.9e-07 66_[+2]_422 25783 9.1e-07 140_[+2]_348 24074 1.5e-06 84_[+2]_404 21707 2e-06 32_[+2]_456 10937 2.9e-06 32_[+2]_456 25381 4e-06 211_[+2]_277 11366 5.5e-06 143_[+2]_345 25466 1.3e-05 206_[+2]_282 25236 1.6e-05 168_[+2]_320 6635 1.8e-05 86_[+2]_402 23996 2e-05 54_[+2]_434 bd1692 2.5e-05 22_[+2]_466 24900 2.7e-05 145_[+2]_343 20970 3e-05 28_[+2]_460 22021 3.3e-05 299_[+2]_189 23671 3.6e-05 131_[+2]_357 7872 4e-05 46_[+2]_442 25432 4.4e-05 63_[+2]_425 21480 4.8e-05 283_[+2]_205 25372 5.2e-05 431_[+2]_57 23072 5.2e-05 78_[+2]_410 7550 5.7e-05 156_[+2]_332 23576 6.1e-05 411_[+2]_77 21558 8.6e-05 230_[+2]_258 7689 9.3e-05 176_[+2]_312 42258 0.0001 301_[+2]_187 24596 0.00011 153_[+2]_335 21381 0.00011 167_[+2]_321 37707 0.00012 135_[+2]_353 268316 0.00016 392_[+2]_96 5835 0.00017 95_[+2]_393 31984 0.00017 84_[+2]_404 23511 0.00019 42_[+2]_446 21559 0.00019 277_[+2]_211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=35 37803 ( 451) TTGTTGTTGGTG 1 21656 ( 67) GTGGTGGTGCTG 1 25783 ( 141) TTGTTGTTGCTG 1 24074 ( 85) TTGTTGTTGTTG 1 21707 ( 33) GTGGTGGAGGTG 1 10937 ( 33) TTGGTGATGCTG 1 25381 ( 212) GTGGTGTAGCTG 1 11366 ( 144) TTCGTGGTGCTG 1 25466 ( 207) GTGTTGATGTTG 1 25236 ( 169) CTGGTGCTGGTG 1 6635 ( 87) TCGGTGTTGTTG 1 23996 ( 55) TTGTTGGAGCCG 1 bd1692 ( 23) GTGTTGATGGTT 1 24900 ( 146) GTGTTGGTAGTG 1 20970 ( 29) ATGGTGGCGTTG 1 22021 ( 300) GTCTTGCTGCTG 1 23671 ( 132) TCGGTGGCGGTG 1 7872 ( 47) ATGTTGGTGTTT 1 25432 ( 64) GTGGTGTGGGCG 1 21480 ( 284) TTGGCGTAGGTG 1 25372 ( 432) TCGTTGTTGGTT 1 23072 ( 79) TTGGTGGCGCCT 1 7550 ( 157) CTGTTGTTGCCG 1 23576 ( 412) GTCGTGGAGGCG 1 21558 ( 231) TGGGTGTTGGTT 1 7689 ( 177) TTGTCGGTGCCG 1 42258 ( 302) GTGGTGCTTGTG 1 24596 ( 154) ATGGTGCTGCCT 1 21381 ( 168) TTCTTGCCGTTG 1 37707 ( 136) ATCGTGTTGTTT 1 268316 ( 393) TTGGTGGAGGGT 1 5835 ( 96) TTGGTGTGATTG 1 31984 ( 85) TTGTTGCAATTG 1 23511 ( 43) TTGGTGATGGAT 1 21559 ( 278) GTCTTGTCGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 23472 bayes= 10.21 E= 8.2e-001 -122 -205 46 94 -1177 -147 -299 172 -1177 -47 186 -1177 -1177 -1177 133 67 -1177 -205 -1177 181 -1177 -1177 213 -1177 -122 -47 59 47 -41 -73 -200 116 -163 -1177 196 -323 -1177 41 81 9 -321 -25 -299 147 -1177 -1177 165 9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 35 E= 8.2e-001 0.114286 0.057143 0.314286 0.514286 0.000000 0.085714 0.028571 0.885714 0.000000 0.171429 0.828571 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.057143 0.000000 0.942857 0.000000 0.000000 1.000000 0.000000 0.114286 0.171429 0.342857 0.371429 0.200000 0.142857 0.057143 0.600000 0.085714 0.000000 0.885714 0.028571 0.000000 0.314286 0.400000 0.285714 0.028571 0.200000 0.028571 0.742857 0.000000 0.000000 0.714286 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]TG[GT]TG[TG][TA]G[GCT][TC][GT] -------------------------------------------------------------------------------- Time 36.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 24 llr = 253 E-value = 2.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::82:44::3::33: pos.-specific C 216:1852352:7:4a probability G ::41:1:1:51:323: matrix T 89:171:36:5a:51: 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 TTCATCCATCTTCTCC consensus G ATCGA GAG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 37803 435 1.38e-07 AGAGTGCTGC TTCATCCATGCTGTGC TTGTTGTTGG 21707 418 1.61e-07 GTCGTCTTCC TTCATCATTCTTCAAC CGTGTTGTGA 23671 62 1.94e-07 GGCGTTGCTT TTCATCAATGTTGAGC TCATTCGTTC bd1890 432 2.30e-07 AACTTATCCG TTCATCAGTCTTGTCC CCGCCATTTT 24028 303 4.05e-07 CCTTTTCTTC TTCATCCTTGATCGAC GTTGATACTT 268316 336 6.77e-07 CCTCTTCCTA TTGAACAATCATCTCC AAAGTTGCCA 20970 261 7.63e-07 CTTCGACCCC TTCATCACCGTTCGGC GGCTTCTTCT 25783 446 1.10e-06 AAGGAACCAC CTCATCACCGTTCTCC CCCTCCCCCC 25372 242 1.38e-06 CTCATCAACT TTCTTCCTTCTTCACC TTGAGTCCCG 7550 357 1.75e-06 ATAGTAACAT TTGATCCTTCGTGTAC CAGTTGGTGA 269057 472 3.03e-06 ACCCGCAAGA TTCACCAACCATGTCC TTTTTGAAGC 21480 108 3.71e-06 CGTAAACTTC TTCTTCCCTGCTCTGC CCCTTCCTCT 22021 253 7.82e-06 AAGGGATGAT TTCGTCACCCATCACC CATCACTAGT 21558 458 1.01e-05 TGGAGACGCC CTCGTCCGTCTTCTAC CCTCTGCACC 22339 4 1.09e-05 TAT TTGATGATCGATGTGC TCTAAACTGT 23982 398 1.19e-05 CATTACATGT CTGATCCAGGCTCTCC GTCAGACAAA 31984 244 1.50e-05 TTTAGTTGAT CTGAAGCATCTTCTCC GTATCACATT 24918 343 1.50e-05 GAAAATGCAA TTGATCAGAGCTCTGC CAGTAACTTG 24596 485 1.63e-05 GTGACTTTCC TCCAACCACCATCAAC 23996 156 2.53e-05 ATGCAACCGA TTGAGTCTTCTTGTGC GCAAGAAACT 25626 441 3.11e-05 CAACACATCG TCGATTCACCATCGCC ATCATCGTAC bd1692 340 3.32e-05 TGATGCTCGT TTGATCGTTGTTGGTC ATTCAGTCCT 11360 347 3.55e-05 CTTCTCGATT TTCACTCACGTTCATC CTGGAGTCCC 10937 443 4.86e-05 CGTCTCACAA TACAACCATCGTCAAC ACAATACAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37803 1.4e-07 434_[+3]_50 21707 1.6e-07 417_[+3]_67 23671 1.9e-07 61_[+3]_423 bd1890 2.3e-07 431_[+3]_53 24028 4e-07 302_[+3]_182 268316 6.8e-07 335_[+3]_149 20970 7.6e-07 260_[+3]_224 25783 1.1e-06 445_[+3]_39 25372 1.4e-06 241_[+3]_243 7550 1.8e-06 356_[+3]_128 269057 3e-06 471_[+3]_13 21480 3.7e-06 107_[+3]_377 22021 7.8e-06 252_[+3]_232 21558 1e-05 457_[+3]_27 22339 1.1e-05 3_[+3]_481 23982 1.2e-05 397_[+3]_87 31984 1.5e-05 243_[+3]_241 24918 1.5e-05 342_[+3]_142 24596 1.6e-05 484_[+3] 23996 2.5e-05 155_[+3]_329 25626 3.1e-05 440_[+3]_44 bd1692 3.3e-05 339_[+3]_145 11360 3.5e-05 346_[+3]_138 10937 4.9e-05 442_[+3]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=24 37803 ( 435) TTCATCCATGCTGTGC 1 21707 ( 418) TTCATCATTCTTCAAC 1 23671 ( 62) TTCATCAATGTTGAGC 1 bd1890 ( 432) TTCATCAGTCTTGTCC 1 24028 ( 303) TTCATCCTTGATCGAC 1 268316 ( 336) TTGAACAATCATCTCC 1 20970 ( 261) TTCATCACCGTTCGGC 1 25783 ( 446) CTCATCACCGTTCTCC 1 25372 ( 242) TTCTTCCTTCTTCACC 1 7550 ( 357) TTGATCCTTCGTGTAC 1 269057 ( 472) TTCACCAACCATGTCC 1 21480 ( 108) TTCTTCCCTGCTCTGC 1 22021 ( 253) TTCGTCACCCATCACC 1 21558 ( 458) CTCGTCCGTCTTCTAC 1 22339 ( 4) TTGATGATCGATGTGC 1 23982 ( 398) CTGATCCAGGCTCTCC 1 31984 ( 244) CTGAAGCATCTTCTCC 1 24918 ( 343) TTGATCAGAGCTCTGC 1 24596 ( 485) TCCAACCACCATCAAC 1 23996 ( 156) TTGAGTCTTCTTGTGC 1 25626 ( 441) TCGATTCACCATCGCC 1 bd1692 ( 340) TTGATCGTTGTTGGTC 1 11360 ( 347) TTCACTCACGTTCATC 1 10937 ( 443) TACAACCATCGTCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 23280 bayes= 9.57892 E= 2.1e+000 -1123 -51 -1123 163 -267 -151 -1123 170 -1123 140 72 -1123 165 -1123 -145 -169 -67 -151 -245 140 -1123 174 -145 -110 65 119 -245 -1123 65 -51 -87 12 -267 49 -245 112 -1123 119 101 -1123 13 -51 -145 77 -1123 -1123 -1123 189 -1123 149 55 -1123 13 -1123 -45 101 -9 66 35 -169 -1123 208 -1123 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 2.1e+000 0.000000 0.166667 0.000000 0.833333 0.041667 0.083333 0.000000 0.875000 0.000000 0.625000 0.375000 0.000000 0.833333 0.000000 0.083333 0.083333 0.166667 0.083333 0.041667 0.708333 0.000000 0.791667 0.083333 0.125000 0.416667 0.541667 0.041667 0.000000 0.416667 0.166667 0.125000 0.291667 0.041667 0.333333 0.041667 0.583333 0.000000 0.541667 0.458333 0.000000 0.291667 0.166667 0.083333 0.458333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.291667 0.000000 0.166667 0.541667 0.250000 0.375000 0.291667 0.083333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[CG]ATC[CA][AT][TC][CG][TA]T[CG][TA][CGA]C -------------------------------------------------------------------------------- Time 53.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10937 1.31e-04 32_[+2(2.92e-06)]_329_\ [+1(7.71e-05)]_53_[+3(4.86e-05)]_42 11360 4.98e-02 346_[+3(3.55e-05)]_138 11366 3.12e-03 143_[+2(5.48e-06)]_220_\ [+1(6.52e-05)]_109 20970 2.52e-05 28_[+2(3.04e-05)]_220_\ [+3(7.63e-07)]_17_[+1(7.10e-05)]_191 21085 1.12e-02 139_[+1(1.93e-06)]_345 21381 1.64e-01 500 21480 1.01e-04 45_[+1(4.57e-05)]_46_[+3(3.71e-06)]_\ 160_[+2(4.76e-05)]_205 21558 1.19e-04 230_[+2(8.65e-05)]_68_\ [+1(1.12e-05)]_131_[+3(1.01e-05)]_27 21559 1.70e-02 292_[+1(4.57e-05)]_192 21656 1.00e-04 66_[+2(4.93e-07)]_156_\ [+1(2.60e-05)]_250 21707 1.71e-07 32_[+2(1.98e-06)]_172_\ [+1(1.91e-05)]_185_[+3(1.61e-07)]_67 22021 1.82e-05 74_[+1(4.31e-06)]_162_\ [+3(7.82e-06)]_31_[+2(3.32e-05)]_189 22339 5.05e-03 3_[+3(1.09e-05)]_62_[+1(3.81e-05)]_\ 403 22953 1.54e-02 346_[+1(1.44e-06)]_138 23072 2.70e-02 78_[+2(5.19e-05)]_410 23511 4.63e-02 500 23576 2.51e-02 411_[+2(6.12e-05)]_56_\ [+1(7.71e-05)]_5 23671 1.25e-05 61_[+3(1.94e-07)]_54_[+2(3.61e-05)]_\ 357 23802 1.07e-01 369_[+1(7.10e-05)]_115 23982 9.92e-04 397_[+3(1.19e-05)]_4_[+1(1.39e-05)]_\ 67 23996 4.27e-03 54_[+2(1.98e-05)]_89_[+3(2.53e-05)]_\ 329 24028 1.94e-05 88_[+1(2.93e-06)]_198_\ [+3(4.05e-07)]_96_[+3(1.63e-05)]_70 24039 2.17e-01 500 24074 1.69e-05 62_[+1(1.93e-06)]_6_[+2(1.48e-06)]_\ 404 24596 1.95e-03 484_[+3(1.63e-05)] 24684 3.43e-01 500 24900 1.84e-03 145_[+2(2.74e-05)]_294_\ [+1(7.10e-05)]_33 24918 7.81e-04 342_[+3(1.50e-05)]_58_\ [+1(8.91e-06)]_68 25236 1.94e-03 50_[+1(2.60e-05)]_102_\ [+2(1.59e-05)]_104_[+1(9.85e-05)]_200 25372 1.48e-05 164_[+1(1.25e-05)]_61_\ [+3(1.38e-06)]_174_[+2(5.19e-05)]_57 25381 2.15e-04 211_[+2(4.04e-06)]_233_\ [+1(2.56e-06)]_28 25432 1.62e-03 63_[+2(4.38e-05)]_151_\ [+1(3.80e-06)]_258 25466 2.00e-05 206_[+2(1.28e-05)]_99_\ [+1(1.38e-07)]_167 25626 1.37e-02 440_[+3(3.11e-05)]_44 25783 3.01e-05 27_[+2(1.78e-05)]_101_\ [+2(9.14e-07)]_293_[+3(1.10e-06)]_39 268316 3.43e-08 268_[+1(1.03e-08)]_51_\ [+3(6.77e-07)]_149 269057 1.07e-03 9_[+1(3.46e-05)]_446_[+3(3.03e-06)]_\ 13 31984 1.77e-04 243_[+3(1.50e-05)]_201_\ [+1(6.24e-06)]_24 37707 3.13e-03 33_[+1(2.56e-06)]_240_\ [+1(3.81e-05)]_195 37803 5.03e-08 329_[+3(3.79e-05)]_67_\ [+1(2.35e-05)]_6_[+3(1.38e-07)]_[+2(4.93e-07)]_38 42258 5.98e-02 500 5835 8.99e-03 158_[+1(3.15e-05)]_326 6635 2.03e-04 86_[+2(1.78e-05)]_121_\ [+1(6.81e-07)]_19_[+2(9.27e-05)]_234 7550 3.86e-04 156_[+2(5.67e-05)]_188_\ [+3(1.75e-06)]_20_[+3(5.78e-05)]_92 7689 7.96e-04 141_[+1(7.05e-06)]_19_\ [+2(9.27e-05)]_312 7872 1.80e-03 46_[+2(3.97e-05)]_84_[+1(8.91e-06)]_\ 342 bd1692 2.78e-05 22_[+2(2.47e-05)]_119_\ [+1(7.10e-05)]_170_[+3(3.32e-05)]_90_[+1(2.22e-06)]_39 bd1890 1.42e-04 431_[+3(2.30e-07)]_31_\ [+1(2.60e-05)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************