******************************************************************************** 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/409/409.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31831 1.0000 500 43065 1.0000 500 43115 1.0000 500 43235 1.0000 500 43244 1.0000 500 46348 1.0000 500 36358 1.0000 500 5808 1.0000 500 36534 1.0000 500 46578 1.0000 500 46884 1.0000 500 13617 1.0000 500 48278 1.0000 500 48286 1.0000 500 43375 1.0000 500 32665 1.0000 500 43469 1.0000 500 54119 1.0000 500 40593 1.0000 500 49807 1.0000 500 8044 1.0000 500 41238 1.0000 500 50641 1.0000 500 10974 1.0000 500 10925 1.0000 500 44536 1.0000 500 44702 1.0000 500 44735 1.0000 500 44761 1.0000 500 34385 1.0000 500 11403 1.0000 500 34712 1.0000 500 51825 1.0000 500 45402 1.0000 500 45570 1.0000 500 45584 1.0000 500 45604 1.0000 500 45672 1.0000 500 45826 1.0000 500 45955 1.0000 500 12431 1.0000 500 46175 1.0000 500 46435 1.0000 500 42502 1.0000 500 42596 1.0000 500 42605 1.0000 500 42900 1.0000 500 42997 1.0000 500 47015 1.0000 500 43138 1.0000 500 45225 1.0000 500 33765 1.0000 500 43261 1.0000 500 43395 1.0000 500 43396 1.0000 500 54088 1.0000 500 46406 1.0000 500 46501 1.0000 500 47693 1.0000 500 44600 1.0000 500 45479 1.0000 500 35217 1.0000 500 36629 1.0000 500 45603 1.0000 500 34384 1.0000 500 45074 1.0000 500 45155 1.0000 500 45270 1.0000 500 45403 1.0000 500 35400 1.0000 500 32511 1.0000 500 45632 1.0000 500 45104 1.0000 500 34586 1.0000 500 49982 1.0000 500 8596 1.0000 500 45587 1.0000 500 46009 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/409/409.seqs.fa -oc motifs/409 -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= 78 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= 39000 N= 78 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.237 G 0.221 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.237 G 0.221 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 13 sites = 49 llr = 478 E-value = 4.1e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3::18:4::1a32 pos.-specific C 12:5:a:::5:13 probability G 41:31::a:3:5: matrix T 27a11:6:a::15 bits 2.2 * * 2.0 * * * 1.7 * * ** * 1.5 * * ** * Relative 1.3 * * ** * Entropy 1.1 * ** ** * (14.1 bits) 0.9 * ***** * 0.7 ** ******* 0.4 ************ 0.2 ************* 0.0 ------------- Multilevel GTTCACTGTCAGT consensus A G A G AC sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 42997 273 1.86e-07 CATTGGTCGA ATTCACAGTCAGT CTTTTCACAA 45479 448 7.11e-07 GAAAATAAGT GTTCACTGTGAAC ACAATCGCAG 42502 398 7.11e-07 TCCCTCGTTT GTTCACAGTGAAT GGCGTGTGGT 43469 176 7.11e-07 TCATTTTCTC ATTCACAGTCAAT CAACTTTCCG 44761 398 8.52e-07 ACTGTTGGCG ATTGACTGTGAGT CACAACCATC 43138 315 1.10e-06 CGGCTCAATT TTTCACAGTCAGC CAGATACGTT 43065 137 1.35e-06 GTGGACTTGC ATTGACTGTGAGC TGCACCACTA 43261 83 1.82e-06 AATGATCCGG TTTGACTGTGAGT GTTCCTAATC 54088 349 2.07e-06 TAGCATCCGC ACTCACAGTCAGT ACATGGTGTA 45225 146 2.07e-06 GCCAAAACTA GTTCTCTGTCAGT GCCATTACGA 40593 35 2.07e-06 TAAATCACCC ATTTACTGTCAGT GGATTTGGCA 45270 356 2.49e-06 TTGTGGTTCG TTTCACAGTCAAC TTTTCCGCTC 36534 427 2.49e-06 TTTGCATGGC GCTCACAGTCAAT GGCGAGGCAT 12431 125 2.93e-06 TGTGTTTACT GTTGACTGTAAGT GGCGCGTGCA 50641 102 3.31e-06 CGGTCAGCGC GTTCACAGTAAGC AAAAGGGGGT 49982 430 5.01e-06 CTGTGCAATA GTTGACTGTGATC GTGAGACTTT 45632 162 5.57e-06 TCTCGACCTA GTTTACAGTCAAC AGAGCACTAT 44600 73 5.57e-06 AGTCAATTCG GCTGACTGTGAAT TAGATTTAAT 44702 237 5.57e-06 TATCTGTTCT ATTTACTGTGAGC TCTGTCTTTT 33765 288 7.19e-06 AGTCACATAC CTTCACAGTCAAT GCGCAGCACA 47015 241 7.19e-06 CGGTTTCCGT ATTTACTGTGAAT CACTGTAACA 41238 172 8.90e-06 CACAAATCGT GTTGACTGTGATA AAAATGTTTA 45155 315 9.96e-06 AAAAGGTGGG GGTGACTGTGAGC GACAATCGAT 48286 451 9.96e-06 TCACCAACGG TTTCTCAGTCAGT CTCAGCAAAA 48278 451 9.96e-06 TCACCAACGG TTTCTCAGTCAGT CTCAGCAAAA 45570 368 1.12e-05 CAATGCCCAG ATTAACAGTCAGA AACTGTCAAC 44735 258 1.26e-05 CAGTATTTTT ACTGACTGTGAGA TTGATACCGC 45672 23 1.36e-05 AGAGATATTG GCTAACTGTCAAT GGATGTACCC 34712 62 1.36e-05 CTACCATATT GCTGACTGTGATT GTGTCGTCTA 45604 452 1.68e-05 AGAGCTGCTG ATTCACAGTAAAA TGGACAAGCA 46348 230 1.83e-05 GTCTTTTGTT TCTCACAGTCAAA AGATATTTTA 42605 346 1.99e-05 CAGTAGAAGA AATCACAGTCAGC CCTCTCTCTA 46501 212 2.39e-05 TACCTACTTG TTTCACGGTCAGT CCCATGAACT 8596 332 2.63e-05 CGGGTATGAT GATGACTGTCAAC CGAAAACGGA 45955 456 2.63e-05 TAACAGATAC GTTCACTGCCAGC GTTTTGTTGC 46884 215 2.63e-05 AAACTAGACT ATTGACTGTAATC AACAGGATCT 54119 216 2.81e-05 AAGCAAATTC CTTGACTGTGAAA CAAAGCGGAA 45826 321 3.06e-05 TACTATTAGT TGTTACTGTCAGT CAGCAATAAC 51825 350 3.65e-05 TAGGAAAAGT ACTCACTGTCAGG AAGTACGACC 42596 82 3.91e-05 GCAGTTTATA GTTAACTGTAATT TTTAGCGGTC 43235 349 3.91e-05 GACGACAGGC GTCCACTGTCAGA CACCGAACCC 45402 124 4.19e-05 AGAGATTCTT CTTCGCTGTCAGC GAAGTTCCAG 34385 383 4.57e-05 ATCGATATAT TGTGACAGTGAAC GCTTTATATC 43396 352 7.83e-05 GACAGTACCC GTTCGCAGTCACA CCTTGCAGCA 43395 349 7.83e-05 GAGAGTACCC GTTCGCAGTCACA CCCAGCAGCA 49807 77 8.36e-05 GTGGCTGAGG ATTATCTGTGATT TCTCCTTCTT 42900 195 1.06e-04 TGGAATACTA TTTCTCTGTGACA AATGTATTAT 36358 77 1.06e-04 TCCGATAGGT GGTTTCAGTCAAT GAAAGCTTTG 45584 228 1.12e-04 AGAGACTCGT ACTAACTGTAATT TAATGGAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42997 1.9e-07 272_[+1]_215 45479 7.1e-07 447_[+1]_40 42502 7.1e-07 397_[+1]_90 43469 7.1e-07 175_[+1]_312 44761 8.5e-07 397_[+1]_90 43138 1.1e-06 314_[+1]_173 43065 1.4e-06 136_[+1]_351 43261 1.8e-06 82_[+1]_405 54088 2.1e-06 348_[+1]_139 45225 2.1e-06 145_[+1]_342 40593 2.1e-06 34_[+1]_453 45270 2.5e-06 355_[+1]_132 36534 2.5e-06 426_[+1]_61 12431 2.9e-06 124_[+1]_363 50641 3.3e-06 101_[+1]_386 49982 5e-06 429_[+1]_58 45632 5.6e-06 161_[+1]_326 44600 5.6e-06 72_[+1]_415 44702 5.6e-06 236_[+1]_251 33765 7.2e-06 287_[+1]_200 47015 7.2e-06 240_[+1]_247 41238 8.9e-06 171_[+1]_316 45155 1e-05 314_[+1]_173 48286 1e-05 450_[+1]_37 48278 1e-05 450_[+1]_37 45570 1.1e-05 367_[+1]_120 44735 1.3e-05 257_[+1]_230 45672 1.4e-05 22_[+1]_465 34712 1.4e-05 61_[+1]_426 45604 1.7e-05 451_[+1]_36 46348 1.8e-05 229_[+1]_258 42605 2e-05 345_[+1]_142 46501 2.4e-05 211_[+1]_276 8596 2.6e-05 331_[+1]_156 45955 2.6e-05 455_[+1]_32 46884 2.6e-05 214_[+1]_273 54119 2.8e-05 215_[+1]_272 45826 3.1e-05 320_[+1]_167 51825 3.6e-05 349_[+1]_138 42596 3.9e-05 81_[+1]_406 43235 3.9e-05 348_[+1]_139 45402 4.2e-05 123_[+1]_364 34385 4.6e-05 382_[+1]_105 43396 7.8e-05 351_[+1]_136 43395 7.8e-05 348_[+1]_139 49807 8.4e-05 76_[+1]_411 42900 0.00011 194_[+1]_293 36358 0.00011 76_[+1]_411 45584 0.00011 227_[+1]_260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=49 42997 ( 273) ATTCACAGTCAGT 1 45479 ( 448) GTTCACTGTGAAC 1 42502 ( 398) GTTCACAGTGAAT 1 43469 ( 176) ATTCACAGTCAAT 1 44761 ( 398) ATTGACTGTGAGT 1 43138 ( 315) TTTCACAGTCAGC 1 43065 ( 137) ATTGACTGTGAGC 1 43261 ( 83) TTTGACTGTGAGT 1 54088 ( 349) ACTCACAGTCAGT 1 45225 ( 146) GTTCTCTGTCAGT 1 40593 ( 35) ATTTACTGTCAGT 1 45270 ( 356) TTTCACAGTCAAC 1 36534 ( 427) GCTCACAGTCAAT 1 12431 ( 125) GTTGACTGTAAGT 1 50641 ( 102) GTTCACAGTAAGC 1 49982 ( 430) GTTGACTGTGATC 1 45632 ( 162) GTTTACAGTCAAC 1 44600 ( 73) GCTGACTGTGAAT 1 44702 ( 237) ATTTACTGTGAGC 1 33765 ( 288) CTTCACAGTCAAT 1 47015 ( 241) ATTTACTGTGAAT 1 41238 ( 172) GTTGACTGTGATA 1 45155 ( 315) GGTGACTGTGAGC 1 48286 ( 451) TTTCTCAGTCAGT 1 48278 ( 451) TTTCTCAGTCAGT 1 45570 ( 368) ATTAACAGTCAGA 1 44735 ( 258) ACTGACTGTGAGA 1 45672 ( 23) GCTAACTGTCAAT 1 34712 ( 62) GCTGACTGTGATT 1 45604 ( 452) ATTCACAGTAAAA 1 46348 ( 230) TCTCACAGTCAAA 1 42605 ( 346) AATCACAGTCAGC 1 46501 ( 212) TTTCACGGTCAGT 1 8596 ( 332) GATGACTGTCAAC 1 45955 ( 456) GTTCACTGCCAGC 1 46884 ( 215) ATTGACTGTAATC 1 54119 ( 216) CTTGACTGTGAAA 1 45826 ( 321) TGTTACTGTCAGT 1 51825 ( 350) ACTCACTGTCAGG 1 42596 ( 82) GTTAACTGTAATT 1 43235 ( 349) GTCCACTGTCAGA 1 45402 ( 124) CTTCGCTGTCAGC 1 34385 ( 383) TGTGACAGTGAAC 1 43396 ( 352) GTTCGCAGTCACA 1 43395 ( 349) GTTCGCAGTCACA 1 49807 ( 77) ATTATCTGTGATT 1 42900 ( 195) TTTCTCTGTGACA 1 36358 ( 77) GGTTTCAGTCAAT 1 45584 ( 228) ACTAACTGTAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 38064 bayes= 10.0691 E= 4.1e-024 26 -195 88 -41 -273 -37 -144 136 -1226 -353 -1226 186 -141 105 37 -114 159 -1226 -185 -114 -1226 208 -1226 -1226 59 -1226 -343 108 -1226 -1226 218 -1226 -1226 -353 -1226 186 -115 116 65 -1226 188 -1226 -1226 -1226 26 -195 109 -92 -41 37 -343 80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 49 E= 4.1e-024 0.326531 0.061224 0.408163 0.204082 0.040816 0.183673 0.081633 0.693878 0.000000 0.020408 0.000000 0.979592 0.102041 0.489796 0.285714 0.122449 0.816327 0.000000 0.061224 0.122449 0.000000 1.000000 0.000000 0.000000 0.408163 0.000000 0.020408 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.020408 0.000000 0.979592 0.122449 0.530612 0.346939 0.000000 1.000000 0.000000 0.000000 0.000000 0.326531 0.061224 0.469388 0.142857 0.204082 0.306122 0.020408 0.469388 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GAT]TT[CG]AC[TA]GT[CG]A[GA][TCA] -------------------------------------------------------------------------------- Time 46.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 30 llr = 327 E-value = 5.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1241::::1:242::: pos.-specific C 8:4:::4:344:1:2a probability G :42::3:5:34::::: matrix T 14:9a75562167a8: bits 2.2 * 2.0 * 1.7 * * * 1.5 ** * * Relative 1.3 ** *** Entropy 1.1 * ** * *** (15.7 bits) 0.9 * ***** * *** 0.7 * ***** ***** 0.4 ********** ***** 0.2 **************** 0.0 ---------------- Multilevel CGATTTTGTCCTTTTC consensus TC GCTCGGAA sequence AG TA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8596 50 7.61e-08 GAAATTATAC CTATTTTTTCCATTTC TCCTTCCCTA 43244 364 1.46e-07 TGCGATGTTT CGATTGTTTGGATTTC CTAGGAATAT 45074 210 1.75e-07 CATCGAAGAA CACTTTCGTCGATTTC ACGCTCTTCT 42596 144 1.75e-07 CAACGATCAT CGGTTGCTTGGTTTTC GGATGTCGAT 32511 394 2.43e-07 CCAACTTCTA CTCTTTCGTCGTATTC TACAAATACA 47693 394 2.43e-07 CCAACTTCTA CTCTTTCGTCGTATTC TACAAATACA 46406 294 3.90e-07 TGCATTCTTT CACTTTTTTTGTTTTC CACAACACTG 40593 70 4.49e-07 GTCTGATCAC CGATTTTGCGAATTTC CTCTTACATC 34385 51 5.90e-07 GACCGCTTTC CGCTTGCGTCGTTTCC GATGTGTGGA 49807 106 7.71e-07 TCTTCCTCAT CGATTTCTCCGTCTTC GGATCCCGCC 43395 292 9.97e-07 TGTATGTCGA CGATTTCTACCATTTC TTCTTGTGCG 35400 452 2.01e-06 TTCGAAATTA CTCTTTTGTGAACTTC GCATCAGCCA 46009 60 3.37e-06 ACAGGGAAAC CTATTGCGCCTTTTTC ACATGTTATC 45225 112 3.71e-06 AGATAGATAC TTGTTTCGTGATTTTC CTTGTGAGGC 43375 280 3.71e-06 CCTCTTTTTG ATATTTTGTTGATTTC CTTACGGTAT 43396 295 6.99e-06 TGTATATCGA CAATTTCTGCCATTTC TTCTCGTGCG 12431 326 7.61e-06 ATAATAGTCT CACTTTCGTCCACTCC TCCCATTCGA 45270 93 8.99e-06 GTCAGCCTGT AGGTTGTTCGCATTTC AATAAACATC 45479 226 8.99e-06 ATATATGGTG CTGTTTTGCGCTCTCC TACTCACTGT 42605 215 8.99e-06 GACATGTGGT CGCTTTTTCCAAATCC GAGTCCCACC 44536 449 1.05e-05 ACTGGGTAAA CTATTTCTTTCTTATC GATCAGGAGA 43469 124 1.14e-05 ACGGGTATTC AAGTTTTGCTGTTTTC CCACTTCCAC 45632 132 1.32e-05 ATGCTCCAAT CTAATGTGTTCTATTC CTTTTCTCGA 45155 174 1.32e-05 CCCGCAGTGT CGGTGTTTCTGTTTTC GCACAGGAAG 35217 364 1.32e-05 TCGCTTCCTT TGCTTATGTGCTTTTC TCCGAGTGTT 45955 241 1.42e-05 GCATCCATTA CGCTTGTTATATATTC GGTCATATAA 34586 200 1.53e-05 GCTTTTTTTG TTAATGTTTCCTTTTC GAAATAATAG 45570 187 1.88e-05 AGCTTTGCTT CAGTTTATTGAATTTC TTGTCGAGGT 45587 193 2.15e-05 ATTTAAATAC TGCTTTTTACTTTTTC CGACATTTCT 43115 371 2.15e-05 CGTCGAACGA CGAATGCGTGCTATCC ATCACACCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8596 7.6e-08 49_[+2]_435 43244 1.5e-07 363_[+2]_121 45074 1.7e-07 209_[+2]_275 42596 1.7e-07 143_[+2]_341 32511 2.4e-07 393_[+2]_91 47693 2.4e-07 393_[+2]_91 46406 3.9e-07 293_[+2]_191 40593 4.5e-07 69_[+2]_415 34385 5.9e-07 50_[+2]_434 49807 7.7e-07 105_[+2]_379 43395 1e-06 291_[+2]_193 35400 2e-06 451_[+2]_33 46009 3.4e-06 59_[+2]_425 45225 3.7e-06 111_[+2]_373 43375 3.7e-06 279_[+2]_205 43396 7e-06 294_[+2]_190 12431 7.6e-06 325_[+2]_159 45270 9e-06 92_[+2]_392 45479 9e-06 225_[+2]_259 42605 9e-06 214_[+2]_270 44536 1.1e-05 448_[+2]_36 43469 1.1e-05 123_[+2]_361 45632 1.3e-05 131_[+2]_353 45155 1.3e-05 173_[+2]_311 35217 1.3e-05 363_[+2]_121 45955 1.4e-05 240_[+2]_244 34586 1.5e-05 199_[+2]_285 45570 1.9e-05 186_[+2]_298 45587 2.2e-05 192_[+2]_292 43115 2.2e-05 370_[+2]_114 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=30 8596 ( 50) CTATTTTTTCCATTTC 1 43244 ( 364) CGATTGTTTGGATTTC 1 45074 ( 210) CACTTTCGTCGATTTC 1 42596 ( 144) CGGTTGCTTGGTTTTC 1 32511 ( 394) CTCTTTCGTCGTATTC 1 47693 ( 394) CTCTTTCGTCGTATTC 1 46406 ( 294) CACTTTTTTTGTTTTC 1 40593 ( 70) CGATTTTGCGAATTTC 1 34385 ( 51) CGCTTGCGTCGTTTCC 1 49807 ( 106) CGATTTCTCCGTCTTC 1 43395 ( 292) CGATTTCTACCATTTC 1 35400 ( 452) CTCTTTTGTGAACTTC 1 46009 ( 60) CTATTGCGCCTTTTTC 1 45225 ( 112) TTGTTTCGTGATTTTC 1 43375 ( 280) ATATTTTGTTGATTTC 1 43396 ( 295) CAATTTCTGCCATTTC 1 12431 ( 326) CACTTTCGTCCACTCC 1 45270 ( 93) AGGTTGTTCGCATTTC 1 45479 ( 226) CTGTTTTGCGCTCTCC 1 42605 ( 215) CGCTTTTTCCAAATCC 1 44536 ( 449) CTATTTCTTTCTTATC 1 43469 ( 124) AAGTTTTGCTGTTTTC 1 45632 ( 132) CTAATGTGTTCTATTC 1 45155 ( 174) CGGTGTTTCTGTTTTC 1 35217 ( 364) TGCTTATGTGCTTTTC 1 45955 ( 241) CGCTTGTTATATATTC 1 34586 ( 200) TTAATGTTTCCTTTTC 1 45570 ( 187) CAGTTTATTGAATTTC 1 45587 ( 193) TGCTTTTTACTTTTTC 1 43115 ( 371) CGAATGCGTGCTATCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 37830 bayes= 11.5745 E= 5.7e-005 -144 170 -1155 -102 -44 -1155 97 44 56 63 8 -1155 -144 -1155 -1155 173 -1155 -1155 -273 184 -302 -1155 44 130 -302 87 -1155 98 -1155 -1155 118 89 -144 17 -273 115 -1155 87 59 -21 -44 63 73 -202 56 -1155 -1155 115 -44 -83 -1155 130 -302 -1155 -1155 184 -1155 -51 -1155 162 -1155 208 -1155 -1155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 30 E= 5.7e-005 0.100000 0.766667 0.000000 0.133333 0.200000 0.000000 0.433333 0.366667 0.400000 0.366667 0.233333 0.000000 0.100000 0.000000 0.000000 0.900000 0.000000 0.000000 0.033333 0.966667 0.033333 0.000000 0.300000 0.666667 0.033333 0.433333 0.000000 0.533333 0.000000 0.000000 0.500000 0.500000 0.100000 0.266667 0.033333 0.600000 0.000000 0.433333 0.333333 0.233333 0.200000 0.366667 0.366667 0.066667 0.400000 0.000000 0.000000 0.600000 0.200000 0.133333 0.000000 0.666667 0.033333 0.000000 0.000000 0.966667 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[GTA][ACG]TT[TG][TC][GT][TC][CGT][CGA][TA][TA]TTC -------------------------------------------------------------------------------- Time 90.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 26 llr = 264 E-value = 2.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::8:21::a61 pos.-specific C 7:22a3::3:34 probability G 3:8::2927::3 matrix T :a:::3:8:::3 bits 2.2 * 2.0 * * 1.7 * * * 1.5 ** * * * Relative 1.3 **** **** Entropy 1.1 ***** **** (14.6 bits) 0.9 ***** ***** 0.7 ***** ***** 0.4 ***** ***** 0.2 ***** ****** 0.0 ------------ Multilevel CTGACTGTGAAC consensus G C C CG sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 51825 439 3.10e-07 TTGTCTTAAC CTGACCGTGAAG CGGCAACGAC 44702 374 3.10e-07 CGGCTTGACA CTGACAGTGAAC TGACTTCGGT 34712 20 4.04e-07 TCGCGACATT CTGACTGTGACC ATAGAGCTGG 45225 323 7.22e-07 AGGTAGGTAG GTGACTGTGAAC AAGAGCTCCA 43469 221 1.32e-06 CTACCTTATT CTGACAGTGAAT ACGTAATGAT 45270 174 1.82e-06 CAAAAAATGA CTGACTGTGACT ACCAGAATCA 45155 489 1.92e-06 GCAATCGTCT CTGACTGTCACC 42502 112 2.12e-06 TTGGATAAAT GTGACTGTGAAT AGGAGCTTGA 54119 174 5.00e-06 CGAAATAATA CTGACTGGGAAG CATGACACGG 43138 216 6.61e-06 TTTTGATTCG CTGACAGGGAAG CGACAAATAC 46435 180 8.74e-06 CCTTGCCAAA CTGCCTGTCACC ACGCAACCGA 43261 64 1.30e-05 GACATGGACA GTGCCAGTGAAT GATCCGGTTT 43244 252 1.39e-05 CGAATTCTTG GTGCCGGTCAAC CCAATCCCAT 48286 434 1.47e-05 TCTCCAGCAA GTGCCCGTCACC AACGGTTTCT 48278 434 1.47e-05 TCTCCAGCAA GTGCCCGTCACC AACGGTTTCT 12431 43 1.64e-05 GTTGAGTTCA CTCACAGTCAAG GAGCATCATC 5808 367 1.64e-05 TGGCAGTTCC GTCACCGTCAAC ACAAAATTTG 54088 420 1.75e-05 AATCTACGGT CTGACTGGCACT GTGAATATTC 45672 267 2.04e-05 CGTTTCACGA CTGACGATGACC TGCGTCTATT 36358 9 2.04e-05 TTTTCTGT CTGACCATGACG ACGGGCAGGG 46009 443 2.31e-05 ACGAAAGATA CTGACCCTGAAG TGCATTTCCA 42900 164 2.52e-05 GGTGATAGAT CTGACGGGGAAA CACTTTCATT 42596 425 2.52e-05 TACGGTGACG CTGACGGTGATT TTGCGCTGCA 45570 332 2.52e-05 AAACTGTATT GTCACAGTCAAG CGTGAGAGAG 44735 23 2.52e-05 TTGATCTTGT CGGACCGTGAAT GGGCGAGACG 46348 353 4.47e-05 ACTTTTTGAT GTCACGGTGAAA GTGATGTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 51825 3.1e-07 438_[+3]_50 44702 3.1e-07 373_[+3]_115 34712 4e-07 19_[+3]_469 45225 7.2e-07 322_[+3]_166 43469 1.3e-06 220_[+3]_268 45270 1.8e-06 173_[+3]_315 45155 1.9e-06 488_[+3] 42502 2.1e-06 111_[+3]_377 54119 5e-06 173_[+3]_315 43138 6.6e-06 215_[+3]_273 46435 8.7e-06 179_[+3]_309 43261 1.3e-05 63_[+3]_425 43244 1.4e-05 251_[+3]_237 48286 1.5e-05 433_[+3]_55 48278 1.5e-05 433_[+3]_55 12431 1.6e-05 42_[+3]_446 5808 1.6e-05 366_[+3]_122 54088 1.8e-05 419_[+3]_69 45672 2e-05 266_[+3]_222 36358 2e-05 8_[+3]_480 46009 2.3e-05 442_[+3]_46 42900 2.5e-05 163_[+3]_325 42596 2.5e-05 424_[+3]_64 45570 2.5e-05 331_[+3]_157 44735 2.5e-05 22_[+3]_466 46348 4.5e-05 352_[+3]_136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=26 51825 ( 439) CTGACCGTGAAG 1 44702 ( 374) CTGACAGTGAAC 1 34712 ( 20) CTGACTGTGACC 1 45225 ( 323) GTGACTGTGAAC 1 43469 ( 221) CTGACAGTGAAT 1 45270 ( 174) CTGACTGTGACT 1 45155 ( 489) CTGACTGTCACC 1 42502 ( 112) GTGACTGTGAAT 1 54119 ( 174) CTGACTGGGAAG 1 43138 ( 216) CTGACAGGGAAG 1 46435 ( 180) CTGCCTGTCACC 1 43261 ( 64) GTGCCAGTGAAT 1 43244 ( 252) GTGCCGGTCAAC 1 48286 ( 434) GTGCCCGTCACC 1 48278 ( 434) GTGCCCGTCACC 1 12431 ( 43) CTCACAGTCAAG 1 5808 ( 367) GTCACCGTCAAC 1 54088 ( 420) CTGACTGGCACT 1 45672 ( 267) CTGACGATGACC 1 36358 ( 9) CTGACCATGACG 1 46009 ( 443) CTGACCCTGAAG 1 42900 ( 164) CTGACGGGGAAA 1 42596 ( 425) CTGACGGTGATT 1 45570 ( 332) GTCACAGTCAAG 1 44735 ( 23) CGGACCGTGAAT 1 46348 ( 353) GTCACGGTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 38142 bayes= 11.0485 E= 2.9e-001 -1134 147 65 -1134 -1134 -1134 -252 183 -1134 -62 194 -1134 157 -30 -1134 -1134 -1134 208 -1134 -1134 -24 19 -20 19 -182 -262 200 -1134 -1134 -1134 -52 165 -1134 55 156 -1134 188 -1134 -1134 -1134 118 55 -1134 -281 -182 70 28 -1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 26 E= 2.9e-001 0.000000 0.653846 0.346154 0.000000 0.000000 0.000000 0.038462 0.961538 0.000000 0.153846 0.846154 0.000000 0.807692 0.192308 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.230769 0.269231 0.192308 0.307692 0.076923 0.038462 0.884615 0.000000 0.000000 0.000000 0.153846 0.846154 0.000000 0.346154 0.653846 0.000000 1.000000 0.000000 0.000000 0.000000 0.615385 0.346154 0.000000 0.038462 0.076923 0.384615 0.269231 0.269231 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG]TGAC[TCA]GT[GC]A[AC][CGT] -------------------------------------------------------------------------------- Time 135.84 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31831 3.27e-01 500 43065 7.03e-03 136_[+1(1.35e-06)]_89_\ [+1(5.57e-06)]_249 43115 4.31e-02 370_[+2(2.15e-05)]_114 43235 1.49e-01 348_[+1(3.91e-05)]_139 43244 4.51e-05 232_[+2(7.61e-06)]_3_[+3(1.39e-05)]_\ 100_[+2(1.46e-07)]_121 46348 3.92e-03 229_[+1(1.83e-05)]_110_\ [+3(4.47e-05)]_136 36358 1.82e-02 8_[+3(2.04e-05)]_480 5808 6.28e-02 366_[+3(1.64e-05)]_122 36534 4.41e-04 78_[+1(3.65e-05)]_335_\ [+1(2.49e-06)]_61 46578 8.34e-01 500 46884 9.37e-02 214_[+1(2.63e-05)]_273 13617 9.99e-01 500 48278 2.20e-03 433_[+3(1.47e-05)]_5_[+1(9.96e-06)]_\ 37 48286 2.20e-03 433_[+3(1.47e-05)]_5_[+1(9.96e-06)]_\ 37 43375 5.12e-03 279_[+2(3.71e-06)]_205 32665 6.60e-01 500 43469 2.86e-07 123_[+2(1.14e-05)]_36_\ [+1(7.11e-07)]_32_[+3(1.32e-06)]_53_[+1(8.36e-05)]_202 54119 1.55e-03 173_[+3(5.00e-06)]_30_\ [+1(2.81e-05)]_164_[+1(7.83e-05)]_95 40593 2.45e-06 34_[+1(2.07e-06)]_22_[+2(4.49e-07)]_\ 415 49807 3.65e-04 84_[+2(2.77e-05)]_5_[+2(7.71e-07)]_\ 379 8044 9.78e-01 500 41238 2.90e-02 171_[+1(8.90e-06)]_316 50641 2.67e-02 86_[+1(4.57e-05)]_2_[+1(3.31e-06)]_\ 386 10974 6.33e-01 500 10925 7.48e-01 500 44536 7.29e-02 448_[+2(1.05e-05)]_36 44702 3.33e-05 236_[+1(5.57e-06)]_124_\ [+3(3.10e-07)]_115 44735 3.55e-03 22_[+3(2.52e-05)]_223_\ [+1(1.26e-05)]_230 44761 2.21e-03 397_[+1(8.52e-07)]_90 34385 8.44e-07 50_[+2(5.90e-07)]_226_\ [+2(8.33e-05)]_75_[+3(1.32e-06)]_105 11403 1.91e-01 500 34712 1.24e-04 19_[+3(4.04e-07)]_30_[+1(1.36e-05)]_\ 426 51825 1.49e-04 349_[+1(3.65e-05)]_76_\ [+3(3.10e-07)]_50 45402 1.61e-01 123_[+1(4.19e-05)]_364 45570 7.14e-05 186_[+2(1.88e-05)]_129_\ [+3(2.52e-05)]_24_[+1(1.12e-05)]_120 45584 2.83e-01 500 45604 4.63e-02 451_[+1(1.68e-05)]_36 45672 2.09e-03 22_[+1(1.36e-05)]_231_\ [+3(2.04e-05)]_222 45826 8.04e-02 320_[+1(3.06e-05)]_167 45955 8.56e-04 240_[+2(1.42e-05)]_199_\ [+1(2.63e-05)]_32 12431 6.80e-06 42_[+3(1.64e-05)]_70_[+1(2.93e-06)]_\ 188_[+2(7.61e-06)]_159 46175 7.29e-01 500 46435 2.70e-02 179_[+3(8.74e-06)]_309 42502 3.74e-05 111_[+3(2.12e-06)]_274_\ [+1(7.11e-07)]_90 42596 3.45e-06 81_[+1(3.91e-05)]_49_[+2(1.75e-07)]_\ 265_[+3(2.52e-05)]_64 42605 2.48e-03 214_[+2(8.99e-06)]_115_\ [+1(1.99e-05)]_142 42900 1.75e-02 163_[+3(2.52e-05)]_325 42997 3.59e-04 272_[+1(1.86e-07)]_215 47015 5.07e-02 240_[+1(7.19e-06)]_247 43138 6.16e-05 215_[+3(6.61e-06)]_87_\ [+1(1.10e-06)]_101_[+1(2.16e-05)]_59 45225 1.58e-07 111_[+2(3.71e-06)]_18_\ [+1(2.07e-06)]_164_[+3(7.22e-07)]_166 33765 1.03e-02 287_[+1(7.19e-06)]_200 43261 4.71e-04 63_[+3(1.30e-05)]_7_[+1(1.82e-06)]_\ 405 43395 1.27e-03 291_[+2(9.97e-07)]_41_\ [+1(7.83e-05)]_139 43396 5.69e-03 294_[+2(6.99e-06)]_41_\ [+1(7.83e-05)]_136 54088 2.02e-04 348_[+1(2.07e-06)]_58_\ [+3(1.75e-05)]_69 46406 4.16e-03 293_[+2(3.90e-07)]_191 46501 8.00e-02 211_[+1(2.39e-05)]_276 47693 4.91e-03 393_[+2(2.43e-07)]_91 44600 1.98e-05 73_[+3(7.22e-07)]_415 45479 3.66e-05 225_[+2(8.99e-06)]_206_\ [+1(7.11e-07)]_40 35217 2.20e-02 363_[+2(1.32e-05)]_121 36629 5.06e-01 500 45603 9.78e-01 500 34384 8.52e-01 500 45074 3.00e-03 209_[+2(1.75e-07)]_275 45155 4.91e-06 173_[+2(1.32e-05)]_125_\ [+1(9.96e-06)]_161_[+3(1.92e-06)] 45270 9.56e-07 92_[+2(8.99e-06)]_65_[+3(1.82e-06)]_\ 170_[+1(2.49e-06)]_132 45403 7.27e-01 500 35400 5.08e-03 451_[+2(2.01e-06)]_33 32511 4.91e-03 393_[+2(2.43e-07)]_91 45632 1.17e-03 131_[+2(1.32e-05)]_14_\ [+1(5.57e-06)]_326 45104 2.70e-01 500 34586 1.11e-01 199_[+2(1.53e-05)]_285 49982 7.52e-03 429_[+1(5.01e-06)]_58 8596 1.03e-05 49_[+2(7.61e-08)]_266_\ [+1(2.63e-05)]_156 45587 2.64e-02 192_[+2(2.15e-05)]_292 46009 8.06e-04 59_[+2(3.37e-06)]_367_\ [+3(2.31e-05)]_46 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************