******************************************************************************** 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/421/421.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10264 1.0000 500 1051 1.0000 500 11430 1.0000 500 1249 1.0000 500 13485 1.0000 500 16390 1.0000 500 17919 1.0000 500 20816 1.0000 500 21140 1.0000 500 2159 1.0000 500 22795 1.0000 500 22979 1.0000 500 23162 1.0000 500 24353 1.0000 500 25036 1.0000 500 25895 1.0000 500 260925 1.0000 500 260934 1.0000 500 261019 1.0000 500 261087 1.0000 500 264439 1.0000 500 268594 1.0000 500 269095 1.0000 500 35094 1.0000 500 3554 1.0000 500 37120 1.0000 500 39241 1.0000 500 41425 1.0000 500 5626 1.0000 500 7645 1.0000 500 795 1.0000 500 8407 1.0000 500 9375 1.0000 500 bd643 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/421/421.seqs.fa -oc motifs/421 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.230 G 0.236 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.230 G 0.236 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 33 llr = 322 E-value = 7.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 353:542564446731952: pos.-specific C 5458128:34264:48:26: probability G ::111:::1:2::211::17 matrix T 211234:4:21:113:1313 bits 2.1 1.9 1.7 1.5 * * Relative 1.3 * * Entropy 1.1 * * ** * (14.1 bits) 0.8 * ** ** ** * 0.6 * * **** *** ** ** 0.4 ***** **** *** ***** 0.2 ******************** 0.0 -------------------- Multilevel CACCAACAAAACAACCAACG consensus ACA TT TCCCACGA TAT sequence T C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 795 17 4.08e-10 TTGTCAACAA CAACAACAACACCATCAACG CGTTGCTGAA 269095 135 1.01e-09 TCTAAACTTT CCCCTTCAACGCAACCAACG CAATGTTGGG 261087 432 7.41e-09 CAAACAATCA AACCAACAAACAAATCAACG GTACCAACGC 17919 245 8.68e-08 CGTCGGCTGC TTCCATCAACCCCAACAACG ACAACCTGCA 3554 479 1.41e-07 CTTCTCCTTC CTCCAACTCCAACACCATCG CC 16390 112 1.41e-07 GACGAGAAAC CACCAACAGCGACACCACCG GATGAGGCAG 260934 419 1.14e-06 GATTCTGAAG CAGCAACTACTACACCAAAG TATCGTTGAA 23162 287 1.85e-06 CCACGTTGGC CAACATCAATGCAGCCATGG TGTATATTCT 2159 426 2.62e-06 GTGGAACTGC AACCAACAACCACAACTACT TGGAACTCGG 5626 435 2.93e-06 CGTTTGTGCG AACTAACAACACAAGCATAG CATTTAGTGC 9375 478 3.66e-06 TCGTGGAAGC ATACACATACAAAAACAACG GCG 37120 430 5.05e-06 GTCTACCCAT ACCCATCAACGCATGCATCT CTACACGTCG 7645 473 7.61e-06 TCCCCCACTA TCACACAAACACAGACATCT TTCAAAGC 41425 466 7.61e-06 GTTCTTCTCA TCCTTTCACTAACAACAACG CTACGCCAAG 11430 349 7.61e-06 CGGCCCTTCA CTACAGCTCACAAAACAACG CAGAACTAAT 260925 131 1.02e-05 ACATGAGCAC TAACCTCAAAGCATTCATCG GCATAGCCAC 22795 408 1.02e-05 GAGCTCATAA AACCCAATCAAACATCAACG CGAAGACCTT 25895 128 1.49e-05 CTCTCTCTTC ACCCGACAAATCAAAAAAAG GTAAGGGTAC 24353 75 1.95e-05 ATCCCGAGCA CAACACACACACAGCCAAAG CCGTCTGCTG 35094 127 2.33e-05 TTTTTATTCA TCCTTTCTGACAAATCAACT ATTGAAACTT 264439 133 2.33e-05 TCAGCGGCTG CCACGACAAAAGAAACACAG CAGATTAGGA 8407 343 2.53e-05 GTAAAGTACA CAACATCTCTACAGCGATAG GTGATAGTTC 25036 301 2.76e-05 CCCCTCAACT CCCCTTCTGTCACATCAAGT AGCAAGCAAT 21140 356 2.76e-05 TTGTTGGTTG CAGTTCCACACCCACAAACG ACACACGGTG 10264 19 3.84e-05 GACAAAATTG TCTGAACAAAACAGTCACCT TGTCGCTTCC 13485 452 4.87e-05 CGTTTGCTCA CATCATCTACTCCACTACCT TTGACTCTAC 22979 296 6.13e-05 TCTCGTCTCA CCTCTCCTGAACTTCCAACG CACAAGAATT 20816 426 6.61e-05 TTATTTTTTC CAGTTACACCAAAATCACGT CGTCATCACT 268594 16 9.49e-05 CTGTACACCC ACCCTCCTCTACCGTAACCT GCAAGGCCAT 39241 356 1.62e-04 CTCAAACCGA ACAGAACACACCTAACATTG AGAACCTCTC 1051 276 1.73e-04 ATGCAAGAAG CACCGTATAAGCAGCGATGG ATATCTTCAT 1249 393 2.21e-04 AGTATATGTG TAAGTCCTAAGAAACAATAT AATTAAATCC bd643 143 2.80e-04 GAACAAACTT AACCTTCTAATCATACTATT CTCTACTTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 795 4.1e-10 16_[+1]_464 269095 1e-09 134_[+1]_346 261087 7.4e-09 431_[+1]_49 17919 8.7e-08 244_[+1]_236 3554 1.4e-07 478_[+1]_2 16390 1.4e-07 111_[+1]_369 260934 1.1e-06 418_[+1]_62 23162 1.9e-06 286_[+1]_194 2159 2.6e-06 425_[+1]_55 5626 2.9e-06 434_[+1]_46 9375 3.7e-06 477_[+1]_3 37120 5e-06 429_[+1]_51 7645 7.6e-06 472_[+1]_8 41425 7.6e-06 465_[+1]_15 11430 7.6e-06 348_[+1]_132 260925 1e-05 130_[+1]_350 22795 1e-05 407_[+1]_73 25895 1.5e-05 127_[+1]_353 24353 2e-05 74_[+1]_406 35094 2.3e-05 126_[+1]_354 264439 2.3e-05 132_[+1]_348 8407 2.5e-05 342_[+1]_138 25036 2.8e-05 300_[+1]_180 21140 2.8e-05 355_[+1]_125 10264 3.8e-05 18_[+1]_462 13485 4.9e-05 451_[+1]_29 22979 6.1e-05 295_[+1]_185 20816 6.6e-05 425_[+1]_55 268594 9.5e-05 15_[+1]_465 39241 0.00016 355_[+1]_125 1051 0.00017 275_[+1]_205 1249 0.00022 392_[+1]_88 bd643 0.00028 142_[+1]_338 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=33 795 ( 17) CAACAACAACACCATCAACG 1 269095 ( 135) CCCCTTCAACGCAACCAACG 1 261087 ( 432) AACCAACAAACAAATCAACG 1 17919 ( 245) TTCCATCAACCCCAACAACG 1 3554 ( 479) CTCCAACTCCAACACCATCG 1 16390 ( 112) CACCAACAGCGACACCACCG 1 260934 ( 419) CAGCAACTACTACACCAAAG 1 23162 ( 287) CAACATCAATGCAGCCATGG 1 2159 ( 426) AACCAACAACCACAACTACT 1 5626 ( 435) AACTAACAACACAAGCATAG 1 9375 ( 478) ATACACATACAAAAACAACG 1 37120 ( 430) ACCCATCAACGCATGCATCT 1 7645 ( 473) TCACACAAACACAGACATCT 1 41425 ( 466) TCCTTTCACTAACAACAACG 1 11430 ( 349) CTACAGCTCACAAAACAACG 1 260925 ( 131) TAACCTCAAAGCATTCATCG 1 22795 ( 408) AACCCAATCAAACATCAACG 1 25895 ( 128) ACCCGACAAATCAAAAAAAG 1 24353 ( 75) CAACACACACACAGCCAAAG 1 35094 ( 127) TCCTTTCTGACAAATCAACT 1 264439 ( 133) CCACGACAAAAGAAACACAG 1 8407 ( 343) CAACATCTCTACAGCGATAG 1 25036 ( 301) CCCCTTCTGTCACATCAAGT 1 21140 ( 356) CAGTTCCACACCCACAAACG 1 10264 ( 19) TCTGAACAAAACAGTCACCT 1 13485 ( 452) CATCATCTACTCCACTACCT 1 22979 ( 296) CCTCTCCTGAACTTCCAACG 1 20816 ( 426) CAGTTACACCAAAATCACGT 1 268594 ( 16) ACCCTCCTCTACCGTAACCT 1 39241 ( 356) ACAGAACACACCTAACATTG 1 1051 ( 276) CACCGTATAAGCAGCGATGG 1 1249 ( 393) TAAGTCCTAAGAAACAATAT 1 bd643 ( 143) AACCTTCTAATCATACTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 16354 bayes= 8.98552 E= 7.4e-006 19 108 -1169 -34 96 66 -1169 -115 33 108 -138 -156 -1169 172 -138 -83 104 -192 -138 17 57 -11 -296 43 -81 189 -1169 -1169 104 -292 -1169 66 119 25 -96 -1169 68 89 -1169 -83 68 8 -16 -115 57 133 -296 -1169 112 66 -1169 -215 133 -1169 -16 -115 19 66 -196 2 -113 178 -196 -315 182 -1169 -1169 -215 96 -34 -1169 17 -32 140 -96 -215 -1169 -1169 150 31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 33 E= 7.4e-006 0.303030 0.484848 0.000000 0.212121 0.515152 0.363636 0.000000 0.121212 0.333333 0.484848 0.090909 0.090909 0.000000 0.757576 0.090909 0.151515 0.545455 0.060606 0.090909 0.303030 0.393939 0.212121 0.030303 0.363636 0.151515 0.848485 0.000000 0.000000 0.545455 0.030303 0.000000 0.424242 0.606061 0.272727 0.121212 0.000000 0.424242 0.424242 0.000000 0.151515 0.424242 0.242424 0.212121 0.121212 0.393939 0.575758 0.030303 0.000000 0.575758 0.363636 0.000000 0.060606 0.666667 0.000000 0.212121 0.121212 0.303030 0.363636 0.060606 0.272727 0.121212 0.787879 0.060606 0.030303 0.939394 0.000000 0.000000 0.060606 0.515152 0.181818 0.000000 0.303030 0.212121 0.606061 0.121212 0.060606 0.000000 0.000000 0.666667 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CAT][AC][CA]C[AT][ATC]C[AT][AC][AC][ACG][CA][AC][AG][CAT]CA[AT][CA][GT] -------------------------------------------------------------------------------- Time 9.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 24 llr = 249 E-value = 1.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 42::7:13::4::53: pos.-specific C :321:12361:3:::: probability G 6::9::62:73:a2:a matrix T :58:29:34237:36: bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 ** * * * Entropy 1.1 * ** * * * * (15.0 bits) 0.8 * ** * ** ** * 0.6 * ***** ** ** ** 0.4 * ***** ** ** ** 0.2 ******* ******** 0.0 ---------------- Multilevel GTTGATGACGATGATG consensus AC T CCTTTC TA sequence T G G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 264439 96 5.16e-10 TGTGAATGGC GTTGATGCCGATGATG TTGGTGTGCC 7645 229 6.34e-08 GGAGAAAGCG GATGATGATGATGATG ACAGCGGAAG 1249 152 2.85e-07 GGCAGCGGCG GCTGATGCCGGCGAAG AGCCTTTGGC 23162 76 7.49e-07 TGATGGAGAG GTTGATGTTTGTGGTG GTGACGTATT 39241 31 1.23e-06 TCATCCTTTT GATGATGCCGATGCTG CTAAGTGAAC 2159 268 1.23e-06 ATGATGATAC GTCGATGGCCATGATG AACTGGGTGG 16390 10 1.74e-06 GATGAAACT GTCGTTGTTGTTGATG GGACGAATCC bd643 459 2.71e-06 AACAAAGGTA ACCGATGACTTTGATG ACTCTCTTCC 11430 110 3.01e-06 CGTCCAGGCC ATTGACGACGGTGAAG GTAAAGGATG 35094 45 3.34e-06 GCACAGTAGA GTTGATCATCACGATG AGCGCTGGAT 1051 333 4.51e-06 AATTTGGTGA AGTGATGTTGGTGTTG ATAAGTGAAC 261087 234 6.01e-06 AGTTTTGTGG GATGTTCGTGATGGTG TATGAGATGA 268594 200 6.59e-06 CTCGTAGCAT GTTGATGGTGAGGTAG GAGCTATTGT 25036 191 8.64e-06 GGACATAGGG ATTGTTACCGATGTAG AGCGGTCGTC 261019 351 1.12e-05 TGGGTTCCGT ACTGATCCCTCTGATG CCTACGTTTG 5626 273 1.44e-05 CATCAACTTG ACTGATTACGTTGGAG GCCGTCTCAA 3554 174 1.44e-05 TTGGAGTAAG ACTGGTGGCGGTGGAG TGTAAGATAT 20816 69 1.44e-05 AAAGGGGTGT ATTCTTGTCGTCGATG GACGCTTCTG 795 119 1.68e-05 TCACGTCTCA GTTGAAGATTGTGTTG CCGGAGGAGG 37120 211 1.96e-05 GAGTGTCACC ACTGATAGCGATGTGG TGGAAATCGA 25895 397 2.12e-05 AACTGACATT GTTGTTCTTTTCGTTG GTTCACCTCG 260934 347 2.46e-05 TCGCTGCAAT GCTCACCACGTTGATG ATGGGTCGAA 8407 434 6.61e-05 ACATCGAACG GACGATACCCACGAAG TGCACCACTT 260925 237 8.31e-05 TACAATCTCG GCTGCTGTTGTCGGCG CCATTGCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264439 5.2e-10 95_[+2]_389 7645 6.3e-08 228_[+2]_256 1249 2.9e-07 151_[+2]_333 23162 7.5e-07 75_[+2]_409 39241 1.2e-06 30_[+2]_454 2159 1.2e-06 267_[+2]_217 16390 1.7e-06 9_[+2]_475 bd643 2.7e-06 458_[+2]_26 11430 3e-06 109_[+2]_375 35094 3.3e-06 44_[+2]_440 1051 4.5e-06 332_[+2]_152 261087 6e-06 233_[+2]_251 268594 6.6e-06 199_[+2]_285 25036 8.6e-06 190_[+2]_294 261019 1.1e-05 350_[+2]_134 5626 1.4e-05 272_[+2]_212 3554 1.4e-05 173_[+2]_311 20816 1.4e-05 68_[+2]_416 795 1.7e-05 118_[+2]_366 37120 2e-05 210_[+2]_274 25895 2.1e-05 396_[+2]_88 260934 2.5e-05 346_[+2]_138 8407 6.6e-05 433_[+2]_51 260925 8.3e-05 236_[+2]_248 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=24 264439 ( 96) GTTGATGCCGATGATG 1 7645 ( 229) GATGATGATGATGATG 1 1249 ( 152) GCTGATGCCGGCGAAG 1 23162 ( 76) GTTGATGTTTGTGGTG 1 39241 ( 31) GATGATGCCGATGCTG 1 2159 ( 268) GTCGATGGCCATGATG 1 16390 ( 10) GTCGTTGTTGTTGATG 1 bd643 ( 459) ACCGATGACTTTGATG 1 11430 ( 110) ATTGACGACGGTGAAG 1 35094 ( 45) GTTGATCATCACGATG 1 1051 ( 333) AGTGATGTTGGTGTTG 1 261087 ( 234) GATGTTCGTGATGGTG 1 268594 ( 200) GTTGATGGTGAGGTAG 1 25036 ( 191) ATTGTTACCGATGTAG 1 261019 ( 351) ACTGATCCCTCTGATG 1 5626 ( 273) ACTGATTACGTTGGAG 1 3554 ( 174) ACTGGTGGCGGTGGAG 1 20816 ( 69) ATTCTTGTCGTCGATG 1 795 ( 119) GTTGAAGATTGTGTTG 1 37120 ( 211) ACTGATAGCGATGTGG 1 25895 ( 397) GTTGTTCTTTTCGTTG 1 260934 ( 347) GCTCACCACGTTGATG 1 8407 ( 434) GACGATACCCACGAAG 1 260925 ( 237) GCTGCTGTTGTCGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16490 bayes= 9.87026 E= 1.3e-004 50 -1123 140 -1123 -67 54 -250 77 -1123 -46 -1123 163 -1123 -146 196 -1123 142 -246 -250 -37 -267 -146 -1123 170 -108 -14 140 -269 14 12 -18 -11 -1123 134 -1123 63 -1123 -88 150 -37 65 -246 8 12 -1123 12 -250 140 -1123 -1123 208 -1123 91 -246 -18 -11 14 -246 -250 122 -1123 -1123 208 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 1.3e-004 0.375000 0.000000 0.625000 0.000000 0.166667 0.333333 0.041667 0.458333 0.000000 0.166667 0.000000 0.833333 0.000000 0.083333 0.916667 0.000000 0.708333 0.041667 0.041667 0.208333 0.041667 0.083333 0.000000 0.875000 0.125000 0.208333 0.625000 0.041667 0.291667 0.250000 0.208333 0.250000 0.000000 0.583333 0.000000 0.416667 0.000000 0.125000 0.666667 0.208333 0.416667 0.041667 0.250000 0.291667 0.000000 0.250000 0.041667 0.708333 0.000000 0.000000 1.000000 0.000000 0.500000 0.041667 0.208333 0.250000 0.291667 0.041667 0.041667 0.625000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][TC]TG[AT]T[GC][ACTG][CT][GT][ATG][TC]G[ATG][TA]G -------------------------------------------------------------------------------- Time 20.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 20 llr = 218 E-value = 3.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::1::131141293: pos.-specific C :392:a4:65:67:86 probability G :2::2:4::321:1:3 matrix T a6188:27425321:2 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 * * ** ** Entropy 1.1 * * ** * ** (15.7 bits) 0.8 * **** ** *** 0.6 ****** ** ***** 0.4 ****** ** ****** 0.2 **************** 0.0 ---------------- Multilevel TTCTTCCTCCTCCACC consensus C CG GATGATT AG sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 17919 80 7.27e-10 TTTTCTTCAA TTCTTCCTCCACCACC GTCACTGCGC 260934 131 8.77e-08 CACACGTGGT TTCTTCCTCGACTACC GAAGGAGAAG 264439 431 1.41e-07 CCAACTGTCT TCCTTCCACCATCACC AAACTTTGCT 39241 100 2.17e-07 GTGGTTGAGT TTCTTCGTCCTTCAAG AAGAAAAAAT 8407 68 6.41e-07 TGTTGTCCAC TTTTTCTTTCTCCACC GTGGCAGCCG 11430 482 9.23e-07 AACACTAACT TCCTTCCTTCTACACC ACA 35094 159 1.45e-06 TGAAACTTAA TTCCTCGTCGTCTACT TTACACATGG 37120 399 1.61e-06 ACCGCGTTGC TGCCTCTTCCTTCACG GCAAAGTCTA 13485 219 1.61e-06 CGTCAGCACC TCCTTCCTCCTCCTCG GTTCTTCATC 261019 266 4.36e-06 GTATATAAGG TTCTTCGATATTCAAC ATGAGCAAGA 261087 90 4.78e-06 CTCGTACCAA TCCTTCTTTTTCCGCC CCACGTGGCA 24353 108 7.37e-06 TCTGCTGTTT TTCTTCGTCTGCTGCC CCTTCACTTT 20816 483 9.42e-06 AGTTGTACTG TTCTTCCAACTCAACT AA 3554 442 1.02e-05 ACGAAAACGA TTCCGCCTCCGCAACT CCTCCAACTC 16390 84 1.28e-05 GAATCGAGTA TGCTGCGACGACAACG ACGACGAGAA bd643 396 1.39e-05 GAATGTAGCT TGCCTCGTTTATTACC AGTCGATTGC 1051 111 1.39e-05 CAAAGCTTGG TTCTTCTACGGGCACG ATTTTGGCTT 268594 462 2.27e-05 ACATCACCGT TCCATCATCCATCAAC GGCATTGAAC 23162 196 2.93e-05 AGTTGCAAAT TGTTGCGTTGACCAAC GCTGCTACTC 260925 419 4.46e-05 GCGAAGTGCC TTCTGCAATATCCAAT GTCCTCTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17919 7.3e-10 79_[+3]_405 260934 8.8e-08 130_[+3]_354 264439 1.4e-07 430_[+3]_54 39241 2.2e-07 99_[+3]_385 8407 6.4e-07 67_[+3]_417 11430 9.2e-07 481_[+3]_3 35094 1.4e-06 158_[+3]_326 37120 1.6e-06 398_[+3]_86 13485 1.6e-06 218_[+3]_266 261019 4.4e-06 265_[+3]_219 261087 4.8e-06 89_[+3]_395 24353 7.4e-06 107_[+3]_377 20816 9.4e-06 482_[+3]_2 3554 1e-05 441_[+3]_43 16390 1.3e-05 83_[+3]_401 bd643 1.4e-05 395_[+3]_89 1051 1.4e-05 110_[+3]_374 268594 2.3e-05 461_[+3]_23 23162 2.9e-05 195_[+3]_289 260925 4.5e-05 418_[+3]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=20 17919 ( 80) TTCTTCCTCCACCACC 1 260934 ( 131) TTCTTCCTCGACTACC 1 264439 ( 431) TCCTTCCACCATCACC 1 39241 ( 100) TTCTTCGTCCTTCAAG 1 8407 ( 68) TTTTTCTTTCTCCACC 1 11430 ( 482) TCCTTCCTTCTACACC 1 35094 ( 159) TTCCTCGTCGTCTACT 1 37120 ( 399) TGCCTCTTCCTTCACG 1 13485 ( 219) TCCTTCCTCCTCCTCG 1 261019 ( 266) TTCTTCGATATTCAAC 1 261087 ( 90) TCCTTCTTTTTCCGCC 1 24353 ( 108) TTCTTCGTCTGCTGCC 1 20816 ( 483) TTCTTCCAACTCAACT 1 3554 ( 442) TTCCGCCTCCGCAACT 1 16390 ( 84) TGCTGCGACGACAACG 1 bd643 ( 396) TGCCTCGTTTATTACC 1 1051 ( 111) TTCTTCTACGGGCACG 1 268594 ( 462) TCCATCATCCATCAAC 1 23162 ( 196) TGTTGCGTTGACCAAC 1 260925 ( 419) TTCTGCAATATCCAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16490 bayes= 9.93744 E= 3.4e-001 -1097 -1097 -1097 189 -1097 12 -24 103 -1097 197 -1097 -143 -240 -20 -1097 148 -1097 -1097 -24 157 -1097 212 -1097 -1097 -141 61 57 -43 18 -1097 -1097 138 -240 139 -1097 38 -141 112 8 -84 40 -1097 -65 89 -240 139 -224 16 -82 150 -1097 -43 168 -1097 -124 -242 -8 171 -1097 -1097 -1097 126 8 -43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 3.4e-001 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.200000 0.550000 0.000000 0.900000 0.000000 0.100000 0.050000 0.200000 0.000000 0.750000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.100000 0.350000 0.350000 0.200000 0.300000 0.000000 0.000000 0.700000 0.050000 0.600000 0.000000 0.350000 0.100000 0.500000 0.250000 0.150000 0.350000 0.000000 0.150000 0.500000 0.050000 0.600000 0.050000 0.300000 0.150000 0.650000 0.000000 0.200000 0.850000 0.000000 0.100000 0.050000 0.250000 0.750000 0.000000 0.000000 0.000000 0.550000 0.250000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TCG]C[TC][TG]C[CGT][TA][CT][CG][TA][CT][CT]A[CA][CGT] -------------------------------------------------------------------------------- Time 29.69 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10264 3.50e-02 18_[+1(3.84e-05)]_462 1051 1.26e-04 110_[+3(1.39e-05)]_206_\ [+2(4.51e-06)]_152 11430 5.20e-07 109_[+2(3.01e-06)]_223_\ [+1(7.61e-06)]_113_[+3(9.23e-07)]_3 1249 5.10e-04 28_[+2(9.28e-05)]_107_\ [+2(2.85e-07)]_333 13485 9.21e-04 218_[+3(1.61e-06)]_217_\ [+1(4.87e-05)]_29 16390 9.21e-08 9_[+2(1.74e-06)]_58_[+3(1.28e-05)]_\ 12_[+1(1.41e-07)]_369 17919 1.64e-09 79_[+3(7.27e-10)]_149_\ [+1(8.68e-08)]_6_[+3(1.80e-06)]_214 20816 1.09e-04 68_[+2(1.44e-05)]_341_\ [+1(6.61e-05)]_37_[+3(9.42e-06)]_2 21140 5.02e-02 355_[+1(2.76e-05)]_125 2159 4.19e-05 267_[+2(1.23e-06)]_142_\ [+1(2.62e-06)]_55 22795 5.77e-02 366_[+1(7.12e-05)]_21_\ [+1(1.02e-05)]_47_[+1(9.49e-05)]_6 22979 9.57e-02 295_[+1(6.13e-05)]_185 23162 9.35e-07 75_[+2(7.49e-07)]_104_\ [+3(2.93e-05)]_75_[+1(1.85e-06)]_194 24353 5.79e-04 74_[+1(1.95e-05)]_13_[+3(7.37e-06)]_\ 377 25036 2.93e-03 190_[+2(8.64e-06)]_94_\ [+1(2.76e-05)]_180 25895 2.66e-03 127_[+1(1.49e-05)]_249_\ [+2(2.12e-05)]_88 260925 3.74e-04 130_[+1(1.02e-05)]_86_\ [+2(8.31e-05)]_166_[+3(4.46e-05)]_66 260934 7.34e-08 130_[+3(8.77e-08)]_200_\ [+2(2.46e-05)]_56_[+1(1.14e-06)]_62 261019 8.60e-04 265_[+3(4.36e-06)]_69_\ [+2(1.12e-05)]_134 261087 7.79e-09 89_[+3(4.78e-06)]_128_\ [+2(6.01e-06)]_182_[+1(7.41e-09)]_49 264439 8.76e-11 95_[+2(5.16e-10)]_21_[+1(2.33e-05)]_\ 278_[+3(1.41e-07)]_54 268594 1.62e-04 15_[+1(9.49e-05)]_164_\ [+2(6.59e-06)]_246_[+3(2.27e-05)]_23 269095 4.63e-06 134_[+1(1.01e-09)]_346 35094 2.33e-06 44_[+2(3.34e-06)]_66_[+1(2.33e-05)]_\ 12_[+3(1.45e-06)]_95_[+2(4.27e-05)]_215 3554 4.07e-07 173_[+2(1.44e-05)]_252_\ [+3(1.02e-05)]_21_[+1(1.41e-07)]_2 37120 3.20e-06 210_[+2(1.96e-05)]_172_\ [+3(1.61e-06)]_15_[+1(5.05e-06)]_10_[+3(4.72e-05)]_25 39241 9.61e-07 30_[+2(1.23e-06)]_53_[+3(2.17e-07)]_\ 385 41425 3.47e-02 465_[+1(7.61e-06)]_15 5626 5.66e-04 272_[+2(1.44e-05)]_146_\ [+1(2.93e-06)]_46 7645 7.84e-06 228_[+2(6.34e-08)]_228_\ [+1(7.61e-06)]_8 795 1.89e-07 16_[+1(4.08e-10)]_82_[+2(1.68e-05)]_\ 219_[+1(7.61e-06)]_127 8407 1.71e-05 67_[+3(6.41e-07)]_259_\ [+1(2.53e-05)]_71_[+2(6.61e-05)]_51 9375 1.77e-02 477_[+1(3.66e-06)]_3 bd643 1.20e-04 395_[+3(1.39e-05)]_47_\ [+2(2.71e-06)]_26 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************