******************************************************************************** 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/469/469.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10816 1.0000 500 10906 1.0000 500 11461 1.0000 500 1460 1.0000 500 19626 1.0000 500 19895 1.0000 500 20644 1.0000 500 20953 1.0000 500 21307 1.0000 500 21581 1.0000 500 21676 1.0000 500 21752 1.0000 500 21861 1.0000 500 22802 1.0000 500 22959 1.0000 500 23988 1.0000 500 24434 1.0000 500 24435 1.0000 500 25440 1.0000 500 25782 1.0000 500 25879 1.0000 500 260958 1.0000 500 264261 1.0000 500 264357 1.0000 500 264576 1.0000 500 2693 1.0000 500 3035 1.0000 500 37041 1.0000 500 38047 1.0000 500 4157 1.0000 500 8980 1.0000 500 bd1770 1.0000 500 bd1844 1.0000 500 bd1961 1.0000 500 bd736 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/469/469.seqs.fa -oc motifs/469 -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= 35 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= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.236 G 0.240 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.236 G 0.240 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 27 llr = 275 E-value = 1.3e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 31:::::::2:1:2:1 pos.-specific C 66255a:4a:6435a4 probability G 1:5:::3::::12::: matrix T :3355:76:74453:4 bits 2.1 1.9 * * * 1.7 * * * 1.5 * * * Relative 1.2 * * * Entropy 1.0 *** *** * (14.7 bits) 0.8 *** **** * 0.6 *********** * * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCGCTCTTCTCCTCCC consensus ATTTC GC ATTCT T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 22802 442 5.96e-09 CTCTCTCGGC CCGCCCTCCTCTTCCC TCTACCCCGT 20644 38 9.95e-08 CGCCCCCCCC CCTTCCTTCTCTCCCT CTCCTCCTAC 37041 403 3.23e-07 GCTGAACAGC CCTCTCTTCTTCCTCC CACTATTCGA 21861 431 3.84e-07 AGTGACCAAG ACGCTCTCCTTTTCCT GCCGTACCAC 21307 426 5.32e-07 CCAAAATACA CAGTCCTTCTCCTTCT CGTGTGCCCA 1460 24 5.32e-07 TCATCACTCC CACCTCTTCTCCTCCC AACGAAGCTG bd1961 377 1.10e-06 GACAACATCT CTCCTCTCCTCTCCCC TCTCCGCCGC 24434 290 1.62e-06 TGAGAGGCTT CTTTCCGTCTCCGCCC AAAACGAGAA 8980 469 2.06e-06 CTTCCTGGCT GTGCCCTTCTCTTCCT ACGTCCATGA 19895 343 2.58e-06 CAACGTCTAC ACTCTCGTCTTCTTCT CAAATAGGCA 11461 317 2.58e-06 CCTCGTGCGT CCTCCCGCCTTTGCCT CTGCTGCTTT 21581 175 3.55e-06 AACAAAGCAT GCGTTCTTCTCTCTCC CTCTGTCTGG 10906 477 5.80e-06 CCTGCCTCAA ACGTCCTCCTCCTACA CCTCAACA 38047 353 6.37e-06 AAGGTCTGAG CTGCCCGCCACTGCCC ATCCGTGAAC bd736 40 9.92e-06 AACAGCGACA CCCTCCGCCTCCTCCG GAAGACTCTT 25440 228 1.08e-05 GACACTACAT CAGCCCTTCCTCTCCT TTATTCGATC 25879 311 1.38e-05 GTTTTCCAAC ACGTCCACCTCCTACC ACCTCCAAAA 25782 153 2.05e-05 CCACGGTGAG TTTTTCTTCTTCTTCT CACTTACTTC 4157 112 2.37e-05 TGTTCGAGGC ACTTTCGACTTCTCCT GTGGTTTGGA 264576 96 2.37e-05 TTCTGTTTGT ACTCTCTTCATGCACC AGGCGAACAG 19626 484 2.74e-05 CTTCGACAAA CAGTTCTTCATGCTCT T 3035 485 3.62e-05 GTACTCTCGA CCGTTCCTCTCACACC 10816 324 4.13e-05 AACATGCTCA CTGCTCTCCACTTTGC AGCCTTCGCC 264261 223 4.70e-05 TACGATTTTT CTGTCCTTTTTCGACT GGGGGTTAAC 264357 389 5.32e-05 CCTGAACACC ACCCTCTTCACATCCA ATCAAGCAGC 260958 336 6.01e-05 GCTTGATCAG CCTCCTTCCTCGCACT TCTTGAGGCT 24435 229 6.01e-05 ACAGTAACGA ATCTTCGTCATTGTCC CCATCATGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22802 6e-09 441_[+1]_43 20644 9.9e-08 37_[+1]_447 37041 3.2e-07 402_[+1]_82 21861 3.8e-07 430_[+1]_54 21307 5.3e-07 425_[+1]_59 1460 5.3e-07 23_[+1]_461 bd1961 1.1e-06 376_[+1]_108 24434 1.6e-06 289_[+1]_195 8980 2.1e-06 468_[+1]_16 19895 2.6e-06 342_[+1]_142 11461 2.6e-06 316_[+1]_168 21581 3.6e-06 174_[+1]_310 10906 5.8e-06 476_[+1]_8 38047 6.4e-06 352_[+1]_132 bd736 9.9e-06 39_[+1]_445 25440 1.1e-05 227_[+1]_257 25879 1.4e-05 310_[+1]_174 25782 2e-05 152_[+1]_332 4157 2.4e-05 111_[+1]_373 264576 2.4e-05 95_[+1]_389 19626 2.7e-05 483_[+1]_1 3035 3.6e-05 484_[+1] 10816 4.1e-05 323_[+1]_161 264261 4.7e-05 222_[+1]_262 264357 5.3e-05 388_[+1]_96 260958 6e-05 335_[+1]_149 24435 6e-05 228_[+1]_256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=27 22802 ( 442) CCGCCCTCCTCTTCCC 1 20644 ( 38) CCTTCCTTCTCTCCCT 1 37041 ( 403) CCTCTCTTCTTCCTCC 1 21861 ( 431) ACGCTCTCCTTTTCCT 1 21307 ( 426) CAGTCCTTCTCCTTCT 1 1460 ( 24) CACCTCTTCTCCTCCC 1 bd1961 ( 377) CTCCTCTCCTCTCCCC 1 24434 ( 290) CTTTCCGTCTCCGCCC 1 8980 ( 469) GTGCCCTTCTCTTCCT 1 19895 ( 343) ACTCTCGTCTTCTTCT 1 11461 ( 317) CCTCCCGCCTTTGCCT 1 21581 ( 175) GCGTTCTTCTCTCTCC 1 10906 ( 477) ACGTCCTCCTCCTACA 1 38047 ( 353) CTGCCCGCCACTGCCC 1 bd736 ( 40) CCCTCCGCCTCCTCCG 1 25440 ( 228) CAGCCCTTCCTCTCCT 1 25879 ( 311) ACGTCCACCTCCTACC 1 25782 ( 153) TTTTTCTTCTTCTTCT 1 4157 ( 112) ACTTTCGACTTCTCCT 1 264576 ( 96) ACTCTCTTCATGCACC 1 19626 ( 484) CAGTTCTTCATGCTCT 1 3035 ( 485) CCGTTCCTCTCACACC 1 10816 ( 324) CTGCTCTCCACTTTGC 1 264261 ( 223) CTGTCCTTTTTCGACT 1 264357 ( 389) ACCCTCTTCACATCCA 1 260958 ( 336) CCTCCTTCCTCGCACT 1 24435 ( 229) ATCTTCGTCATTGTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 9.86371 E= 1.3e-005 19 133 -169 -283 -81 123 -1140 16 -1140 -35 100 33 -1140 114 -1140 86 -1140 103 -1140 97 -1140 203 -1140 -283 -281 -267 11 133 -281 65 -1140 116 -1140 203 -1140 -283 -22 -267 -1140 149 -1140 133 -1140 62 -181 91 -111 49 -1140 33 -37 97 -22 103 -1140 16 -1140 203 -269 -1140 -181 91 -269 75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 27 E= 1.3e-005 0.296296 0.592593 0.074074 0.037037 0.148148 0.555556 0.000000 0.296296 0.000000 0.185185 0.481481 0.333333 0.000000 0.518519 0.000000 0.481481 0.000000 0.481481 0.000000 0.518519 0.000000 0.962963 0.000000 0.037037 0.037037 0.037037 0.259259 0.666667 0.037037 0.370370 0.000000 0.592593 0.000000 0.962963 0.000000 0.037037 0.222222 0.037037 0.000000 0.740741 0.000000 0.592593 0.000000 0.407407 0.074074 0.444444 0.111111 0.370370 0.000000 0.296296 0.185185 0.518519 0.222222 0.481481 0.000000 0.296296 0.000000 0.962963 0.037037 0.000000 0.074074 0.444444 0.037037 0.444444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][CT][GT][CT][TC]C[TG][TC]C[TA][CT][CT][TC][CTA]C[CT] -------------------------------------------------------------------------------- Time 9.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 35 llr = 289 E-value = 1.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::31:1:::5:: pos.-specific C 17:11:2::12: probability G 124:27::a1:8 matrix T 81476289:381 bits 2.1 1.9 * 1.7 * 1.5 ** Relative 1.2 *** ** Entropy 1.0 * *** ** (11.9 bits) 0.8 * * *** ** 0.6 ** ****** ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCGTTGTTGATG consensus GT G C T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 19895 459 5.74e-07 TGTTCATTGT TCATTGTTGTTG TTTTGTTAAT bd1770 164 1.60e-06 GATTCTGCCT TCGATGTTGATG TGAAATGAAA 25879 98 3.46e-06 GCTCCTTGCT TCTTTGTTGATT GAAGAAAGCT 1460 312 4.07e-06 GAAGAGTGAA TCAATGTTGATG TATTGTGGTG 22802 239 4.82e-06 CCTCTTGATG TCACTGTTGATG GAGCAACTGG 37041 159 7.31e-06 TGGTGACCGG CCATTGTTGATG TATTTGCAGT 264576 419 9.52e-06 GGATGATACG TCGTGTTTGTTG CTCAGACTCT 21307 123 1.01e-05 GAAGTACGTT GCGTTGCTGATG ATTAGATTCT 11461 25 1.01e-05 TTCGCAGAAT TGGATGTTGATG TACGCAAGTT 20953 246 1.13e-05 TTTTGTGGTT TGGTTGTTGCTG CCTGCTGGAC 19626 345 1.59e-05 CGAGCATTTA TCTTGGTTGGTG TAGGAACAAG 25782 297 1.79e-05 GACGGAGGAT TTGTTGTTGACG CTTCAGCAGC 23988 240 1.79e-05 TAAGACGGTG TCTCTTTTGATG TCACTTCTGA 24435 2 2.59e-05 T TGGTGTTTGATG AATTGAAGGG 3035 204 2.95e-05 CATTCACTGT TCGCTGTTGTCG CTAGTCACAC 25440 387 2.95e-05 GTGTGCGTGC TCTTGTCTGATG CACCGTCTCT 21581 108 2.95e-05 TGGTGCGTGG TCTTTGCTGTTT GTTTTGTTAC bd1961 244 3.46e-05 AAGGGTACCA TTTTTTTTGTTG GTTATGAACT 10816 31 3.46e-05 CACAACGATA TGATGGCTGATG GCGAGGGATG 38047 134 4.29e-05 CGACGTCAAT TGATTATTGTTG AAGCTCCTAC 20644 415 4.29e-05 GCTACGTCAA TCACTGTTGATT AGCCAACAGC 4157 238 5.95e-05 GGCAGGGCCG CCGTGGTTGACG GAAGGAGGGA 24434 165 8.54e-05 TTGGCATGGC CGTTCGTTGATG TATACAGCCA 8980 18 9.62e-05 TAACATATAA TTGTTACTGATG AATAAAGATG 22959 168 1.06e-04 ATTGTGCTGG TCTACGTTGTCG ACATTTTGTG 21861 390 1.24e-04 AGGGCTTATG TAATTGTTGACG GATTGGTGTA bd736 180 1.51e-04 AACAGAAGTT GCTTTCTTGTTG TAATTCTAGA 10906 94 1.51e-04 TAGAATCACT TCTTTGCTGGTT ATAAGGCGGT 264357 247 1.62e-04 TTCTTGGCAA TCTTTGCTATTG GGATACTCGA 21752 225 1.62e-04 ACATCTCAAC GCGTTGTTGTTC ACGAGTTGCA 264261 59 3.05e-04 CGTTGTGCCG GTTTGTTTGTTG AGACTTTGAT 2693 243 3.51e-04 CGGTCGACGG TCGTCGTGGCTG ACATCAAGTA 21676 20 4.12e-04 TTGATCGGCG TCGTCGTCGTCG TCGTAGGTGT 260958 416 5.38e-04 CCACAATACA TCAACATTGATT CACTCTTCAT bd1844 208 6.35e-04 CAGAGGAGAT GGTTGATTGCTG TACGAATATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19895 5.7e-07 458_[+2]_30 bd1770 1.6e-06 163_[+2]_325 25879 3.5e-06 97_[+2]_391 1460 4.1e-06 311_[+2]_177 22802 4.8e-06 238_[+2]_250 37041 7.3e-06 158_[+2]_330 264576 9.5e-06 418_[+2]_70 21307 1e-05 122_[+2]_366 11461 1e-05 24_[+2]_464 20953 1.1e-05 245_[+2]_243 19626 1.6e-05 344_[+2]_144 25782 1.8e-05 296_[+2]_192 23988 1.8e-05 239_[+2]_249 24435 2.6e-05 1_[+2]_487 3035 3e-05 203_[+2]_285 25440 3e-05 386_[+2]_102 21581 3e-05 107_[+2]_381 bd1961 3.5e-05 243_[+2]_245 10816 3.5e-05 30_[+2]_458 38047 4.3e-05 133_[+2]_355 20644 4.3e-05 414_[+2]_74 4157 5.9e-05 237_[+2]_251 24434 8.5e-05 164_[+2]_324 8980 9.6e-05 17_[+2]_471 22959 0.00011 167_[+2]_321 21861 0.00012 389_[+2]_99 bd736 0.00015 179_[+2]_309 10906 0.00015 93_[+2]_395 264357 0.00016 246_[+2]_242 21752 0.00016 224_[+2]_264 264261 0.0003 58_[+2]_430 2693 0.00035 242_[+2]_246 21676 0.00041 19_[+2]_469 260958 0.00054 415_[+2]_73 bd1844 0.00064 207_[+2]_281 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=35 19895 ( 459) TCATTGTTGTTG 1 bd1770 ( 164) TCGATGTTGATG 1 25879 ( 98) TCTTTGTTGATT 1 1460 ( 312) TCAATGTTGATG 1 22802 ( 239) TCACTGTTGATG 1 37041 ( 159) CCATTGTTGATG 1 264576 ( 419) TCGTGTTTGTTG 1 21307 ( 123) GCGTTGCTGATG 1 11461 ( 25) TGGATGTTGATG 1 20953 ( 246) TGGTTGTTGCTG 1 19626 ( 345) TCTTGGTTGGTG 1 25782 ( 297) TTGTTGTTGACG 1 23988 ( 240) TCTCTTTTGATG 1 24435 ( 2) TGGTGTTTGATG 1 3035 ( 204) TCGCTGTTGTCG 1 25440 ( 387) TCTTGTCTGATG 1 21581 ( 108) TCTTTGCTGTTT 1 bd1961 ( 244) TTTTTTTTGTTG 1 10816 ( 31) TGATGGCTGATG 1 38047 ( 134) TGATTATTGTTG 1 20644 ( 415) TCACTGTTGATT 1 4157 ( 238) CCGTGGTTGACG 1 24434 ( 165) CGTTCGTTGATG 1 8980 ( 18) TTGTTACTGATG 1 22959 ( 168) TCTACGTTGTCG 1 21861 ( 390) TAATTGTTGACG 1 bd736 ( 180) GCTTTCTTGTTG 1 10906 ( 94) TCTTTGCTGGTT 1 264357 ( 247) TCTTTGCTATTG 1 21752 ( 225) GCGTTGTTGTTC 1 264261 ( 59) GTTTGTTTGTTG 1 2693 ( 243) TCGTCGTGGCTG 1 21676 ( 20) TCGTCGTCGTCG 1 260958 ( 416) TCAACATTGATT 1 bd1844 ( 208) GGTTGATTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17115 bayes= 9.03342 E= 1.1e-004 -1177 -146 -75 154 -318 148 -26 -121 -1 -1177 63 49 -86 -105 -1177 149 -1177 -72 -7 125 -118 -304 151 -62 -1177 -24 -1177 160 -1177 -304 -307 183 -318 -1177 202 -1177 99 -146 -207 37 -1177 -46 -1177 165 -1177 -304 179 -89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 35 E= 1.1e-004 0.000000 0.085714 0.142857 0.771429 0.028571 0.657143 0.200000 0.114286 0.257143 0.000000 0.371429 0.371429 0.142857 0.114286 0.000000 0.742857 0.000000 0.142857 0.228571 0.628571 0.114286 0.028571 0.685714 0.171429 0.000000 0.200000 0.000000 0.800000 0.000000 0.028571 0.028571 0.942857 0.028571 0.000000 0.971429 0.000000 0.514286 0.085714 0.057143 0.342857 0.000000 0.171429 0.000000 0.828571 0.000000 0.028571 0.828571 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CG][GTA]T[TG]G[TC]TG[AT]TG -------------------------------------------------------------------------------- Time 18.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 26 llr = 285 E-value = 2.9e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 34335224277348:861381 pos.-specific C 7544:35543175:a1:7318 probability G ::22:3324:::12:12:311 matrix T :21152::::2:1:::221:: bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.2 * *** Entropy 1.0 * * * *** ** (15.8 bits) 0.8 * * * * *** * ** 0.6 ** * * *** ***** ** 0.4 ** * ************ ** 0.2 ***** *************** 0.0 --------------------- Multilevel CCCCTGCCCAACCACAACAAC consensus AAAAACGAGCTAA G C sequence A A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1770 446 1.46e-09 CCGTAAAGCT CCAGTGCACAACAACAACCAC AAATAACACC 23988 380 9.28e-09 ACAAAACATA CCACTGGGCAACAACAACGAC GTTACTGCTT 38047 468 1.53e-07 CACCGCCGCC ATCAACAACAACAACAACAAC AAAGGCAAGA 20953 165 1.75e-07 CCGAAAGACG CCATAACAACAACACAACAAC TAACTCACCG 260958 446 3.30e-07 ATTGCAATCG CCTCAGCCCAAACACAGAAAC TTGCCACATT 2693 450 7.47e-07 TGCAGAACAG CCCATTCCAAACCGCAACCAG TGAATAGAAA 4157 375 8.34e-07 CAGAGCGGCC CCCGACGACATCAACGACGAC GACGAGACGA bd736 18 1.28e-06 CGTAACCGTC ATCGTTACGAACAACAGCGAC ACCCTCCGCC 21581 370 1.28e-06 AGGACACAAA AAACACGCACTCAACAGCAAC ACAACGCGGC 1460 479 1.74e-06 CTTCCCCGAG CCCCTACCGCCACACCACCAC C 24435 415 1.93e-06 AAGATTCAGC CACAACCAGATCCACCAAAAC TGAAATTTGT 19626 20 1.93e-06 ACAATGGCAT CATCTCGCAAACTGCAACAAC ATGCTCTCAA 24434 480 2.85e-06 AGACACACTC CTCCAACACACAAACAACACC bd1961 76 3.13e-06 TGACTGTTGC CACCTTCCGAGCCACATTGAC TTCCTCCTCG 264576 261 4.12e-06 ATCCCCTCGA CCGCATAGGAACTACAACTAC ATCAGAGCCT 25440 433 4.93e-06 TAAAACCCCA ACGATGACCCTCCGCAGCAAC CCTAGCAGTC 25782 85 5.39e-06 CGCTCGCTGT CCACTCCGCAACGGCAACGGC TGTGGAAGGG 264357 329 6.97e-06 AACAGAGTGA AACGAAGAGAAAGACAATGAC AGCGATATGC 10816 9 9.69e-06 ACGATGCG ATGATGCCGCAACACAACGAT ATGATGGCTG 11461 224 1.23e-05 AGTCATCTAA CAAAAGTCAAACCACATCCAG GACGATATTT 22802 170 1.43e-05 GATTCATGGC AACAAACAGCAAAGCATTCAC CCGTATTCCA 20644 479 1.55e-05 TGTCCATCAT CAGTATCAGCAACACATCCAA G 21752 408 1.67e-05 CAACCAGAAA CCGGCACCAATCAACGACCAC CACCGACGAC 25879 388 2.23e-05 CCACCGACGG CAACTGGGCATCAACAGACGC AGAGACGAAT 8980 411 2.56e-05 CCATTGCTTG ACATTGGCCAACCACAACTCA ACAGGTGTAT 21861 475 2.74e-05 CTCCCACCAT CATATCAAGCAACACAGTACC CACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1770 1.5e-09 445_[+3]_34 23988 9.3e-09 379_[+3]_100 38047 1.5e-07 467_[+3]_12 20953 1.7e-07 164_[+3]_315 260958 3.3e-07 445_[+3]_34 2693 7.5e-07 449_[+3]_30 4157 8.3e-07 374_[+3]_105 bd736 1.3e-06 17_[+3]_462 21581 1.3e-06 369_[+3]_110 1460 1.7e-06 478_[+3]_1 24435 1.9e-06 414_[+3]_65 19626 1.9e-06 19_[+3]_460 24434 2.8e-06 479_[+3] bd1961 3.1e-06 75_[+3]_404 264576 4.1e-06 260_[+3]_219 25440 4.9e-06 432_[+3]_47 25782 5.4e-06 84_[+3]_395 264357 7e-06 328_[+3]_151 10816 9.7e-06 8_[+3]_471 11461 1.2e-05 223_[+3]_256 22802 1.4e-05 169_[+3]_310 20644 1.5e-05 478_[+3]_1 21752 1.7e-05 407_[+3]_72 25879 2.2e-05 387_[+3]_92 8980 2.6e-05 410_[+3]_69 21861 2.7e-05 474_[+3]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=26 bd1770 ( 446) CCAGTGCACAACAACAACCAC 1 23988 ( 380) CCACTGGGCAACAACAACGAC 1 38047 ( 468) ATCAACAACAACAACAACAAC 1 20953 ( 165) CCATAACAACAACACAACAAC 1 260958 ( 446) CCTCAGCCCAAACACAGAAAC 1 2693 ( 450) CCCATTCCAAACCGCAACCAG 1 4157 ( 375) CCCGACGACATCAACGACGAC 1 bd736 ( 18) ATCGTTACGAACAACAGCGAC 1 21581 ( 370) AAACACGCACTCAACAGCAAC 1 1460 ( 479) CCCCTACCGCCACACCACCAC 1 24435 ( 415) CACAACCAGATCCACCAAAAC 1 19626 ( 20) CATCTCGCAAACTGCAACAAC 1 24434 ( 480) CTCCAACACACAAACAACACC 1 bd1961 ( 76) CACCTTCCGAGCCACATTGAC 1 264576 ( 261) CCGCATAGGAACTACAACTAC 1 25440 ( 433) ACGATGACCCTCCGCAGCAAC 1 25782 ( 85) CCACTCCGCAACGGCAACGGC 1 264357 ( 329) AACGAAGAGAAAGACAATGAC 1 10816 ( 9) ATGATGCCGCAACACAACGAT 1 11461 ( 224) CAAAAGTCAAACCACATCCAG 1 22802 ( 170) AACAAACAGCAAAGCATTCAC 1 20644 ( 479) CAGTATCAGCAACACATCCAA 1 21752 ( 408) CCGGCACCAATCAACGACCAC 1 25879 ( 388) CAACTGGGCATCAACAGACGC 1 8980 ( 411) ACATTGGCCAACCACAACTCA 1 21861 ( 475) CATATCAAGCAACACAGTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16800 bayes= 9.8647 E= 2.9e-004 25 155 -1134 -1134 57 97 -1134 -78 25 70 -32 -120 25 70 -32 -120 83 -261 -1134 92 -17 19 36 -46 -43 108 17 -278 57 97 -64 -1134 -17 70 68 -1134 141 38 -1134 -1134 133 -162 -264 -20 41 147 -1134 -1134 57 97 -164 -178 164 -1134 -32 -1134 -1134 208 -1134 -1134 170 -162 -164 -1134 124 -1134 -6 -78 -117 163 -1134 -78 41 38 17 -178 164 -103 -164 -1134 -175 177 -164 -278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 2.9e-004 0.307692 0.692308 0.000000 0.000000 0.384615 0.461538 0.000000 0.153846 0.307692 0.384615 0.192308 0.115385 0.307692 0.384615 0.192308 0.115385 0.461538 0.038462 0.000000 0.500000 0.230769 0.269231 0.307692 0.192308 0.192308 0.500000 0.269231 0.038462 0.384615 0.461538 0.153846 0.000000 0.230769 0.384615 0.384615 0.000000 0.692308 0.307692 0.000000 0.000000 0.653846 0.076923 0.038462 0.230769 0.346154 0.653846 0.000000 0.000000 0.384615 0.461538 0.076923 0.076923 0.807692 0.000000 0.192308 0.000000 0.000000 1.000000 0.000000 0.000000 0.846154 0.076923 0.076923 0.000000 0.615385 0.000000 0.230769 0.153846 0.115385 0.730769 0.000000 0.153846 0.346154 0.307692 0.269231 0.076923 0.807692 0.115385 0.076923 0.000000 0.076923 0.807692 0.076923 0.038462 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA][CA][CA][CA][TA][GCA][CG][CA][CGA][AC][AT][CA][CA]ACA[AG]C[ACG]AC -------------------------------------------------------------------------------- Time 27.97 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10816 1.60e-04 8_[+3(9.69e-06)]_1_[+2(3.46e-05)]_\ 281_[+1(4.13e-05)]_161 10906 7.29e-03 476_[+1(5.80e-06)]_8 11461 5.98e-06 24_[+2(1.01e-05)]_187_\ [+3(1.23e-05)]_72_[+1(2.58e-06)]_168 1460 1.10e-07 23_[+1(5.32e-07)]_272_\ [+2(4.07e-06)]_155_[+3(1.74e-06)]_1 19626 1.40e-05 19_[+3(1.93e-06)]_304_\ [+2(1.59e-05)]_127_[+1(2.74e-05)]_1 19895 2.37e-05 342_[+1(2.58e-06)]_100_\ [+2(5.74e-07)]_30 20644 1.44e-06 37_[+1(9.95e-08)]_361_\ [+2(4.29e-05)]_52_[+3(1.55e-05)]_1 20953 3.79e-05 164_[+3(1.75e-07)]_60_\ [+2(1.13e-05)]_243 21307 5.54e-05 122_[+2(1.01e-05)]_82_\ [+1(4.13e-05)]_12_[+1(4.70e-05)]_165_[+1(5.32e-07)]_59 21581 2.75e-06 107_[+2(2.95e-05)]_55_\ [+1(3.55e-06)]_179_[+3(1.28e-06)]_110 21676 7.29e-01 500 21752 6.16e-03 407_[+3(1.67e-05)]_72 21861 2.02e-05 430_[+1(3.84e-07)]_28_\ [+3(2.74e-05)]_5 22802 1.43e-08 169_[+3(1.43e-05)]_48_\ [+2(4.82e-06)]_171_[+1(6.38e-05)]_4_[+1(5.96e-09)]_43 22959 1.22e-01 500 23988 1.07e-06 239_[+2(1.79e-05)]_128_\ [+3(9.28e-09)]_100 24434 7.08e-06 164_[+2(8.54e-05)]_113_\ [+1(1.62e-06)]_174_[+3(2.85e-06)] 24435 4.26e-05 1_[+2(2.59e-05)]_215_[+1(6.01e-05)]_\ 170_[+3(1.93e-06)]_65 25440 2.43e-05 227_[+1(1.08e-05)]_8_[+1(8.50e-05)]_\ 119_[+2(2.95e-05)]_34_[+3(4.93e-06)]_47 25782 2.97e-05 84_[+3(5.39e-06)]_47_[+1(2.05e-05)]_\ 128_[+2(1.79e-05)]_192 25879 1.73e-05 97_[+2(3.46e-06)]_201_\ [+1(1.38e-05)]_61_[+3(2.23e-05)]_92 260958 1.15e-04 335_[+1(6.01e-05)]_94_\ [+3(3.30e-07)]_34 264261 7.29e-02 222_[+1(4.70e-05)]_262 264357 5.48e-04 328_[+3(6.97e-06)]_39_\ [+1(5.32e-05)]_96 264576 1.54e-05 95_[+1(2.37e-05)]_149_\ [+3(4.12e-06)]_137_[+2(9.52e-06)]_70 2693 1.15e-03 449_[+3(7.47e-07)]_30 3035 2.78e-03 203_[+2(2.95e-05)]_179_\ [+2(8.54e-05)]_78_[+1(3.62e-05)] 37041 4.18e-05 98_[+2(2.22e-05)]_48_[+2(7.31e-06)]_\ 232_[+1(3.23e-07)]_82 38047 9.59e-07 133_[+2(4.29e-05)]_207_\ [+1(6.37e-06)]_19_[+3(4.08e-05)]_59_[+3(1.53e-07)]_12 4157 1.87e-05 111_[+1(2.37e-05)]_110_\ [+2(5.95e-05)]_125_[+3(8.34e-07)]_105 8980 6.66e-05 17_[+2(9.62e-05)]_381_\ [+3(2.56e-05)]_37_[+1(2.06e-06)]_16 bd1770 3.82e-08 31_[+2(1.79e-05)]_120_\ [+2(1.60e-06)]_36_[+2(1.97e-05)]_222_[+3(1.46e-09)]_34 bd1844 4.05e-01 500 bd1961 2.47e-06 75_[+3(3.13e-06)]_147_\ [+2(3.46e-05)]_121_[+1(1.10e-06)]_108 bd736 2.83e-05 17_[+3(1.28e-06)]_1_[+1(9.92e-06)]_\ 445 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************