AlignACE version 2.2 July 7, 1998 AlignACE -jRAD.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YBR114W 600 bp YBR114W rad16 1-2373 Radiation repair protein, putative DNA helicase #2 YCR066W 594 bp YCR066W RAD18 1-1464 Zn finger protein, putative ATPase #3 YDL059C 600 bp YDL059C RAD59 1-717 A mutation in this gene results in RADiation sensitivity and recombination defects, which are general properties of the RAD52 epistasis group mutants. rad59 is epistatic to rad52 for its repair and recombination defects. The RAD59 gene product has homology to the Rad52 protein. #4 YDR004W 446 bp YDR004W rad57 1-1383 RecA homolog (similar to DMC1, RAD51, and RAD55), interacts with Rad 55p by two-hybrid analysis #5 YDR030C 300 bp YDR030C RAD28 1-1521 Protein involved in the same pathway as Rad26p, has beta-transducin (WD-40) repeats #6 YDR076W 385 bp YDR076W rad55 1-1221 RecA homolog (related to DMC1, RAD51, RAD57), interacts with Rad51p and Rad57p by two-hybrid analysis #7 YDR217C 300 bp YDR217C rad9 1-3930 cell cycle arrest protein #8 YDR419W 600 bp YDR419W RAD30 1-1899 similar to E. coli DinB and S. cerevisiae REV1 #9 YEL037C 446 bp YEL037C rad23 1-1197 ubiquitin-like protein #10 YER095W 600 bp YER095W rad51 1-1203 RecA homolog\; Rad51p colocalizes to ~65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p by two-hybrid analysis\; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer #11 YER162C 300 bp YER162C rad4 1-2265 Nucleotide excision repair protein #12 YER171W 430 bp YER171W rad3 1-2337 DNA repair helicase component of transcription factor b #13 YER173W 300 bp YER173W rad24 1-1980 checkpoint protein #14 YGL163C 600 bp YGL163C rad54 1-2697 Required for X-ray damage repair, mitotic recombination, and full meiotic recombination. mRNA increases in meiosis. #15 YGL058W 425 bp YGL058W rad6 1-519 ubiquitin conjugating (E2) enzyme, separate domains of Rad6p interact with Ubr1 (an E3 ubiquitin ligase needed for multiubiquitination), and Rad18p (a single-stranded DNA-binding protein). The C-terminal 23 residues are critical for sporulation and histone polyubiquitinating activity, but not UV repair or induced mutagenesis. #16 YGR258C 600 bp YGR258C rad2 1-3096 homolog of xeroderma pigmentosum group G (XPG) protein, copufurifies with transcription factor, TFIIH, mRNA is cell cycle regulated and induced by DNA damage and by meiosis (different cis-sites utilized in damage and meiotic induction #17 YJR035W 345 bp YJR035W RAD26 1-3258 DNA-dependent ATPase, homologous to human Cockayne syndrome B gene ERCC6, that is a putative helicase #18 YJR052W 300 bp YJR052W rad7 1-1698 Nucleotide excision repair protein involved in G(sub)2 repair of inactive genes #19 YKL113C 600 bp YKL113C RAD27 1-1149 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing #20 YLR032W 300 bp YLR032W RAD5 1-3510 putative ATPase\/DNA helicase #21 YML095C 300 bp YML095C rad10 1-633 Endonuclease (with Rad1p) that degrades single-stranded DNA for repair #22 YML032C 300 bp YML032C rad52 1-1515 Interacts with Rad51p by two hybrid analysis. mRNA is induced in meiosis during recombination #23 YMR201C 492 bp YMR201C RAD14 1-27, 112-1200 human xeroderma pigmentosum group A DNA repair gene homolog #24 YNL250W 600 bp YNL250W rad50 1-3939 protein contains a purine-binding domain, two heptad repeats and a hydrophobic tail, Rad50p interacts with Mre11p and Xrs2p in two-hybrid and immunoprecipitation analyses\; it co-localizes to spots with Mre11p and Xrs2p in a rad50s background #25 YOR368W 300 bp YOR368W rad17 1-1206 encodes a putative 3'->5'exonuclease #26 YPL153C 600 bp YPL153C rad53 1-2466 protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation #27 YPL022W 384 bp YPL022W rad1 1-3303 UV endonuclease Motif number 1 GTGCTTTAGTTTTTATCTTCGTTATGTGGA 1 13 1 TTTTATCTTC 0.6731 -588 TGCGCCTCCGTTTCTTTTTCTTCCCTTTTC 1 395 1 TTTCTTTTTC 0.949132 -206 TTTCTTCCCTTTTCATTTCCCTTTTCTTTT 1 411 1 TTTCATTTCC 0.659726 -190 TCCCTTTTCTTTTTTTTTTCAAGTTTCGGA 1 428 1 TTTTTTTTTC 0.945956 -173 AAGAATTGACTTTTTTTTTTTTTTTTTTTT 2 99 1 TTTTTTTTTT 0.903805 -496 TTTTTTTTTTTTTTTTTTTCATTTTCTTTT 2 110 1 TTTTTTTTTC 0.945956 -485 TTTTTTTCATTTTCTTTTCCTCACCGAAAA 2 122 1 TTTCTTTTCC 0.903035 -473 ATGATACAAATTTTTTTTCTAAGTTTTATA 2 343 1 TTTTTTTTCT 0.824239 -252 TTTTGATCTCTTTTATTTTTACTTGCCCCG 2 453 1 TTTTATTTTT 0.661703 -142 AGCCAGTAAATTTTGTTTTCTTCATGGAAA 3 148 1 TTTTGTTTTC 0.871373 -453 CTGTACTTCTTTTTTTTTTCAGCACTCTTA 4 64 0 TTTTTTTTTC 0.945956 -383 GTACAGAAGTTTTCGTTTCTTTGAAAGTCG 4 88 1 TTTCGTTTCT 0.659265 -359 TGTTCATCATTTTCATTTTTTGAATTCAAC 4 388 0 TTTCATTTTT 0.675862 -59 TTCGGAGTTTTTTTTTTTTCCTACGCTTAA 5 180 0 TTTTTTTTTC 0.945956 -121 CAAGTGCATTTTTCTTTTTTTCTTCATAAT 6 35 1 TTTCTTTTTT 0.909221 -351 AATATTACAATTTTTTTTCCTTTATTGCAT 6 63 0 TTTTTTTTCC 0.897292 -323 CCAGCTACCGTTTCTTCTTTTATTTTTTAT 6 153 1 TTTCTTCTTT 0.849841 -233 TTTTATTCCTTTTTTTCTTCAGTAGAATAT 6 177 1 TTTTTTCTTC 0.908178 -209 TTGAACCTATTTTCTTCTTCTTGAACATAC 8 386 0 TTTCTTCTTC 0.913371 -215 ATTTTTTTATTTTCTTCTCTTTCATTATGG 9 177 1 TTTCTTCTCT 0.738551 -270 ACTGAGAAAATTTTTTCTCCAGTCCCCACT 10 478 0 TTTTTTCTCC 0.831554 -123 TGTTTTTTATTTTTTTTTTTGCGCGAAACT 14 373 0 TTTTTTTTTT 0.903805 -228 TTATTTCCTTTTTTTTCTTTTTGTTTGTAA 14 404 0 TTTTTTCTTT 0.841499 -197 TTCCATTCGCTTTCATTTTTATTTTTCCAG 15 275 0 TTTCATTTTT 0.675862 -151 GTTCTTTCCTTTTTTTCTCTTACACATTCC 15 301 0 TTTTTTCTCT 0.72602 -125 CTTGAATTTTTTTTTTTTTCTTTTTTGGTA 16 278 1 TTTTTTTTTC 0.945956 -323 GTTGCTGTTTTTTTTTTTTCATTGTTAATT 16 369 1 TTTTTTTTTC 0.945956 -232 ATTATCACTATTTTTTTTTCTTTCTAGTAT 16 396 1 TTTTTTTTTC 0.945956 -205 CTTTTCTTTTTTTTTTTTTCACTCTCCCTT 16 456 0 TTTTTTTTTC 0.945956 -145 GGCGGCATCTTTTCTTTTTCTTTTCTTTTT 16 475 0 TTTCTTTTTC 0.949132 -126 TCTTCCCTTCTTTTTTTTTCTTCCACTTTT 17 266 0 TTTTTTTTTC 0.945956 -80 CGCAGTTTCTTTTCTTTTTTTCTGGAAAAT 18 144 1 TTTCTTTTTT 0.909221 -157 GCTTGCCACTTTTCGTTTTTCACGAAAAAA 19 154 1 TTTCGTTTTT 0.794933 -447 ATTTTTTCTTCCGGTGTCCGT 19 590 0 TTTTTTCTTC 0.908178 -11 TACAAGTATTTTTTGTTTCTAGAATAGAAT 20 53 0 TTTTGTTTCT 0.644762 -248 AAGTTACAATTTTCTTTTTTGTTCTAACGA 21 225 0 TTTCTTTTTT 0.909221 -76 TGTAATGTCCTTTCGTCTTCTCAATCACAC 22 162 1 TTTCGTCTTC 0.803177 -139 CCGCTATATTTTTCGTCTTTTCTTAACAGA 22 255 0 TTTCGTCTTT 0.686566 -46 ACAACCCTTGTTTTTTTTTTTTTTTTTGTT 23 318 1 TTTTTTTTTT 0.903805 -175 GGTGAAGGCATTTTTTTTTTTTGACTAAGT 24 400 0 TTTTTTTTTT 0.903805 -201 ATAAGTAAGTTTTTGTTTTTTCTCAGTGTT 26 25 0 TTTTGTTTTT 0.784316 -576 CTATAAATGTTTTCATTTCCAAGTCTACCC 26 384 0 TTTCATTTCC 0.659726 -217 CGTCCCGACTTTTTTTTTTCATTAGACGCG 27 232 0 TTTTTTTTTC 0.945956 -153 ********** Masking position 6 Map Score: 54.8817 Number of sites scoring better than the average of aligned sites = 14169 Number in coding regions = 2734 Number in noncoding regions = 11435 Number of orfs with sites within 600 bp upstream = 2535 Fraction of orfs with sites within 600 bp upstream = 0.407164 Motif number 2 CCATGGCGGGAAAAGGGTAACAGATTTTTTCGAG 1 302 0 AAAAGGAAGA 0.577591 -299 AGGAGGGGGGAAAAATAGAAGCAACGCAGAAGTC 1 355 0 AAAAAAAAAA 0.790635 -246 AAAGGGAAATGAAAAGGGAAGAAAAAGAAACGGA 1 401 0 GAAAAGAAAA 0.921941 -200 CCGAAACTTGAAAAAAAAAAGAAAAGGGAAATGA 1 423 0 AAAAAAAAAA 0.790635 -178 GTGAGGAAAAGAAAATGAAAAAAAAAAAAAAAAA 2 112 0 GAAAAGAAAA 0.921941 -483 AAAAGAGATCAAAAAGGTAAGTGAAGTGAATGGA 2 433 0 AAAAAGAAGA 0.88843 -162 TAAGAGTGCTGAAAAAAAAAAGAAGTACAGAAGT 4 64 1 GAAAAAAAAA 0.610112 -383 GTTGAATTCAAAAAATGAAAATGATGAACAACCA 4 388 1 AAAAAGAAGA 0.88843 -59 AGAAAAAAAGAAAAATGCACTTGACAATTAGAGT 6 24 0 AAAAAGACGA 0.642348 -362 TCATAATGCAATAAAGGAAAAAAAATTGTAATAT 6 58 1 ATAAAGAAAA 0.670813 -328 CTACTGAAGAAAAAAAGGAATAAAAAATAAAAGA 6 168 0 AAAAAGAAAA 0.966105 -218 GTTTGATATGAAAAATAGAAAAAAATACATAGTA 6 258 1 AAAAAAAAAA 0.790635 -128 TAGTGCACTTGAAAAAGCAATAAAATTTTATTTC 7 46 0 GAAAAGAAAA 0.921941 -255 GAGAAGTAAAAAAAATGAACATAAACCACATATA 8 133 0 AAAAAGACAA 0.865386 -468 TTTAGTTAATGAAAATGGAATTAACGAAAGAGAA 8 162 0 GAAAAGAAAA 0.921941 -439 AGTTTCGCGCAAAAAAAAAAATAAAAAACAATTA 14 373 1 AAAAAAAAAA 0.790635 -228 ACAAAAAGAAAAAAAAGGAAATAATAGAAGATCT 14 410 1 AAAAAGAAAA 0.966105 -191 CTGGAAAAATAAAAATGAAAGCGAATGGAATGTG 15 275 1 AAAAAGAAGA 0.88843 -151 GTGTAAGAGAAAAAAAGGAAAGAACTATCAAGTT 15 306 1 AAAAAGAAAA 0.966105 -120 AAAAGCTACCAAAAAAGAAAAAAAAAAAAATTCA 16 280 0 AAAAAGAAAA 0.966105 -321 TGAAAAAAAAAAAACAGCAACAAAATGTGGTATT 16 356 0 AAAACGAAAA 0.770647 -245 GTGAAAAAAAAAAAAAGAAAAGAAAAAGAAAAGA 16 464 1 AAAAAGAAAA 0.966105 -137 AAGGGATTGAAAAACTGTACGTAAATCATTGAAG 16 521 1 AAAACGACAA 0.431125 -80 GTAGAACAATAAAAATGCACTTAACAAGTTCCGT 17 162 1 AAAAAGACAA 0.865386 -184 GCGATGCAATAAAAGTGGAAGAAAAAAAAAGAAG 17 256 1 AAAAGGAAAA 0.830347 -90 ATTTTCCAGAAAAAAAGAAAAGAAACTGCGCAAG 18 140 0 AAAAAGAAAA 0.966105 -161 TTATGGAAGCAAAAATGGAATAAAGGATTGGGAC 18 186 1 AAAAAGAAAA 0.966105 -115 ATTAAAGTAAATAAATGAAATAAATGAAATAGAT 19 383 0 ATAAAGAAAA 0.670813 -218 ATGTCCTCTCAAAAAAGTATGTAAATGAATAGCT 21 116 0 AAAAAGATAA 0.551948 -185 ACGCAACACAAAAAAGGGCATAAACAAAGTTGGT 21 266 1 AAAAAGCAAA 0.61729 -35 TTCAAACAAAAAAAAAAAAAAAAACAAGGGTTGT 23 318 0 AAAAAAAAAA 0.790635 -175 GAGAAAAGAGGAAAGTGAAAAGAAGGTAAGGAAT 23 411 1 GAAAGGAAAA 0.669763 -82 TGAGGCAAGAACAAAGGCAACAAACAGGGACAAG 24 468 0 ACAAAGAAAA 0.631375 -133 CTCTGATCAAGAAAAGGTAAGAAAGCAGAAAAGG 26 467 1 GAAAAGAAAA 0.921941 -134 GTTTAAAAAATGTAATCAACCTGTCCCGT 27 6 1 AAAAAGAAAA 0.966105 -379 ***** * ** ** Masking position 4 Map Score: 43.2453 Number of sites scoring better than the average of aligned sites = 2115 Number in coding regions = 796 Number in noncoding regions = 1319 Number of orfs with sites within 600 bp upstream = 938 Fraction of orfs with sites within 600 bp upstream = 0.150659 Motif number 3 AATCTTCGGCTTTTTCGCGTTGAATTCAAA 4 370 1 TTTTTCGCGT 0.941473 -77 GTCCCCTAAGTTCTTCACGTGTTCTCTTCT 6 222 1 TTCTTCACGT 0.723202 -164 CGTTACCCTATGCTACGCGTCATTTCCGCT 10 396 1 TGCTACGCGT 0.971937 -205 ATAAAAAGTATTTTACGCGTTACCCAATAT 14 338 1 TTTTACGCGT 0.980734 -263 TCATTGAAGGTTCTACACGTCATCCATGAA 16 546 1 TTCTACACGT 0.892102 -55 ATTTGCGCGATGTTACGCGTCGCGTTTCCT 19 473 0 TGTTACGCGT 0.976738 -128 TGGCTGAAAATTTTACGCGTCATAAACCCT 20 160 1 TTTTACGCGT 0.980734 -141 CGTTAACTTTTGTTACGCGTCTCTAGCCAC 25 205 0 TGTTACGCGT 0.976738 -96 TTTCTGCCAATTTTACGCGTCACTCCCGTT 26 342 0 TTTTACGCGT 0.980734 -259 ********** Masking position 4 Map Score: 7.87534 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 11 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 GGCGGCTAAAAATCAAAGGGAAGAGGGGATGTA 1 232 0 AAAAAGGAAG 0.960772 -369 AAGAAAAAGAAACGGAGGCGCAGGAGGAAGGAG 1 384 0 AAGAGGGCAG 0.729298 -217 GAAAAGGGAAATGAAAAGGGAAGAAAAAGAAAC 1 404 0 ATAAAGGAAG 0.769306 -197 AAACTTGAAAAAAAAAAGAAAAGGGAAATGAAA 1 421 0 AAAAAGAAAG 0.727859 -180 AGAGATCAAAAAGGTAAGTGAAGTGAATGGAAA 2 431 0 AATAAGGAAG 0.88062 -164 CAGTAACGGCAAGGAAGGATAAGAACATCATTG 3 488 1 AAAAGGTAAG 0.473371 -113 AGAGTGCTGAAAAAAAAAAGAAGTACAGAAGTT 4 66 1 AAAAAAGAAG 0.868339 -381 TAATAAGTTAAAGATAGGTGAAGAAGATGTCTG 5 80 0 AATAGGGAAG 0.822241 -221 ATTAGCTAAGATGTGAAAAGAAGTATGTAATAT 6 88 0 ATGAAAGAAG 0.555178 -298 AAAGGAATAAAAAATAAAAGAAGAAACGGTAGC 6 156 0 AATAAAGAAG 0.66515 -230 TTCATATCAAACGCGATGAGAAGAGAACACGTG 6 237 0 ACGATGGAAG 0.3094 -149 AAATGGAATTAACGAAAGAGAAGTAAAAAAAAT 8 151 0 AAAAAGGAAG 0.960772 -450 AAACCTTTCAATTAGAAAAGAAGGCCATGCACA 8 220 0 ATGAAAGAAG 0.555178 -381 GCCTAGCCATAATGAAAGAGAAGAAAATAAAAA 9 180 0 AAAAAGGAAG 0.960772 -267 AGGGGCGATGAAAAGAGAGGAAGAAAGAGTTTA 10 106 0 AAGAGAGAAG 0.851807 -495 GAAACTACGGAAGATAGAAGAAGTAACTGAGAA 10 500 0 AATAGAGAAG 0.554684 -101 ATCTTGAGTAAAATAAGGTGAAGGTAAATATAA 13 76 0 AAAAGGGAAG 0.938867 -225 TAGAAGATCTAACTGAAGCGAAGGCCAAAACTC 14 434 1 AAGAAGGAAG 0.971461 -167 GAAAAATAAAAATGAAAGCGAATGGAATGTGTA 15 278 1 AAAAAGGAAT 0.402512 -148 TGTGTAAGAGAAAAAAAGGAAAGAACTATCAAG 15 305 1 AAAAAGAAAG 0.727859 -121 AGTGAAAAAAAAAAAAAGAAAAGAAAAAGAAAA 16 463 1 AAAAAGAAAG 0.727859 -138 CATCGCCCTTAACTGAAATGAAGCTAAGGTATA 17 229 0 AAGAAAGAAG 0.901638 -117 GGAAGAAAAAAAAAGAAGGGAAGAGGTTTGATA 17 272 1 AAGAAGGAAG 0.971461 -74 TATTTTCCAGAAAAAAAGAAAAGAAACTGCGCA 18 142 0 AAAAAGAAAG 0.727859 -159 TCTAGAAATCACGAGAGGGGAAGAA 18 286 1 ACGAGGGAAG 0.820466 -15 AGAATCACTAACGGGAAGAGCAGACTCTTTGGC 22 201 0 ACGAAGGCAG 0.479127 -100 GAAAAGAGGAAAGTGAAAAGAAGGTAAGGAATT 23 413 1 AAGAAAGAAG 0.901638 -80 AGATGAAGACAAACGAGGTGAAGGCATTTTTTT 24 413 0 AAGAGGGAAG 0.955248 -188 TTTCCGGCTTAATTAAAAGGAAGCAGGCTATTA 26 219 0 AAAAAAGAAG 0.868339 -382 ATCTCTGATCAAGAAAAGGTAAGAAAGCAGAAA 26 465 1 AAAAAGTAAG 0.589064 -136 ** **** **** Masking position 6 Map Score: 22.2745 Number of sites scoring better than the average of aligned sites = 1482 Number in coding regions = 958 Number in noncoding regions = 524 Number of orfs with sites within 600 bp upstream = 439 Fraction of orfs with sites within 600 bp upstream = 0.0705108 Motif number 5 TTCATTAGCTTAAAGCATAGGATACCGAGAAACCGTAACGGT 1 46 1 TAAAGAGAAA 0.974767 -555 TGCAATTGATTATACCATAGAAGAGCGGGAAAAGAAGTTAGT 2 267 0 TAAAGAGAAA 0.974767 -328 TAAAGATATGTAAAATATAAAACTTAGAAAAAAAATTTGTAT 2 346 0 TAAAAAGAAA 0.760861 -249 CTTACGGATTTTTAATACAGTATTTAGCTGAAGTTTCCATTC 2 398 1 TAAAGAGGAA 0.924335 -197 TAAATTTACTTCGAAGACAGAAGCCAGTAAATTTTGTTTTCT 3 127 1 TAAAGAGAAT 0.886875 -474 CTTTTTCAAGTGCACTAAAGTATAAGGCAAAATTTTTTTAAT 7 63 1 TAAAGAGAAA 0.974767 -238 AGAAACGCCATAGAAAAGAGCATAGTGAGAAAATCTTCAACA 7 261 1 TAAAGAGAAA 0.974767 -40 TCTTATGTATTAGAGTAGAGAATATTTTAAAATAATAAACTA 8 66 1 TAAAGATAAA 0.89858 -535 TAATTTCGGATTAACTAAAGTACCTATATAATTATACCTTAT 8 481 1 TAAAGATAAT 0.64261 -120 ATTTACAGTCTCCAATAGAGCAGTCAGATAATGATCGGTAAT 11 68 0 TAAAGAGAAT 0.886875 -233 CAACCCAAGATGAAATATAGTATTTCTATGAATGGCTAACAG 12 350 0 TAAAGATGAA 0.738721 -81 CGTTACCCAATATAGCAAAGTTTCGCGCAAAAAAAAAAATAA 14 355 1 TAAAGTGAAA 0.734313 -246 GAAGCAAAAATGGAATAAAGGATTGGGACGAAGTTAGTGAAA 18 191 1 TAAAGAGGAA 0.924967 -110 CTTTTCGTTTTTCACGAAAAAAACAGGCGAAAAAAAATGCTA 19 162 1 TAAAAAGAAA 0.760861 -439 CACCACAGTTTGGATAATAGAACATATGAAAAACAACCTCGT 22 17 1 TAAAGATAAA 0.89858 -284 TACCACGGTAGATAATACAGTATCATTCTAAAAGTACCATTT 26 76 0 GAAAGATAAA 0.646504 -525 CGTGGTATCGGCAACTATAGGACGGAGATAAAGCATGCCAAA 26 111 1 GAAAGAGAAA 0.888568 -490 TCTTAAGCTTTAAAAGAGAGAATAGTGAGAAAAGATAGTGTT 26 551 1 TAAAGAGAAA 0.974767 -50 GCGACTTTTCTTCATCATTGAAGTTAGAAAAAGCTTTACTCG 27 153 1 TAATGAGAAA 0.734311 -232 * * * ** * * *** Masking position 7 Map Score: 10.0977 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 290 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 6 GAAATGAAAAGGGAAGAAAAAGAAACGGAGG 1 399 0 GGGAGAAAAA 0.819677 -202 ATTGCAGAAGAGGCAGGAAAAAATTGTAATC 2 303 1 AGGAGGAAAA 0.901931 -292 AATGCCACATTAGAAGAAAAACCATCCGCAA 2 532 1 TAGAGAAAAA 0.745854 -63 TTATTGCATTATGAAGAAAAAAAGAAAAATG 6 41 0 ATGAGAAAAA 0.871853 -345 TAAACCTTTCAATTAGAAAAGAAGGCCATGC 8 223 0 AATAGAAAAG 0.448254 -378 ACTTAAAAACAGGGAGAAAAACCTAAGTGTA 9 295 0 AGGAGAAAAA 0.966465 -152 AAGTCTTTAGAGGAAGGAAAATTGGATGGTA 9 363 0 AGGAGGAAAA 0.901931 -84 ACTATATAGATGGTAGAAAAGCAAGAGGAGA 11 161 0 TGGAGAAAAG 0.922161 -140 AAAGCCGCGCTAGGAGAAAAATATTCTGCTC 14 77 1 TAGAGAAAAA 0.745854 -524 CACGTCATCCATGAAGAAAAGCATTTTCGGG 16 561 1 ATGAGAAAAG 0.866373 -40 GCAATAAAAGTGGAAGAAAAAAAAAGAAGGG 17 261 1 TGGAGAAAAA 0.925549 -85 AAACGGACACCGGAAGAAAAAAT 19 588 1 CGGAGAAAAA 0.819677 -13 GCTAAGTTGTAGGGAGAAAAGAGGAAAGTGA 23 398 1 AGGAGAAAAG 0.964869 -95 CTTAGTGTTTATGTAGGAAAACTTTGATGGA 25 174 0 ATGAGGAAAA 0.684651 -127 CGCGTAAAATTGGCAGAAAAATCATCACCGT 26 353 1 TGGAGAAAAA 0.925549 -248 AAAGGTAAGAAAGCAGAAAAGGACGGTAGAG 26 479 1 AAGAGAAAAG 0.866373 -122 AAGAGAGAATAGTGAGAAAAGATAGTGTTAC 26 564 1 AGTAGAAAAG 0.77485 -37 AACTTCAATGATGAAGAAAAGTCGCAAAATA 27 147 0 ATGAGAAAAG 0.866373 -238 TCATCATTGAAGTTAGAAAAAGCTTTACTCG 27 164 1 AGTAGAAAAA 0.783143 -221 *** ******* Masking position 5 Map Score: 9.86116 Number of sites scoring better than the average of aligned sites = 1748 Number in coding regions = 1017 Number in noncoding regions = 731 Number of orfs with sites within 600 bp upstream = 561 Fraction of orfs with sites within 600 bp upstream = 0.090106 Motif number 7 ATTTTATTTCATATGTATCTAACGCTAACAA 7 25 0 ATATGTATTA 0.882893 -276 TTTCAGGCAAATATATATTTAGTTAATGAAA 8 182 0 ATATATATTA 0.923297 -419 ATTATTATCGGTATATATGTACAACTATATG 9 49 0 GTATATATTA 0.898363 -398 TCATTCACCTGTATTTATTTACAGTCTCCAA 11 95 0 GTATTTATTA 0.710735 -206 ATATACATATATATATATTTATTTATTATTT 12 301 0 ATATATATTA 0.923297 -130 AAATATATATATATGTATATCTTAAAGTTGA 12 312 1 ATATGTATTC 0.704304 -119 TCAAGGTACCATATATATTTCCTTATAACTG 14 580 1 ATATATATTC 0.791793 -21 CCGGATTAGTGTATGTATATACAAAAAGGCA 15 219 1 GTATGTATTA 0.847002 -207 ATTTATTTATGTATATATTTACAGGCCAATT 17 22 0 GTATATATTA 0.898363 -324 CTTGACGCATATATTTATTTATGTATATATT 17 34 0 ATATTTATTA 0.769909 -312 CTCTTACAATATATATATATATATATACGCA 17 92 1 ATATATATTA 0.923297 -254 AGGTTTGATAATATATATATATATATATATA 17 295 1 ATATATATTA 0.923297 -51 GAGCAATGTTATATATATATATATATATATA 17 306 0 ATATATATTA 0.923297 -40 ******** ** Masking position 7 Map Score: 4.33615 Number of sites scoring better than the average of aligned sites = 4286 Number in coding regions = 284 Number in noncoding regions = 4002 Number of orfs with sites within 600 bp upstream = 557 Fraction of orfs with sites within 600 bp upstream = 0.0894635 Motif number 8 ATTGACTTTTTTTTTTTTTTTTTTTTCATTTTCTTTTCCTCACCG 2 103 1 TTTTTTTCTT 0.926711 -492 AATTTGTATCATTTTTGTTATGATTACAATTTTTTCCTGCCTCTT 2 310 0 ATTTTTTTTT 0.626591 -285 TTCTAAGTTTTATATTTTACATATCTTTATTTTTTGATCCTTACG 2 359 1 TATTTTTTTT 0.886627 -236 ATATTATAAATATATTCTTCCTTTACCTATTTCTTCTCACACATT 4 290 1 TATTTTTCTT 0.947582 -157 TAAAGGAAAAAAAATTGTAATATTACATACTTCTTTTCACATCTT 6 69 1 AATTTTTCTT 0.847215 -317 ATTTTCATATTATATATTATTAATAAGTTCTTTTCCTTATCT 6 354 0 TTTTTTTCTT 0.926711 -32 TAGGTAGCGTTTAATTTTATCCTTAGTACATTTTTAGAGTAATAT 8 315 0 TATTTTTTTT 0.886627 -286 AAATTGAACTATTAATTTGAACCTATTTTCTTCTTCTTGAACATA 8 387 0 AATTTTTCTT 0.84722 -214 ATTTTACAATATTAGTTTAATTTTGGGCAATTCTTATAATTTCGG 8 445 1 AATTTTTCTT 0.84722 -156 ATCAAACCTCTATTCTTTGGTCTTTAACTTTTCTTTGAGTGAATT 9 80 1 TTTTTTTCTT 0.926711 -367 TCATTTTTTCTTAAGTTTTGCTGTCGCTATTTCTTGCCTAGCCAT 9 203 0 TATTTTTCTT 0.947582 -244 GCACCACTTGTGTATTTTCAAGATGTTAAATTTTTGATACATAAG 14 207 0 TATTTTTTTT 0.886627 -394 TTTTTTCTTTTTGTTTGTAATTGTTTTTTATTTTTTTTTTTGCGC 14 379 0 TTTTTTTTTT 0.845445 -222 ATTTATGTCATCAACTCTGCAACTTGATAGTTCTTTCCTTTTTTT 15 315 0 TATTTTTCTT 0.947582 -111 AACTTCGCACTTGAATTTTTTTTTTTTTCTTTTTTGGTAGCTTTT 16 269 1 TATTTTTTTT 0.886627 -332 TTTTTCATTGTTAATTATCACTATTTTTTTTTCTTTCTAGTATAA 16 383 1 TATTTTTCTT 0.947582 -218 TGGCGGCATCTTTTCTTTTTCTTTTCTTTTTTTTTTTTTCACTCT 16 461 0 TTTTTTTTTT 0.845445 -140 TGTTCTACCCTCTATTTTTTAAATGTAATGTTCTTGAATACGCTA 17 125 0 TATTTTTCTT 0.947582 -221 ATGAAGGTTTTGATGTATTATAATGAGGTATTCTTCCTTATATAC 19 501 1 TTTTTTTCTT 0.926711 -100 GACAAACTAATTTTGTATATGCATTCGATTTTCTTAAGCTTTAAA 26 520 1 TTTTTTTCTT 0.926711 -81 ACATCATCTATTTTGTTTCAAGTTCGTACATTTTTTGAAGCGTGT 27 43 0 TTTTTTTTTT 0.845445 -342 CCACGCAGACAAAAGTTTACTCGTCCCGACTTTTTTTTTTCATTA 27 238 0 AATTTTTTTT 0.705794 -147 * * * * * ***** Masking position 14 Map Score: 20.4302 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 536 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 9 TTTCGAGGAGTAACACATTTTGTGCTGTGTGGG 1 276 0 TACAATTTTT 0.861098 -325 GGGAAAAGGGTAACAGATTTTTTCGAGGAGTAA 1 296 0 TACAATTTTT 0.861098 -305 TTTTTTTTTTTTTCATTTTCTTTTCCTCACCGA 2 116 1 TTCATTTCTT 0.842977 -479 TCATATCACATAGCATTTTCTTTTTAATCTTAT 2 219 1 TACATTTCTT 0.924097 -376 TTTGTTATGATTACAATTTTTTCCTGCCTCTTC 2 309 0 TTCATTTTTC 0.629258 -286 GTACTTAGTTTTTCACTTTCTATTGAAAAATGC 2 490 0 TTCATTTCTT 0.842977 -105 TCTTAGTAATTACCATATGTTCTTGTATGTGGC 3 193 1 TACAATGTTT 0.774206 -408 TGTGGCAGTTTAGCACATGCTTTGGACCATTAA 3 529 1 TACAATGCTT 0.819681 -72 GTATGTAATATTACAATTTTTTTTCCTTTATTG 6 66 0 TTCATTTTTT 0.801956 -320 TCCGCATCTATAACATATTCTACTGAAGAAAAA 6 188 0 TACAATTCTC 0.775021 -198 AGATAGTGTGTATCAGTTGTTATTTTATATGTG 8 108 1 TACATTGTTT 0.835506 -493 GACCTTGTTCTATCATTTTTTCTTAAGTTTTGC 9 227 0 TACATTTTTT 0.9018 -220 GTGACCCCAATACCACATTTTGTTGCTGTTTTT 16 348 1 TACAATTTTT 0.861098 -253 TCTAGGACTATTTCAGTTTTTTTTCACTAACTT 18 221 0 TTCATTTTTT 0.801956 -80 AGCAAACTTATATCACTTTCTACTTCTTTCCCT 19 124 0 TACATTTCTC 0.836147 -477 GGTACTAGTCTAGCATTTTTTTTCGCCTGTTTT 19 181 0 TACATTTTTT 0.9018 -420 CGAGGTTGTTTTTCATATGTTCTATTATCCAAA 22 25 0 TTCAATGTTT 0.601901 -276 GAATTATTATTAACACTTTCTCTGGCAGAAATT 25 79 1 TACATTTCTT 0.924097 -222 AATGTTTATTTATCAATTTCTGCCAGAGAAAGT 25 93 0 TACATTTCTC 0.836147 -208 TTTACACATTTAGCAAATGCTCTACCAACGTCC 27 324 0 TACAATGCTT 0.819681 -61 ** ** ***** * Masking position 8 Map Score: 8.92954 Number of sites scoring better than the average of aligned sites = 1053 Number in coding regions = 678 Number in noncoding regions = 375 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 10 TGTCGGTTTTATTAGTCCTTAAGGTCCTAT 1 483 0 ATTAGTCCTT 0.783534 -118 TCTGCAATTGATTATACCATAGAAGAGCGG 2 281 0 ATTATACCAT 0.727165 -314 TTATAAATATATTCTTCCTTTACCTATTTC 4 293 1 ATTCTTCCTT 0.945492 -154 TCTTTTATTTTTTATTCCTTTTTTTCTTCA 6 168 1 TTTATTCCTT 0.882304 -218 TACCTATATAATTATACCTTATCGCGGCGA 8 501 1 ATTATACCTT 0.882304 -100 CTATTAGTGTATTATTCCTTTATAGTAGAC 13 114 1 ATTATTCCTT 0.954721 -187 TAAGTACAAATTTATACCTTAGCTTCATTT 17 217 1 TTTATACCTT 0.727165 -129 GTCCCAATCCTTTATTCCATTTTTGCTTCC 18 190 0 TTTATTCCAT 0.727165 -111 ATAATGAGGTATTCTTCCTTATATACATCG 19 520 1 ATTCTTCCTT 0.945492 -81 TTTTCCACACATTATTCCTTACTGCTAAGC 20 194 1 ATTATTCCTT 0.954721 -107 ATCTATCCAAATTCTTCCATACTGAAAATC 23 117 1 ATTCTTCCAT 0.860472 -376 TGCCAAAGTAATTCTTCCTTTATTAGATGA 26 146 1 ATTCTTCCTT 0.945492 -455 ********** Masking position 3 Map Score: 5.32612 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 136 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 TTCTAATGTGGCATTGCTCAAGTGGTACTT 2 517 0 GCATTGCTCA 0.981829 -78 TGCTCACTTCACATTGCTCATCGTTGCAAA 7 225 0 ACATTGCTCA 0.936467 -76 GAATGCTCAGGGAATGCTCAAGAAGGCCAC 10 306 0 GGAATGCTCA 0.945975 -295 ACAACCGGTTGGAATGCTCAGGGAATGCTC 10 317 0 GGAATGCTCA 0.945975 -284 TATATATATAACATTGCTCAGAGAAACATA 17 318 1 ACATTGCTCA 0.936467 -28 ACTGCTAAGCGCATTGCTCACTTGAAAGTA 20 214 1 GCATTGCTCA 0.981829 -87 ATGATCTTATGCAATGCACATTCCTGCCCT 23 227 0 GCAATGCACA 0.895995 -266 ********** Masking position 3 Map Score: 2.26183 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 43 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 AGCATAGGATACCGAGAAACCGTAACGGTTTC 1 59 1 ACGAGAAACG 0.630171 -542 AAAACCGGTCAACATGAAACCGTTACGGTTTC 1 74 0 ACATGAAACG 0.72443 -527 AGCACTCAAAATCAACAAAAAGTGAGAAGGTT 1 191 1 ACAACAAAAG 0.894609 -410 GAAATGAAAAGGGAAGAAAAAGAAACGGAGGC 1 398 0 GGAAGAAAAG 0.840959 -203 AAAAATAAAAGAGATCAAAAAGGTAAGTGAAG 2 441 0 GGATCAAAAG 0.403961 -154 GATAATGTGTGAGAAGAAATAGGTAAAGGAAG 4 306 0 GGAAGAAAAG 0.840959 -141 TACGTCCCAGAACGAGAAAGAGATAAAATTTT 5 268 0 ACGAGAAAAG 0.847579 -33 ATGTGAAGTGAGCAAGATAGAGAAACGCCATA 7 241 1 ACAAGATAAG 0.552315 -60 GCTTTGATAAAACAAGACAAAGC 8 588 1 ACAAGACAAG 0.646457 -13 TTGCCTAGCCATAATGAAAGAGAAGAAAATAA 9 183 0 AAATGAAAAG 0.672062 -264 ATTATGGCTAGGCAAGAAATAGCGACAGCAAA 9 200 1 GCAAGAAAAG 0.94284 -247 ATGAAAAGAGAGGAAGAAAGAGTTTATGGCAT 10 100 0 AGAAGAAAAG 0.884274 -501 AGTTGAGTGTAGCGACAAAGAGCAGACGTAGT 10 544 1 ACGACAAAAG 0.664461 -57 GCAAATGCCCATCATGAAAGAGCGAGGGCGTA 11 37 1 ACATGAAAAG 0.895606 -264 AAAAACAATTACAAACAAAAAGAAAAAAAAGG 14 396 1 AAAACAAAAG 0.669715 -205 AGCAGCTTTAGTGAAGAAAGAGAAAAGTTGCT 14 505 0 GGAAGAAAAG 0.840959 -96 TATATATGGTACCTTGAAATAGAGCTAAGTTC 14 565 0 ACTTGAAAAG 0.47042 -36 TGGAAAAATAAAAATGAAAGCGAATGGAATGT 15 276 1 AAATGAAACG 0.385738 -150 ATCCTCTGGAAACATCAAAAAGCTACCAAAAA 16 299 0 ACATCAAAAG 0.753401 -302 AAAAAAAAAAGAAAAGAAAAAGAAAAGATGCC 16 470 1 GAAAGAAAAG 0.797579 -131 GCCATTGCCAATAAACAAAAAGAACAGGGAAA 19 99 1 AAAACAAAAG 0.669715 -502 AGCATACATTGGAAAGAAATAGGAAACGGACA 19 565 1 GAAAGAAAAG 0.797579 -36 CTGTGACCCAAACAAGAAAGAGCACTGTAAAA 21 158 0 ACAAGAAAAG 0.959736 -143 AATTTATCGGAACTAGAAAAAGAGTTTGGATC 23 442 1 ACTAGAAAAG 0.71165 -51 TATTCATTGAAACAAGAAACCGATAGTACTTC 24 207 1 ACAAGAAACG 0.879575 -394 CAAGAACAAAGGCAACAAACAGGGACAAGATG 24 465 0 GCAACAAAAG 0.854525 -136 GAAATCTCTGATCAAGAAAAGGTAAGAAAGCA 26 462 1 ACAAGAAAGG 0.674732 -139 * ******* ** Masking position 7 Map Score: 10.241 Number of sites scoring better than the average of aligned sites = 2817 Number in coding regions = 1861 Number in noncoding regions = 956 Number of orfs with sites within 600 bp upstream = 774 Fraction of orfs with sites within 600 bp upstream = 0.124317 Motif number 13 CATGCCATTGATGTATGTAAACCTTTCAATTAGA 8 237 0 ATATGAAACT 0.962895 -364 TATTATCGGTATATATGTACAACTATATGAATTC 9 44 0 ATATGACACT 0.803654 -403 TGCATGCACAATATATGCAAATTTTATGCAGTTC 11 230 1 ATATGAAATT 0.901842 -71 TGTATATGAAATTTATGAAAAATTAAAGTAGCGT 12 225 1 ATATGAAATT 0.901866 -206 ATAAATATATATATATGTATATCTTAAAGTTGAC 12 310 1 ATATGATACT 0.734144 -121 GATAAAGCTTATGTATCAAAAATTTAACATCTTG 14 200 1 ATATCAAATT 0.622792 -401 TTATTTATGAAAATTGGCCTGTAAAT 17 3 1 ATATGAAATG 0.727341 -343 AATAAATGAAATAGATGAAAAACTGGTTACACTA 19 365 0 ATATGAAACT 0.962895 -236 CCTCATTATAATACATCAAAACCTTCATTTGCGC 19 495 0 ATATCAAACT 0.823391 -106 CCTTATATACATCGATGAAAAGCGTTGACAGCAT 19 536 1 ATATGAAACG 0.882803 -65 GAAAGTAATAATTTATGAAAATTTAACTACTTAT 20 102 0 ATATGAAATT 0.901866 -199 GAAAAGTGTCTTAGATGAAAATCTTGCTGTGACC 21 182 0 TTATGAAACT 0.883651 -119 GCTTTGATCTTTAAATGGAAATCTTTAATTCTAA 24 524 1 TTATGAAACT 0.883651 -77 GTAGGAAAACTTTGATGGAAAACTAAAATATATC 25 159 0 TTATGAAACT 0.883651 -142 ** *** *** ** Masking position 9 Map Score: 1.85441 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 224 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 14 TTTATTTCTGGTAATAATAGCAAGAAATAAGAAC 3 44 1 GATATAGAAG 0.970829 -557 GGCAAGGGCAGATATGATAGGAAGCAGTAACGGC 3 464 1 GATGTAGAAG 0.973014 -137 TAGAAAAAAATACATAGTAGCATGACTAACTAAT 6 273 1 TATATAGATG 0.722616 -113 ATACATCAATGGCATGATAGGATGTTGCAACTTT 8 255 1 GATGTAGATG 0.942286 -346 GAAGGAAAATTGGATGGTAGCAAGCTTGTCTGCG 9 348 0 TATGTAGAAG 0.861748 -99 AAGAGTTTATGGCATAGTAGAAAGGCCAATTAAA 10 81 0 GATATAGAAG 0.970829 -520 CCGCCTTACTGCAATAATAAAAAGTATTTTACGC 14 322 1 GATATAAAAG 0.744092 -279 ATACATATTCGGAATATTAGTATGGTGACTACAT 15 182 1 GATATAGATG 0.937771 -244 GTTCGAATGGGTTATACTAGAAAGAAAAAAAAAT 16 405 0 GATATAGAAG 0.970829 -196 CGGCTGGTAAGTTATGATAGAAAGCCAACGCTGT 19 272 1 GATGTAGAAG 0.973014 -329 * *** *** *** Masking position 8 Map Score: 2.55119 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 129 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 15 ACTAAGGTTTGAAAACACCACGCAGCATTACGT 1 521 0 GACACCACGC 0.980503 -80 TATTTTTTTCGTAAGAACCACGCGCTTTAGGCT 3 12 1 GGAACCACGC 0.965988 -589 GGCGAAAAAAGTATAAACCACTTATTGTAGTCT 8 526 1 GAAACCACTT 0.677678 -75 CCGGTCACATGACTACACCACGTTAATAGCGAT 10 172 1 GACACCACGT 0.922312 -429 TCCCCTTTATGGTCCCACCACGCGTACTGTAAA 10 443 0 GCCACCACGC 0.981977 -158 GATCGTCAAAGAAGCAAACACGCATTGATATCT 13 203 1 GCAAACACGC 0.71108 -98 AGCACATGAAGCTGGAACCACGCACCATTA 14 8 0 GGAACCACGC 0.965988 -593 CGTGACACATCTTTGCACCACTTGTGTATTTTC 14 233 0 CGCACCACTT 0.818708 -368 AAATAGCATACATGGCACCACTCAGGTCCAGAA 14 266 0 CGCACCACTC 0.950322 -335 GTGGTATTGGGGTCACACCACTCATTGACTCAC 16 331 0 GACACCACTC 0.954881 -270 TGGATTTTACCACTAAACCACTTGCGCTCACTA 18 71 0 CAAACCACTT 0.586118 -230 TGTAACTTATGAGACAGCCACGCAACACAAAAA 21 247 1 GCAGCCACGC 0.860245 -54 TCTCCGTTGTCCTAACACCACTCCTTCAGTAGC 25 33 0 CACACCACTC 0.934447 -268 TCAACCTGTCCCGTCCAACACGCTTCAAAAAAT 27 26 1 CCCAACACGC 0.797539 -359 CTCTCCTCTCCTATGCGCCACGCAGACAAAAGT 27 267 0 CGCGCCACGC 0.924262 -118 * ********* Masking position 10 Map Score: 4.08307 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 347 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826