******************************************************************************** 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/200/200.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1432 1.0000 500 17349 1.0000 500 1750 1.0000 500 204 1.0000 500 21290 1.0000 500 21710 1.0000 500 21788 1.0000 500 22770 1.0000 500 23601 1.0000 500 23819 1.0000 500 24714 1.0000 500 24965 1.0000 500 25225 1.0000 500 260861 1.0000 500 262136 1.0000 500 263944 1.0000 500 264295 1.0000 500 268059 1.0000 500 27451 1.0000 500 33330 1.0000 500 35031 1.0000 500 3607 1.0000 500 39666 1.0000 500 4111 1.0000 500 4462 1.0000 500 5105 1.0000 500 5144 1.0000 500 9443 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/200/200.seqs.fa -oc motifs/200 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.229 G 0.252 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.229 G 0.252 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 23 llr = 241 E-value = 1.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4::21232:74:74: pos.-specific C ::214::22::2:::: probability G 8228:6814a3:a1:a matrix T 246132:52::3:26: bits 2.1 1.9 * * * 1.7 * * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * * ** * ** (15.1 bits) 0.8 * * * ** **** 0.6 * ** * ** **** 0.4 ******* ******* 0.2 ******** ******* 0.0 ---------------- Multilevel GATGCGGTGGAAGATG consensus TG TTAAC GT A sequence A T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23601 266 2.91e-08 AGCACTAGCA GACGCGGTGGATGATG ACGGGTTGAT 5105 153 6.95e-08 GGGCGAGCGG GTTGCGATGGATGATG GCCGACTTGT 17349 320 2.07e-07 TCTTCGCTCG GTTGTGGTGGGTGAAG GTTCACTCTG 23819 86 3.87e-07 GGAGCCTGGT GTTGTAGTGGAAGAAG GTGGTGGCGC 35031 203 7.96e-07 TACCCTGCCA GTTGTGGCCGACGAAG ACGAATGGTG 262136 110 9.15e-07 AGGTACGTTC TTGGCGGTGGAAGAAG CAGTTTTGGT 9443 177 1.93e-06 TAAGATATTA GTTGTTATCGATGATG TTGCTACTTG 263944 257 1.93e-06 TGATTCTATG GATGCAATAGAAGATG GTGACTCTCC 260861 151 2.18e-06 ATGGAGTAAA GATGATGAAGAAGAAG AAGAAGCAGA 21788 335 2.73e-06 GAGGTGCACC GACGCGGAAGAAGTTG GGTTCGTTGG 21710 139 4.17e-06 TACGTTTGGT TGTGCAGTGGATGATG TGCATGGTGA 39666 429 4.62e-06 AGGGACCAAC GATCTGGCGGGAGATG ATTCCCGTGG 5144 257 5.10e-06 TCTCCGCGGC GATGCGGAAGGAGGAG GCTGGCTGTT 268059 141 6.82e-06 AGAGCGAGAG GAGGAGGGTGACGATG GCGCTGTCAT 4462 280 1.16e-05 TACTCGCGTC GTCGTGGTTGGCGTTG ATGTAGATGC 21290 191 1.26e-05 CCATCTTGCA GATGCCGACGATGTTG TCGGGGAGGA 24714 168 1.36e-05 CGACGGCGGA GTTCATGTCGATGAAG CTGGGTGTGT 25225 61 2.00e-05 TGTCAGCGAG GATGCTACTGACGTTG AAGGGCCAAC 264295 283 2.65e-05 AAGTGTAGGC TACGAGGAGGACGGTG TGCGGTTAGT 27451 3 3.67e-05 GC GGTGTTGCTGGTGGTG TATGGAGGGC 204 170 4.65e-05 CGACCACTTT TGGTAGGTTGAAGATG CATTCACACG 1750 324 4.91e-05 GATGAGTGTG GTGTTGAGGGAAGAAG GAAGGGGCTA 33330 283 5.48e-05 GGGTGGGCGG AGGGCGGACGGAGAAG GTAAAAACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23601 2.9e-08 265_[+1]_219 5105 6.9e-08 152_[+1]_332 17349 2.1e-07 319_[+1]_165 23819 3.9e-07 85_[+1]_399 35031 8e-07 202_[+1]_282 262136 9.1e-07 109_[+1]_375 9443 1.9e-06 176_[+1]_308 263944 1.9e-06 256_[+1]_228 260861 2.2e-06 150_[+1]_334 21788 2.7e-06 334_[+1]_150 21710 4.2e-06 138_[+1]_346 39666 4.6e-06 428_[+1]_56 5144 5.1e-06 256_[+1]_228 268059 6.8e-06 140_[+1]_344 4462 1.2e-05 279_[+1]_205 21290 1.3e-05 190_[+1]_294 24714 1.4e-05 167_[+1]_317 25225 2e-05 60_[+1]_424 264295 2.7e-05 282_[+1]_202 27451 3.7e-05 2_[+1]_482 204 4.6e-05 169_[+1]_315 1750 4.9e-05 323_[+1]_161 33330 5.5e-05 282_[+1]_202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=23 23601 ( 266) GACGCGGTGGATGATG 1 5105 ( 153) GTTGCGATGGATGATG 1 17349 ( 320) GTTGTGGTGGGTGAAG 1 23819 ( 86) GTTGTAGTGGAAGAAG 1 35031 ( 203) GTTGTGGCCGACGAAG 1 262136 ( 110) TTGGCGGTGGAAGAAG 1 9443 ( 177) GTTGTTATCGATGATG 1 263944 ( 257) GATGCAATAGAAGATG 1 260861 ( 151) GATGATGAAGAAGAAG 1 21788 ( 335) GACGCGGAAGAAGTTG 1 21710 ( 139) TGTGCAGTGGATGATG 1 39666 ( 429) GATCTGGCGGGAGATG 1 5144 ( 257) GATGCGGAAGGAGGAG 1 268059 ( 141) GAGGAGGGTGACGATG 1 4462 ( 280) GTCGTGGTTGGCGTTG 1 21290 ( 191) GATGCCGACGATGTTG 1 24714 ( 168) GTTCATGTCGATGAAG 1 25225 ( 61) GATGCTACTGACGTTG 1 264295 ( 283) TACGAGGAGGACGGTG 1 27451 ( 3) GGTGTTGCTGGTGGTG 1 204 ( 170) TGGTAGGTTGAAGATG 1 1750 ( 324) GTGTTGAGGGAAGAAG 1 33330 ( 283) AGGGCGGACGGAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 9.60633 E= 1.3e-006 -257 -1117 163 -58 75 -1117 -54 59 -1117 -40 -22 123 -1117 -140 171 -158 -25 92 -1117 42 -98 -240 127 -26 -25 -1117 163 -1117 2 -40 -154 88 -57 -8 63 -26 -1117 -1117 199 -1117 152 -1117 5 -1117 75 -8 -1117 42 -1117 -1117 199 -1117 143 -1117 -95 -58 60 -1117 -1117 123 -1117 -1117 199 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 1.3e-006 0.043478 0.000000 0.782609 0.173913 0.434783 0.000000 0.173913 0.391304 0.000000 0.173913 0.217391 0.608696 0.000000 0.086957 0.826087 0.086957 0.217391 0.434783 0.000000 0.347826 0.130435 0.043478 0.608696 0.217391 0.217391 0.000000 0.782609 0.000000 0.260870 0.173913 0.086957 0.478261 0.173913 0.217391 0.391304 0.217391 0.000000 0.000000 1.000000 0.000000 0.739130 0.000000 0.260870 0.000000 0.434783 0.217391 0.000000 0.347826 0.000000 0.000000 1.000000 0.000000 0.695652 0.000000 0.130435 0.173913 0.391304 0.000000 0.000000 0.608696 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AT][TG]G[CTA][GT][GA][TA][GCT]G[AG][ATC]GA[TA]G -------------------------------------------------------------------------------- Time 6.70 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 25 llr = 229 E-value = 1.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::311:4:22:: pos.-specific C 29::67:a5:a7 probability G 21:2:::::::1 matrix T 6:77236:28:2 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * ** Entropy 1.1 * *** ** (13.2 bits) 0.8 ** *** *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCTTCCTCCTCC consensus AGTTA AA T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9443 129 3.92e-08 GTCCGGGTGA TCTTCCTCCTCC GAATCCTCTT 262136 397 7.76e-07 CATGGACCAA TCTTTCACCTCC ACGCCTGTAA 24965 324 7.76e-07 TCGGTCTTGG TCTTTCACCTCC GCGCTGATTT 3607 464 1.22e-06 CGCGTTAAGA TCTTCTTCTTCC CTCTTTCCTC 5144 445 2.48e-06 AGAACGCTGT TCATCCTCCACC CTTCACCACC 33330 27 2.48e-06 GATCCCCTGC TCTTCCTCTTCT TCTTGTGCTT 21788 470 4.20e-06 CACCCCCCCA CCTTCTACCTCC ACAAGAGCCA 268059 385 7.81e-06 TCAATGAAAA TCATTTTCCTCC GTTTGGAGCC 204 376 9.06e-06 ACCGAGCTTT CCTGCCTCTTCC AACAGCCTCT 5105 434 1.21e-05 TCAACTCATG TTTTCCACCTCC ATTCTCACCT 24714 205 1.49e-05 ATCGTAGACT TCTTCTTCTTCG TTCGTGGTGG 23601 362 1.49e-05 TTCGTGTTCA TCTTCTTCATCG ATGTCGATGT 4111 18 1.63e-05 CTTCTCCACT TCTGACTCATCC AGTTGTTGCG 39666 153 2.26e-05 CAAGAGCATC ACTTCCTCCACC TCGGAGCTGC 263944 41 3.64e-05 AAACAAACGT GCTTCTTCTTCT GATGAGAAAA 27451 76 4.82e-05 CGGAACTGCC TCGTACACCTCC GTCGGCGTCG 25225 310 6.07e-05 CGGCCACGGC GCTACCACCACC ACCGCCACAC 22770 349 6.07e-05 ATTCAATCTC TCAATCTCATCC TTGTCATAAC 4462 106 6.59e-05 TTCATGTAAA TCACTCACCTCC GGGCTCTTGA 35031 116 6.59e-05 CGAGTGATTG GCTGCCTCTTCG ATGGAGGCAG 17349 301 9.41e-05 GGTTCTTCTG CCTGCTTCATCT TCGCTCGGTT 1432 11 9.41e-05 TCGTACGGCC GCATACACCTCT AACATTGACA 21290 467 1.15e-04 TACCTACCAG CCAGCCACAACC CACAAACCAC 1750 64 1.23e-04 GAAGTACATG TGTTCCTCAACT TGCAAAGGAT 264295 6 1.70e-04 TTGGT TGATGCACCTCC GTCCAAGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9443 3.9e-08 128_[+2]_360 262136 7.8e-07 396_[+2]_92 24965 7.8e-07 323_[+2]_165 3607 1.2e-06 463_[+2]_25 5144 2.5e-06 444_[+2]_44 33330 2.5e-06 26_[+2]_462 21788 4.2e-06 469_[+2]_19 268059 7.8e-06 384_[+2]_104 204 9.1e-06 375_[+2]_113 5105 1.2e-05 433_[+2]_55 24714 1.5e-05 204_[+2]_284 23601 1.5e-05 361_[+2]_127 4111 1.6e-05 17_[+2]_471 39666 2.3e-05 152_[+2]_336 263944 3.6e-05 40_[+2]_448 27451 4.8e-05 75_[+2]_413 25225 6.1e-05 309_[+2]_179 22770 6.1e-05 348_[+2]_140 4462 6.6e-05 105_[+2]_383 35031 6.6e-05 115_[+2]_373 17349 9.4e-05 300_[+2]_188 1432 9.4e-05 10_[+2]_478 21290 0.00011 466_[+2]_22 1750 0.00012 63_[+2]_425 264295 0.00017 5_[+2]_483 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=25 9443 ( 129) TCTTCCTCCTCC 1 262136 ( 397) TCTTTCACCTCC 1 24965 ( 324) TCTTTCACCTCC 1 3607 ( 464) TCTTCTTCTTCC 1 5144 ( 445) TCATCCTCCACC 1 33330 ( 27) TCTTCCTCTTCT 1 21788 ( 470) CCTTCTACCTCC 1 268059 ( 385) TCATTTTCCTCC 1 204 ( 376) CCTGCCTCTTCC 1 5105 ( 434) TTTTCCACCTCC 1 24714 ( 205) TCTTCTTCTTCG 1 23601 ( 362) TCTTCTTCATCG 1 4111 ( 18) TCTGACTCATCC 1 39666 ( 153) ACTTCCTCCACC 1 263944 ( 41) GCTTCTTCTTCT 1 27451 ( 76) TCGTACACCTCC 1 25225 ( 310) GCTACCACCACC 1 22770 ( 349) TCAATCTCATCC 1 4462 ( 106) TCACTCACCTCC 1 35031 ( 116) GCTGCCTCTTCG 1 17349 ( 301) CCTGCTTCATCT 1 1432 ( 11) GCATACACCTCT 1 21290 ( 467) CCAGCCACAACC 1 1750 ( 64) TGTTCCTCAACT 1 264295 ( 6) TGATGCACCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13692 bayes= 9.58536 E= 1.8e-004 -269 -52 -66 130 -1129 194 -166 -270 12 -1129 -265 139 -169 -252 -34 139 -110 148 -265 -38 -1129 165 -1129 11 63 -1129 -1129 120 -1129 212 -1129 -1129 -10 118 -1129 -12 -37 -1129 -1129 162 -1129 212 -1129 -1129 -1129 157 -107 -38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 25 E= 1.8e-004 0.040000 0.160000 0.160000 0.640000 0.000000 0.880000 0.080000 0.040000 0.280000 0.000000 0.040000 0.680000 0.080000 0.040000 0.200000 0.680000 0.120000 0.640000 0.040000 0.200000 0.000000 0.720000 0.000000 0.280000 0.400000 0.000000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.240000 0.520000 0.000000 0.240000 0.200000 0.000000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.680000 0.120000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TC[TA][TG][CT][CT][TA]C[CAT][TA]C[CT] -------------------------------------------------------------------------------- Time 13.26 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 28 llr = 264 E-value = 4.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 23746:7952841881 pos.-specific C 5615:73:47:48127 probability G 3:1:11:111:::::: matrix T :11:32::::1211:2 bits 2.1 1.9 1.7 1.5 Relative 1.3 * * Entropy 1.1 ** * *** (13.6 bits) 0.8 *** * *** 0.6 ********** **** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCACACAAACACCAAC consensus GA ATTC C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 17349 484 1.26e-09 ATACCACCAC CCAAACAAACAACAAC C 25225 336 3.38e-08 CCACACACAC ACACACCACCACCAAC AACACACACC 24714 485 5.45e-07 GGCCGACTCA CACCTCAAACAACAAC 22770 241 6.14e-07 CGGAATTTGA CAACACCAACATCAAT GATTCTGACT 9443 338 7.94e-07 TTCCAATTTT CAACTTCAACAACAAC ACTGCAACTG 1432 467 1.01e-06 GACGGCGATA GAATACAACCACCAAC CCCATCCGAA 21710 289 2.03e-06 AGTCATCAAT ATAATCAACCATCAAC GATACCCCTC 23819 438 3.52e-06 ATGAAGATAA GCAAACAAACTCCACT CCCCAACAGG 264295 435 4.35e-06 AAATCAAATG GCAAACAAACAACGCC TGACCGCCTG 4111 384 5.92e-06 CGCCGACTCT CCACGCAACCTCCCAC GCTGCAGCAA 39666 413 5.92e-06 GTGACAAACT GCACACAGGGACCAAC GATCTGGCGG 27451 269 9.69e-06 AACCAACAGA ACAAACCAAAATCAAA CAACGAAGGC 35031 254 1.17e-05 CGAGAACCAA CCACTCCAAAATCTAC CAGATTGACT 268059 477 1.29e-05 CGAAACCCTC ACAAATCAACGCCAAC GCCGACGA 23601 477 1.29e-05 AAGATTCGTC GCACACAAGCACTAAA ATTCCTTC 33330 246 1.41e-05 TGCCATCCAT CAGCACAACAACAAAC CAGTCAAAAA 21788 432 1.55e-05 CAGCTCAAAC GCTCACAACCAAAAAA CACCCTCCGA 3607 485 1.69e-05 CCTCTTTCCT CCACATCACTACCACC 204 210 1.69e-05 CTTCAAAACC GACCATAAGCATCAAC AGGGGTTTGT 260861 361 2.21e-05 AGAGTGCTAT CTAATCAAACAATAAT CATTATTAGA 21290 425 2.21e-05 CATAAAGATC CAAATGAAAATCCAAC GAAAACAGCA 263944 223 4.01e-05 AAGCAACAAG CTCAAGAGACAACAAC GGAAACACTG 5144 473 5.10e-05 CACCTTTTCA CCTCACAGCGTACAAC GCCTCCTTCC 5105 413 1.09e-04 TCTAGAAGAT TCAGATAAAAATCAAC TCATGTTTTC 4462 29 1.54e-04 ACCAAAAGAT GTTAGCAAAGAACAAT AGGGCGAGAC 24965 466 2.02e-04 CCACTCCCAG CCACGCCACCAACTCG CCACTCCACG 262136 312 2.96e-04 GAGATAATGA GCAAGTAGCCACAACT GTTCGTTGAA 1750 424 5.94e-04 AGCCCCCCTG AAGATGAAACACACAC TTTAGAAGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17349 1.3e-09 483_[+3]_1 25225 3.4e-08 335_[+3]_149 24714 5.4e-07 484_[+3] 22770 6.1e-07 240_[+3]_244 9443 7.9e-07 337_[+3]_147 1432 1e-06 466_[+3]_18 21710 2e-06 288_[+3]_196 23819 3.5e-06 437_[+3]_47 264295 4.3e-06 434_[+3]_50 4111 5.9e-06 383_[+3]_101 39666 5.9e-06 412_[+3]_72 27451 9.7e-06 268_[+3]_216 35031 1.2e-05 253_[+3]_231 268059 1.3e-05 476_[+3]_8 23601 1.3e-05 476_[+3]_8 33330 1.4e-05 245_[+3]_239 21788 1.5e-05 431_[+3]_53 3607 1.7e-05 484_[+3] 204 1.7e-05 209_[+3]_275 260861 2.2e-05 360_[+3]_124 21290 2.2e-05 424_[+3]_60 263944 4e-05 222_[+3]_262 5144 5.1e-05 472_[+3]_12 5105 0.00011 412_[+3]_72 4462 0.00015 28_[+3]_456 24965 0.0002 465_[+3]_19 262136 0.0003 311_[+3]_173 1750 0.00059 423_[+3]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=28 17349 ( 484) CCAAACAAACAACAAC 1 25225 ( 336) ACACACCACCACCAAC 1 24714 ( 485) CACCTCAAACAACAAC 1 22770 ( 241) CAACACCAACATCAAT 1 9443 ( 338) CAACTTCAACAACAAC 1 1432 ( 467) GAATACAACCACCAAC 1 21710 ( 289) ATAATCAACCATCAAC 1 23819 ( 438) GCAAACAAACTCCACT 1 264295 ( 435) GCAAACAAACAACGCC 1 4111 ( 384) CCACGCAACCTCCCAC 1 39666 ( 413) GCACACAGGGACCAAC 1 27451 ( 269) ACAAACCAAAATCAAA 1 35031 ( 254) CCACTCCAAAATCTAC 1 268059 ( 477) ACAAATCAACGCCAAC 1 23601 ( 477) GCACACAAGCACTAAA 1 33330 ( 246) CAGCACAACAACAAAC 1 21788 ( 432) GCTCACAACCAAAAAA 1 3607 ( 485) CCACATCACTACCACC 1 204 ( 210) GACCATAAGCATCAAC 1 260861 ( 361) CTAATCAAACAATAAT 1 21290 ( 425) CAAATGAAAATCCAAC 1 263944 ( 223) CTCAAGAGACAACAAC 1 5144 ( 473) CCTCACAGCGTACAAC 1 5105 ( 413) TCAGATAAAAATCAAC 1 4462 ( 29) GTTAGCAAAGAACAAT 1 24965 ( 466) CCACGCCACCAACTCG 1 262136 ( 312) GCAAGTAGCCACAACT 1 1750 ( 424) AAGATGAAACACACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 8.91886 E= 4.5e-005 -53 102 35 -286 15 132 -1145 -87 147 -110 -182 -128 73 112 -282 -286 123 -1145 -82 -6 -1145 156 -124 -28 147 32 -1145 -1145 173 -1145 -82 -1145 105 64 -124 -1145 -53 156 -124 -286 167 -1145 -282 -87 47 90 -1145 -28 -85 178 -1145 -186 167 -168 -282 -186 167 -36 -1145 -1145 -127 156 -282 -54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 28 E= 4.5e-005 0.178571 0.464286 0.321429 0.035714 0.285714 0.571429 0.000000 0.142857 0.714286 0.107143 0.071429 0.107143 0.428571 0.500000 0.035714 0.035714 0.607143 0.000000 0.142857 0.250000 0.000000 0.678571 0.107143 0.214286 0.714286 0.285714 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.535714 0.357143 0.107143 0.000000 0.178571 0.678571 0.107143 0.035714 0.821429 0.000000 0.035714 0.142857 0.357143 0.428571 0.000000 0.214286 0.142857 0.785714 0.000000 0.071429 0.821429 0.071429 0.035714 0.071429 0.821429 0.178571 0.000000 0.000000 0.107143 0.678571 0.035714 0.178571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][CA]A[CA][AT][CT][AC]A[AC]CA[CAT]CAAC -------------------------------------------------------------------------------- Time 19.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1432 2.78e-04 10_[+2(9.41e-05)]_444_\ [+3(1.01e-06)]_18 17349 1.05e-09 300_[+2(9.41e-05)]_7_[+1(2.07e-07)]_\ 119_[+3(6.45e-05)]_13_[+3(1.26e-09)]_1 1750 1.40e-02 323_[+1(4.91e-05)]_161 204 9.15e-05 169_[+1(4.65e-05)]_24_\ [+3(1.69e-05)]_150_[+2(9.06e-06)]_113 21290 3.27e-04 190_[+1(1.26e-05)]_218_\ [+3(2.21e-05)]_60 21710 8.78e-05 138_[+1(4.17e-06)]_134_\ [+3(2.03e-06)]_196 21788 3.56e-06 308_[+1(2.31e-05)]_10_\ [+1(2.73e-06)]_81_[+3(1.55e-05)]_22_[+2(4.20e-06)]_19 22770 9.55e-05 240_[+3(6.14e-07)]_92_\ [+2(6.07e-05)]_140 23601 1.57e-07 265_[+1(2.91e-08)]_80_\ [+2(1.49e-05)]_34_[+2(8.17e-05)]_57_[+3(1.29e-05)]_8 23819 1.73e-05 85_[+1(3.87e-07)]_14_[+1(5.10e-06)]_\ 306_[+3(3.52e-06)]_47 24714 2.34e-06 167_[+1(1.36e-05)]_21_\ [+2(1.49e-05)]_268_[+3(5.45e-07)] 24965 1.34e-03 30_[+2(5.25e-05)]_281_\ [+2(7.76e-07)]_165 25225 9.45e-07 60_[+1(2.00e-05)]_181_\ [+3(5.34e-06)]_36_[+2(6.07e-05)]_14_[+3(3.38e-08)]_3_[+3(2.42e-05)]_51_\ [+3(7.23e-06)]_8_[+3(2.11e-07)]_12_[+3(1.17e-05)]_11 260861 3.74e-04 74_[+1(2.00e-05)]_60_[+1(2.18e-06)]_\ 194_[+3(2.21e-05)]_124 262136 3.91e-06 109_[+1(9.15e-07)]_271_\ [+2(7.76e-07)]_92 263944 4.07e-05 12_[+1(1.26e-05)]_12_[+2(3.64e-05)]_\ 170_[+3(4.01e-05)]_18_[+1(1.93e-06)]_228 264295 2.13e-04 282_[+1(2.65e-05)]_136_\ [+3(4.35e-06)]_50 268059 1.18e-05 140_[+1(6.82e-06)]_228_\ [+2(7.81e-06)]_80_[+3(1.29e-05)]_8 27451 1.94e-04 2_[+1(3.67e-05)]_57_[+2(4.82e-05)]_\ 162_[+3(7.51e-05)]_3_[+3(9.69e-06)]_216 33330 2.91e-05 26_[+2(2.48e-06)]_207_\ [+3(1.41e-05)]_21_[+1(5.48e-05)]_202 35031 1.06e-05 115_[+2(6.59e-05)]_75_\ [+1(7.96e-07)]_35_[+3(1.17e-05)]_231 3607 3.85e-04 463_[+2(1.22e-06)]_9_[+3(1.69e-05)] 39666 1.08e-05 152_[+2(2.26e-05)]_248_\ [+3(5.92e-06)]_[+1(4.62e-06)]_56 4111 1.14e-03 17_[+2(1.63e-05)]_354_\ [+3(5.92e-06)]_101 4462 9.68e-04 105_[+2(6.59e-05)]_162_\ [+1(1.16e-05)]_205 5105 1.93e-06 152_[+1(6.95e-08)]_265_\ [+2(1.21e-05)]_55 5144 1.12e-05 256_[+1(5.10e-06)]_172_\ [+2(2.48e-06)]_16_[+3(5.10e-05)]_12 9443 2.47e-09 59_[+2(5.91e-06)]_57_[+2(3.92e-08)]_\ 36_[+1(1.93e-06)]_145_[+3(7.94e-07)]_147 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************