AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iiclR_pyro_opreg_100.orf -g0.419 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0198 300 168aa long hypothetical protein #2 PH0583 100 318aa long hypothetical protein #3 PH0803 56 110aa long hypothetical protein #4 PH1150 89 236aa long hypothetical arylmalonate decarboxylase Motif number 1 CTTGGGTTGCTAGATAGGGAGGTACTTTAA 1 46 0 TAGATAGGGA 0.993245 -255 TTAGGGAAGATGGTGAGGAACTTGGGTTGC 1 66 0 TGGTGAGGAA 0.947288 -235 GGTAGGATCAGAGTTAGGGAAGATGGTGAG 1 79 0 GAGTTAGGGA 0.990346 -222 GTCTTAACTCCAGTTAAGGATATTTCAATA 1 127 0 CAGTTAAGGA 0.90597 -174 CTATAAATTTTAGTGAGGGGAGGCTTGAAG 1 156 0 TAGTGAGGGG 0.983673 -145 CTAGGTTTGCTAGATAAGGAAGGTTTTTGT 1 208 0 TAGATAAGGA 0.962141 -93 AAGTGAGGGACCGAGGGTTG 1 291 0 AAGTGAGGGA 0.983601 -10 GTAACTTCTTGGGGGAGGGAAG 2 3 0 GGGGGAGGGA 0.977059 -98 ATAGCAGGGATGGAGAGGGATCAGA 2 86 1 TGGAGAGGGA 0.994046 -15 AAATCCCTATTACATAGGGATTTTAAACTA 4 58 0 TACATAGGGA 0.950075 -32 ********** Masking position 6 Map Score: 17.2627 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 606 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 AACCTTTTGCTTAAGTATTAAAGTACCTCCCTA 1 29 1 TTAAGTTTAG 0.972788 -272 TCTTATCTCTGTGATTATTGAAATATCCTTAAC 1 112 1 GTGATTTTAA 0.824037 -189 TTAACTGGAGTTAAGACTTCAAGCCTCCCCTCA 1 140 1 TTAAGATTAG 0.918676 -161 ATTTATAGCCTTGAGTATTCCAACTCCTTGACA 1 178 1 TTGAGTTTAA 0.981333 -123 GTCCGGTACTTTGATTTTTCTAAGCTTAGCAAT 1 244 0 TTGATTTTAA 0.957355 -57 TCAATAGATGTTAAGTATTTCGGTTTAGTACCT 2 34 1 TTAAGTTTGG 0.962196 -67 TTTCCCCTTATTAAGTCTTTAGGTACTAAACCG 2 54 0 TTAAGTTTGG 0.962197 -47 TATGCTTTATTTGATAATGGGAA 3 1 0 TTGATATGAA 0.753141 -56 TAGGGTAAAGTTAAGTTTGATAACC 3 42 1 TTAAGTTGAA 0.934147 -15 CTAACCTCCTTGATCTTTGGGAACATTATAAA 4 10 1 TTGATCTTGA 0.809399 -80 ****** ** ** Masking position 8 Map Score: 6.98794 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 244 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TGAGGAACTTGGGTTGCTAGATAGGGAGGT 1 53 0 GGGTTGCTAG 0.993857 -248 ACAGAGATAAGATTTGGTAGGATCAGAGTT 1 94 0 GATTTGGTAG 0.973178 -207 TTTACTTCTAGGTTTGCTAGATAAGGAAGG 1 215 0 GGTTTGCTAG 0.996387 -86 TAAGTATTTCGGTTTAGTACCTAAAGACTT 2 45 1 GGTTTAGTAC 0.931197 -56 TATGTAATAGGGATTTCTAGGTGACAGC 4 72 1 GGATTTCTAG 0.96488 -18 ********** Masking position 5 Map Score: 3.72254 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 50 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AAGGTTTTTGTCAAGGAGTTGGAATACTCA 1 189 0 TCAAGGAGTT 0.990172 -112 ATCTAGCAAACCTAGAAGTAAATTGCTAAG 1 223 1 CCTAGAAGTA 0.940406 -78 CTTCCCTCCCCCAAGAAGTTACCTCAATAG 2 11 1 CCAAGAAGTT 0.990172 -90 TTCCCAAAGATCAAGGAGGTTAG 4 4 0 TCAAGGAGGT 0.98336 -86 ********** Masking position 4 Map Score: 1.65706 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 69 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AAAAGGTTTATTAAATATATGAAACC 1 7 0 TTAAATATAT 0.887432 -294 ATATATTTAATAAACCTTTTGCTTAAGTAT 1 17 1 TAAACCTTTT 0.775848 -284 AACCTTTTGCTTAAGTATTAAAGTACCTCC 1 29 1 TTAAGTATTA 0.76645 -272 TTAACTCCAGTTAAGGATATTTCAATAATC 1 124 0 TTAAGGATAT 0.82535 -177 CTCCCCTCACTAAAATTTATAGCCTTGAGT 1 164 1 TAAAATTTAT 0.800689 -137 TCAATAGATGTTAAGTATTTCGGTTTAGTA 2 34 1 TTAAGTATTT 0.959943 -67 TTTCCCCTTATTAAGTCTTTAGGTACTAAA 2 57 0 TTAAGTCTTT 0.88094 -44 CATTATCAAATAAAGCATATAAAACGTTAG 3 15 1 TAAAGCATAT 0.879365 -42 GTTATCAAACTTAACTTTACCCTAACGTTT 3 36 0 TTAACTTTAC 0.636535 -21 GGGAACATTATAAAATTTTTTGAATAAAAT 4 29 1 TAAAATTTTT 0.827199 -61 ATAGGGATTTTAAACTATTTTATTCAAAAA 4 45 0 TAAACTATTT 0.925579 -45 ********** Masking position 4 Map Score: 5.9655 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 387 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 6 ********** No masking Map Score: -1.04207e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: -1.04207e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: -1.04207e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0