AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ifnr_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 cydA 274 Cytochrome Oxidase Subunit I #2 CT065 300 ADP/ATP Translocase #3 CT483 300 hypothetical protein Motif number 1 GGCCTTCTTAAGACCTTCCTTGACTTCGGT 1 102 0 AGACCTTCCT 0.949519 -173 CCTTTCCCAAAGGCCTTCTTAAGACCTTCC 1 113 0 AGGCCTTCTT 0.977404 -162 ACTAGGGATGAGTCCTTTCCCAAAGGCCTT 1 126 0 AGTCCTTTCC 0.944811 -149 TTGTTAAAACAGCCCTTTTCCACAAAATAC 1 182 0 AGCCCTTTTC 0.990204 -93 ATTCTCAGTGAGCCCTTCTGCTTGTTCAGC 2 17 1 AGCCCTTCTG 0.985511 -284 TTCAGCATACAGCCCTTTTCTATTGCCTTC 2 41 1 AGCCCTTTTC 0.990204 -260 TTGCCTTCCGAGACCTTTGGTGGTATACTC 2 63 1 AGACCTTTGG 0.918443 -238 TTTTGGATGTAGGCCTTTTTAAGAAGGATC 3 20 1 AGGCCTTTTT 0.977842 -281 ********** Masking position 1 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 0.864857 -251 CATTATTTTCAGCAAAACAAGAAGCTGTACCAACTCCTT 1 45 1 ACAACAACTA 0.967291 -230 ATAGTATATATACTAAAAAGAATACTAGAAGTTTTTGAT 1 232 1 TCAAAAACTA 0.959753 -43 CGTTGATTTGATCAACAAAGAAAACTTAACAATAAACAC 2 251 1 ACAAAAACTA 0.989702 -50 TCGTCTTTGTAAACAGAGAAGATCCTTCTTAAAAAGGCC 3 31 0 AAAAGAACTT 0.938299 -270 TCTTGTTTATAACGAGAAAGCAAGCTTTAGGAATCGTCT 3 64 0 ACAAAAACTA 0.989702 -237 TCTCGTTATAAACAAGAAACCACCCTAGATCCTTTGTAC 3 86 1 ACAAAAACTA 0.989702 -215 TTGTACATCGAACGAAAAGAAACTCTATACAAACTTTTT 3 119 1 ACAAAGACTA 0.947642 -182 GAGTTTTTTTTACTAATGAATAGTCTTCTCCGACTACAG 3 180 1 TCATGAACTT 0.790775 -121 CTCCGACTACAGAGAGAAATGAGTCTCCTATTCCATAAA 3 207 1 AAAAAAACTT 0.933495 -94 TTTTACTCCCATCTACAGAGGATCCTTTTATTTCAGG 3 274 1 ACAAGAACTT 0.983972 -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 CGGATGAACCGAAGTCAAGGAAGGTCTTAAG 1 95 1 GAGTCAAGGA 0.757207 -180 GTCTCGGAAGGCAATAGAAAAGGGCTGTATG 2 46 0 GAATAGAAAA 0.941992 -255 CCAGGAGGGCGGAATAAAAAATGGCAGAAAT 2 109 0 GAATAAAAAA 0.910281 -192 TCCTCCTCACGTAATCGAAGATTCAGCCGGA 2 161 1 GAATCGAAGA 0.976503 -140 AGATTCAGCCGGAATAGGGAGTCGTGAAATC 2 179 1 GAATAGGGAG 0.803277 -122 AGGGAGTCGTGAAATCAAAATTTTTTCACGA 2 194 1 GAATCAAAAT 0.649462 -107 AATCGTCTTTGTAAACAGAGAAGATCCTTCT 3 41 0 GAAACAGAGA 0.776977 -260 TAAAGAAAGGGGAATAAAAAGTTTGTATAGA 3 142 0 GAATAAAAAG 0.864031 -159 ATTTCTCTCTGTAGTCGGAGAAGACTATTCA 3 196 0 GAGTCGGAGA 0.943453 -105 TTTTTTTTATGGAATAGGAGACTCATTTCTC 3 220 0 GAATAGGAGA 0.976503 -81 AGATGGGAGTAAAATAGGAGATATTTTACCT 3 257 0 AAATAGGAGA 0.748864 -44 CCTGAAATAAAAGGATCCTCTGTA 3 287 0 GAATAAAAGG 0.933505 -14 * ********* Masking position 3 Map Score: 7.77403 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 419 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 AACCGAAGTCAAGGAAGGTCTTAAGAAGGC 1 101 1 AAGGAAGGTC 0.864395 -174 AGGAAGGTCTTAAGAAGGCCTTTGGGAAAG 1 112 1 TAAGAAGGCC 0.918683 -163 GAAGGCCTTTGGGAAAGGACTCATCCCTAG 1 125 1 GGGAAAGGAC 0.901452 -150 AGTATTTTGTGGAAAAGGGCTGTTTTAACA 1 181 1 GGAAAAGGGC 0.986242 -94 TGCTGAACAAGCAGAAGGGCTCACTGAGAA 2 18 0 GCAGAAGGGC 0.95663 -283 GGAAGGCAATAGAAAAGGGCTGTATGCTGA 2 42 0 AGAAAAGGGC 0.983433 -259 AGGGCGGAATAAAAAATGGCAGAAATCCAA 2 105 0 AAAAAATGGC 0.85585 -196 AGATCCTTCTTAAAAAGGCCTACATCCAAA 3 21 0 TAAAAAGGCC 0.931957 -280 CTTAAATATAAAGAAAGGGGAATAAAAAGT 3 151 0 AAGAAAGGGG 0.87891 -150 ********** Masking position 5 Map Score: 5.51937 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 212 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 AAGAAGCTGTACCAACTCCTTGAAACTTAT 1 63 1 ACCAACTCCT 0.91819 -212 GCCCTTTTCCACAAAATACTTTGCCATTAA 1 171 0 ACAAAATACT 0.784855 -104 TCTCCAAATCAAAAACTTCTAGTATTCTTT 1 248 0 AAAAACTTCT 0.93804 -27 AAAAGTCGTGAAAAAATTTTGATTTCACGA 2 200 0 AAAAAATTTT 0.803407 -101 AACAATAAACACAAGCTTTTCAGAGGGTGA 2 278 1 ACAAGCTTTT 0.720686 -23 GAAACTCTATACAAACTTTTTATTCCCCTT 3 137 1 ACAAACTTTT 0.959768 -164 CATTAGTAAAAAAAACTCTTAAATATAAAG 3 168 0 AAAAACTCTT 0.927045 -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 6 CTTCCGAGACCTTTGGTGGTATACTCTTTT 2 67 1 CTTTGGTGGT 0.940085 -234 TACTTTAAATCTTCGTTGATTTGATCAACA 2 238 1 CTTCGTTGAT 0.97209 -63 GTTAAGTTTTCTTTGTTGATCAAATCAACG 2 251 0 CTTTGTTGAT 0.987231 -50 ACCCTAGATCCTTTGTACATCGAACGAAAA 3 107 1 CTTTGTACAT 0.938742 -194 TAAAAGGATCCTCTGTAGATGGGAGTAAAA 3 274 0 CTCTGTAGAT 0.960354 -27 ********** Masking position 2 Map Score: 1.65472 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 32 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 ATTATTTTCAGCAAAACAAGAAGCTGTACC 1 46 1 GCAAAACAAG 0.979382 -229 CTGTCTTCCAGCTAAACTAGGGATGAGTCC 1 141 0 GCTAAACTAG 0.979382 -134 AGGGCTGTATGCTGAACAAGCAGAAGGGCT 2 27 0 GCTGAACAAG 0.985991 -274 GCTTTCTCGTTATAAACAAGAAACCACCCT 3 82 1 TATAAACAAG 0.883765 -219 ********** Masking position 5 Map Score: 0.317584 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 50 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