AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -inarL_ctra_opreg_100.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 CT065 300 ADP/ATP Translocase #2 CT134 300 hypothetical protein #3 CT135 58 hypothetical protein #4 CT483 300 hypothetical protein #5 sdhB 236 Succinate Dehydrogenase #6 sdhC 25 Succinate Dehydrogenase #7 CT593.1 221 hypothetical protein-possible frameshift with CT593 Motif number 1 ACGACTTTTTAAAGAAATACTTTAAATCTTC 1 221 1 AAAGAAATCT 0.93036 -80 TCTACTTAGAGAAAATCTCCTAAGTCGAAGA 2 21 0 GAAAATCTCT 0.863768 -280 CTAGGAACTTAAAAAAATCCTGATAAAAGCT 2 72 0 AAAAAAATCT 0.916613 -229 TCCAATTAAAGAGGATATGCTGGCTGCCCTT 2 185 1 GAGGATATCT 0.885134 -116 GATAGAAAGTAAGGAAATCCTGCGGCGGGAG 2 270 1 AAGGAAATCT 0.935452 -31 CCTTTTTAAGAAGGATCTTCTCTGTTTACAA 4 33 1 AAGGATCTCT 0.932566 -268 CGTTATAAACAAGAAACCACCCTAGATCCTT 4 89 1 AAGAAACCCC 0.825364 -212 CATCGAACGAAAAGAAACTCTATACAAACTT 4 124 1 AAAGAAACCT 0.889809 -177 TTCATTAGTAAAAAAAACTCTTAAATATAAA 4 169 0 AAAAAAACCT 0.869183 -132 TATTCCATAAAAAAAAATACCAAGGTAAAAT 4 235 1 AAAAAAATCC 0.869185 -66 TACCAAGGTAAAATATCTCCTATTTTACTCC 4 252 1 AAATATCTCT 0.623154 -49 CCTGAAATAAAAGGATCCTCTGTAGATGGGA 4 280 0 AAGGATCCCT 0.893153 -21 TGTCGTGCTAGAGAATATTCCAGCGAATATT 5 123 1 GAGAATATCC 0.793067 -114 CTGAAGAGAAAAAATTCTCTCTCCC 6 8 0 GAAAAAATCT 0.869184 -18 GAGATAGTACAAAAATCTTCCTACATTCGTT 7 166 1 AAAAATCTCC 0.863768 -56 ******** ** Masking position 5 Map Score: 13.7378 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 464 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 GCTGAACAAGCAGAAGGGCTCACTGAGAAT 1 17 0 CAGAAGGGCT 0.987008 -284 GAAGGCAATAGAAAAGGGCTGTATGCTGAA 1 41 0 GAAAAGGGCT 0.907521 -260 TCAAGGAGCCCAGGAGGGCGGAATAAAAAA 1 119 0 CAGGAGGGCG 0.985633 -182 GGCTCCTTGAGTGGAGGGCATCTCCTCCTC 1 139 1 GTGGAGGGCA 0.983161 -162 ATTTCACCCTCTGAAAAGCTTGTGTTTATT 1 281 0 CTGAAAAGCT 0.709278 -20 TCATAGGTCTCTAAAGGGCAGCCAGCATAT 2 199 0 CTAAAGGGCA 0.88882 -102 CCTGCGGCGGGAGGAGAGCAGTT 2 288 1 GAGGAGAGCA 0.945015 -13 CTGAAGAGAAAAAATTCTCT 6 16 0 CTGAAGAGAA 0.664458 -10 TATCCCTCAACTGAAAGGCTTCCATCCCTA 7 14 0 CTGAAAGGCT 0.907828 -208 CATGATGTTTGAGGAGGGCTCTTTATGGAA 7 86 1 GAGGAGGGCT 0.988437 -136 GCGTTCATATGAGGAGGGAGATAGTACAAA 7 149 1 GAGGAGGGAG 0.898598 -73 ********** Masking position 5 Map Score: 12.1488 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 181 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 CCAGGAGGGCGGAATAAAAAATGGCAGAAA 1 110 0 GGAATAAAAA 0.977855 -191 AGGGAGTCGTGAAATCAAAATTTTTTCACG 1 194 1 GAAATCAAAA 0.926149 -107 CTCTTTAATTGGAATGAAAACCAATAAGAT 2 168 0 GGAATGAAAA 0.981592 -133 TTGGGGGAACGAAATAAAAAGAGGTAAAGC 3 31 1 GAAATAAAAA 0.965324 -28 TAAAGAAAGGGGAATAAAAAGTTTGTATAG 4 143 0 GGAATAAAAA 0.977855 -158 CCTGAAATAAAAGGATCCTCTGT 4 288 0 GAAATAAAAG 0.880869 -13 CCTATATCGGGAAATGAATATTCGCTGGAA 5 140 0 GAAATGAATA 0.924852 -97 ATCCCGATACGGAATGAATACATCATATAA 7 200 0 GGAATGAATA 0.951269 -22 ********** Masking position 4 Map Score: 11.4709 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 57 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 GATTCAGCCGGAATAGGGAGTCGTGAAATC 1 180 1 GAATAGGGAG 0.944562 -121 GACAGTCTTCGACTTAGGAGATTTTCTCTA 2 16 1 GACTTAGGAG 0.97138 -285 TAGCGATTTCTAATTAGGAGAGACCGAAGC 2 237 1 TAATTAGGAG 0.924911 -64 GTCTAAAAAAGATTTGGGGGAACGAAATAA 3 18 1 GATTTGGGGG 0.821801 -41 TTTTTTTTATGGAATAGGAGACTCATTTCT 4 221 0 GGAATAGGAG 0.931124 -80 AGATGGGAGTAAAATAGGAGATATTTTACC 4 258 0 AAAATAGGAG 0.865976 -43 TGTGAATCCAGAATTACGAGATTACACTCG 5 78 1 GAATTACGAG 0.94127 -159 TTCATTTCCCGATATAGGAGGCTAATTTGA 5 152 1 GATATAGGAG 0.954919 -85 GAGGGACAGCGAATAAGGAGGCGTTCATAT 7 129 1 GAATAAGGAG 0.972111 -93 ********** Masking position 8 Map Score: 7.19997 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 106 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 5 ACAAGCAGAAGGGCTCACTGAGAATGAGCCT 1 8 0 GGGCTATGGA 0.975584 -293 CAATAGAAAAGGGCTGTATGCTGAACAAGCAGAA 1 32 0 GGGCTTTGTA 0.918529 -269 CCGCCCTCCTGGGCTCCTTGAGTGGAGGGCATCT 1 128 1 GGGCTCTGGG 0.991602 -173 AAGCGGGACTGGGCTGCATAAGCAAGATCTATCT 2 138 1 GGGCTCTAGA 0.992449 -163 TTTGGATGTAGGCCTTTTTAAGAAGGATCTTCTC 4 21 1 GGCCTTTAGA 0.975076 -280 TATTTATAGAGGCGTTCCTGGGAAATAATATTGG 5 201 1 GGCGTCTGGA 0.978422 -36 TGTTTGAGGAGGGCTCTTTATGGAAGGGCAGGAA 7 91 1 GGGCTTTAGA 0.984532 -131 CGAATAAGGAGGCGTTCATATGAGGAGGGAGATA 7 138 1 GGCGTCTAGG 0.94182 -84 ***** * ** * * Masking position 9 Map Score: 6.99182 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 6 ATTCCGGCTGAATCTTCGATTACGTGAGGA 1 164 0 AATCTTCGAT 0.979986 -137 AAATACTTTAAATCTTCGTTGATTTGATCA 1 235 1 AATCTTCGTT 0.923546 -66 GGGTGGACAGTCTTCGACTTAGGAGATT 2 9 1 AGTCTTCGAC 0.971143 -292 ATCCTGATAAAAGCTGCGACTCAGAAGCAT 2 57 0 AAGCTGCGAC 0.958914 -244 GGAGAGACCGAAGCTTCGATAGAAAGTAAG 2 253 1 AAGCTTCGAT 0.987178 -48 CTCAACTGAAAGGCTTCCATCCCTAATT 7 9 0 AGGCTTCCAT 0.936043 -213 ********** Masking position 5 Map Score: 3.42551 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 25 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 TTTGGTGGTATACTCTTTTCCTAAAGGTTGGA 1 78 1 TCTCTTTCCT 0.887493 -223 TTGTTAAGTTTTCTTTGTTGATCAAATCAACG 1 251 0 TCTTTGTGAT 0.949419 -50 CCACCCTAGATCCTTTGTACATCGAACGAAAA 4 105 1 TCTTTGTCAT 0.96102 -196 AATAAAAGGATCCTCTGTAGATGGGAGTAAAA 4 274 0 TCTCTGTGAT 0.985675 -27 GATCGCTACATATTCTGTAGATGAGCCAGAAA 5 18 1 TTTCTGTGAT 0.899244 -219 CGCGATTAAGTGCGCTGTTCATCATGATGTTT 7 64 1 TCGCTGTCAT 0.983823 -158 CGCCTCCTTATTCGCTGTCCCTCATGGTTCCT 7 120 0 TCGCTGTCCT 0.976147 -102 * ****** *** Masking position 6 Map Score: 3.32084 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 38 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 TTTTTAAGTTCCTAGTTTCTTCGCAAGTTT 2 88 1 CCTAGTTTCT 0.965428 -213 GCAGGATTTCCTTACTTTCTATCGAAGCTT 2 263 0 CTTACTTTCT 0.947516 -38 CTTAAAAAGGCCTACATCCAAAATAACAAC 4 13 0 CCTACATCCA 0.894038 -288 ATTCCTAAAGCTTGCTTTCTCGTTATAAAC 4 69 1 CTTGCTTTCT 0.847444 -232 AAGAAACCACCCTAGATCCTTTGTACATCG 4 99 1 CCTAGATCCT 0.935197 -202 ATAGCGGGTATCTACTTTCTTATATGAAAT 5 49 0 TCTACTTTCT 0.89566 -188 CAAAAATCTTCCTACATTCGTTTCATTATA 7 175 1 CCTACATTCG 0.948937 -47 ********** Masking position 7 Map Score: 1.3034 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 137 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 CTCTTTTCCTAAAGGTTGGATTTCTGCCAT 1 90 1 AAAGGTTGGA 0.916535 -211 AAGTCGTGAAAAAATTTTGATTTCACGACT 1 198 0 AAAATTTTGA 0.723627 -103 CACCCTCTGAAAAGCTTGTGTTTATTGTTA 1 277 0 AAAGCTTGTG 0.837379 -24 AGTTTCTTCGCAAGTTTTTATATTCTAAGA 2 101 1 CAAGTTTTTA 0.83722 -200 AAAAAGAGGTAAAGCTTTTAAAG 3 46 1 AAAGCTTTTA 0.932695 -13 AGGGGAATAAAAAGTTTGTATAGAGTTTCT 4 136 0 AAAGTTTGTA 0.952799 -165 TAATATTGGGAAAGTTTTGAG 5 226 1 AAAGTTTTGA 0.952799 -11 ********** Masking position 3 Map Score: 0.399257 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 94 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: 3.07908e-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 11 ********** No masking Map Score: 3.07908e-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 12 ********** No masking Map Score: 3.07908e-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