AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ifnr_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 cydA 274 Cytochrome Oxidase Subunit I #2 CT065 300 ADP/ATP Translocase #3 CT483 300 hypothetical protein Motif number 1 ACCGAAGTCAAGGAAGGTCTTAAGAAGGCC 1 102 1 AGGAAGGTCT 0.957739 -173 GGAAGGTCTTAAGAAGGCCTTTGGGAAAGG 1 113 1 AAGAAGGCCT 0.981177 -162 AAGGCCTTTGGGAAAGGACTCATCCCTAGT 1 126 1 GGAAAGGACT 0.953769 -149 GTATTTTGTGGAAAAGGGCTGTTTTAACAA 1 182 1 GAAAAGGGCT 0.991857 -93 GCTGAACAAGCAGAAGGGCTCACTGAGAAT 2 17 0 CAGAAGGGCT 0.987947 -284 GAAGGCAATAGAAAAGGGCTGTATGCTGAA 2 41 0 GAAAAGGGCT 0.991857 -260 GAGTATACCACCAAAGGTCTCGGAAGGCAA 2 63 0 CCAAAGGTCT 0.93137 -238 GATCCTTCTTAAAAAGGCCTACATCCAAAA 3 20 0 AAAAAGGCCT 0.981543 -281 ********** Masking position 5 Map Score: 11.7804 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 89 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 2 GTTTTGCTGAAAATAATGAAAACACTTCAACTGCTAGGG 1 24 0 AAATGAACTA 0.840576 -251 CATTATTTTCAGCAAAACAAGAAGCTGTACCAACTCCTT 1 45 1 ACAACAACTA 0.960575 -230 ATAGTATATATACTAAAAAGAATACTAGAAGTTTTTGAT 1 232 1 TCAAAAACTA 0.951567 -43 CGTTGATTTGATCAACAAAGAAAACTTAACAATAAACAC 2 251 1 ACAAAAACTA 0.987529 -50 TCGTCTTTGTAAACAGAGAAGATCCTTCTTAAAAAGGCC 3 31 0 AAAAGAACTT 0.926085 -270 TCTTGTTTATAACGAGAAAGCAAGCTTTAGGAATCGTCT 3 64 0 ACAAAAACTA 0.987529 -237 TCTCGTTATAAACAAGAAACCACCCTAGATCCTTTGTAC 3 86 1 ACAAAAACTA 0.987529 -215 TTGTACATCGAACGAAAAGAAACTCTATACAAACTTTTT 3 119 1 ACAAAGACTA 0.937153 -182 GAGTTTTTTTTACTAATGAATAGTCTTCTCCGACTACAG 3 180 1 TCATGAACTT 0.756924 -121 CTCCGACTACAGAGAGAAATGAGTCTCCTATTCCATAAA 3 207 1 AAAAAAACTT 0.920411 -94 TTTTACTCCCATCTACAGAGGATCCTTTTATTTCAGG 3 274 1 ACAAGAACTT 0.980613 -27 * * * *** * ** * Masking position 12 Map Score: 11.6878 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 136 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 3 GTCTCGGAAGGCAATAGAAAAGGGCTGTAT 2 47 0 GCAATAGAAA 0.891057 -254 CCAGGAGGGCGGAATAAAAAATGGCAGAAA 2 110 0 GGAATAAAAA 0.963744 -191 TCCTCCTCACGTAATCGAAGATTCAGCCGG 2 161 1 GTAATCGAAG 0.914938 -140 AGATTCAGCCGGAATAGGGAGTCGTGAAAT 2 179 1 GGAATAGGGA 0.810471 -122 AGGGAGTCGTGAAATCAAAATTTTTTCACG 2 194 1 GAAATCAAAA 0.864777 -107 AATCGTCTTTGTAAACAGAGAAGATCCTTC 3 42 0 GTAAACAGAG 0.662728 -259 TAAAGAAAGGGGAATAAAAAGTTTGTATAG 3 143 0 GGAATAAAAA 0.963744 -158 CTATTCATTAGTAAAAAAAACTCTTAAATA 3 173 0 GTAAAAAAAA 0.781548 -128 TTTTTTTTATGGAATAGGAGACTCATTTCT 3 221 0 GGAATAGGAG 0.956925 -80 CCTGAAATAAAAGGATCCTCTGT 3 288 0 GAAATAAAAG 0.906813 -13 ********** Masking position 4 Map Score: 5.65537 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 255 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 4 ATAAGTTTCAAGGAGTTGGTACAGCTTCTT 1 63 0 AGGAGTTGGT 0.920958 -212 TTAATGGCAAAGTATTTTGTGGAAAAGGGC 1 171 1 AGTATTTTGT 0.79111 -104 AAAGAATACTAGAAGTTTTTGATTTGGAGA 1 248 1 AGAAGTTTTT 0.938958 -27 TCGTGAAATCAAAATTTTTTCACGACTTTT 2 200 1 AAAATTTTTT 0.807634 -101 TCACCCTCTGAAAAGCTTGTGTTTATTGTT 2 278 0 AAAAGCTTGT 0.718625 -23 AAGGGGAATAAAAAGTTTGTATAGAGTTTC 3 137 0 AAAAGTTTGT 0.96021 -164 CTTTATATTTAAGAGTTTTTTTTACTAATG 3 168 1 AAGAGTTTTT 0.928894 -133 ********** Masking position 4 Map Score: 2.41559 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 249 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 ATTATTTTCAGCAAAACAAGAAGCTGTACC 1 46 1 GCAAAACAAG 0.804287 -229 AAAACAAGAAGCTGTACCAACTCCTTGAAA 1 58 1 GCTGTACCAA 0.875272 -217 CTGTCTTCCAGCTAAACTAGGGATGAGTCC 1 141 0 GCTAAACTAG 0.902241 -134 GTGCATAGTATATATACTAAAAAGAATACT 1 228 1 TATATACTAA 0.506346 -47 ATTTGGCTCTCCAAATCAAAAACTT 1 260 0 GCTCTCCAAA 0.790927 -15 AGGGCTGTATGCTGAACAAGCAGAAGGGCT 2 27 0 GCTGAACAAG 0.966246 -274 TCGTTGATTTGATCAACAAAGAAAACTTAA 2 250 1 GATCAACAAA 0.8856 -51 GCTTTCTCGTTATAAACAAGAAACCACCCT 3 82 1 TATAAACAAG 0.778601 -219 CTTTTCGTTCGATGTACAAAGGATCTAGGG 3 108 0 GATGTACAAA 0.918231 -193 GAAAAGAAACTCTATACAAACTTTTTATTC 3 132 1 TCTATACAAA 0.883691 -169 ********** Masking position 9 Map Score: 2.7611 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 421 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 CTTAAGAAGGCCTTTGGGAAAGGACTCATC 1 120 1 CCTTTGGGAA 0.990939 -155 AGAAATCCAACCTTTAGGAAAAGAGTATAC 2 85 0 CCTTTAGGAA 0.992373 -216 GAGAAAGCAAGCTTTAGGAATCGTCTTTGT 3 60 0 GCTTTAGGAA 0.986053 -241 ********** Masking position 9 Map Score: 1.56106 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 ACCAGTTGTTAAAACAGCCCTTTTCCACAA 1 187 0 AAAACAGCCC 0.943628 -88 GGCTCACTGAGAATGAGCCT 2 1 0 GAATGAGCCT 0.926127 -300 GGCTCATTCTCAGTGAGCCCTTCTGCTTGT 2 12 1 CAGTGAGCCC 0.982425 -289 GCTTGTTCAGCATACAGCCCTTTTCTATTG 2 36 1 CATACAGCCC 0.978909 -265 GCCCTCCACTCAAGGAGCCCAGGAGGGCGG 2 128 0 CAAGGAGCCC 0.982425 -173 CGTAATCGAAGATTCAGCCGGAATAGGGAG 2 170 1 GATTCAGCCG 0.928405 -131 ********** Masking position 6 Map Score: 1.29342 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 60 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: -1.80235e-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 9 ********** No masking Map Score: -1.80235e-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 10 ********** No masking Map Score: -1.80235e-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