AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iarcA_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 sodM 131 Superoxide Dismutase (Mn) #3 yhxB 151 Phosphomannomutase #4 CT296 108 hypothetical protein #5 CT552 300 hypothetical protein #6 fmu 124 RNA Methyltransferase #7 brnQ 149 Amino Acid (Branched) Transport #8 CT555 174 SWI/SNF family helicase #9 CT556 177 hypothetical protein #10 lpdA 208 Lipoamide Dehydrogenase #11 sdhC 25 Succinate Dehydrogenase #12 CT593.1 221 hypothetical protein-possible frameshift with CT593 #13 ycfH 84 PHP superfamily hydrolase #14 dsbD 152 Thio:disulfide Interchange Protein Motif number 1 TTCTTTGGATTTTTGTGCCTATCCCACTTT 3 10 1 TTTTTTGCCT 0.879532 -142 ACTTTAAGATTATTTCCGCCTATAAAAACCC 4 49 0 TATTTCGCCT 0.848713 -60 TACTTTCGAGTTTATTCGCCTAAATAAGTGA 4 86 1 TTTATCGCCT 0.752024 -23 TTTCTAACCCTTTTTTCTCTTAACTCTCTAT 5 155 1 TTTTTCTCTT 0.908945 -146 TAGCGGACTTTTTTTCCGCTTTTTTCTAAGA 5 198 1 TTTTTCGCTT 0.915511 -103 TTAGAGAAAGTCTTTTTTCCTGTCCCGTTCT 5 240 1 TCTTTTTCCT 0.884431 -61 TTCCTTTTCGCTTCCATCATCTC 6 3 1 CCTTTCGCTT 0.896925 -122 TGCTCGATAGTTTATTCTCTTCCCCAATAGG 6 41 1 TTTATCTCTT 0.634031 -84 TCTAATTCATCCTTTATTCTTTCCAAAGAAC 7 70 1 CCTTTTTCTT 0.77008 -80 AGAAGACACCTATCTACTCCTAAACACTCGT 8 100 1 TATCTCTCCT 0.766787 -75 AACACTCGTTCCTTTCTGCCTAGGTCATGCG 8 122 1 CCTTTTGCCT 0.85429 -53 AATGATTGACCTTTTATTCTTCTTTTTACGT 9 18 1 CTTTTTTCTT 0.746425 -160 TTACCTTGATTTTTTCCTCCTAGGAACTATA 9 50 1 TTTTTCTCCT 0.941512 -128 TCTTTGGGCCTTTTTATGGCTTCCATACTGC 9 138 0 TTTTTTGGCT 0.653919 -40 TCCTATTTTTTCTCTCCTGCTACCACTTCTC 10 22 1 TCTCTCTGCT 0.750982 -187 CTGAAGGACCTCTCTTTTCCTTTCCTAGAAA 10 103 1 TCTCTTTCCT 0.829607 -106 AACATTTCCTCTTCAATGAGTGT 10 196 0 CATTTCTCTT 0.693424 -13 GGAGAGAGAATTTTTTCTCTTCAG 11 12 1 TTTTTCTCTT 0.908945 -14 AAAAACAACTCTTCTGTTGTTTGATGATTTG 14 107 1 CTTCTTTGTT 0.326449 -46 AACACAACACTCTCTCCGGTTTAGCAAATCA 14 131 0 TCTCTCGGTT 0.669973 -22 ***** ***** Masking position 5 Map Score: 16.7277 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 597 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 CTTCTTAAGACCTTCCTTGACTTCGGTTCA 1 99 0 CCTTCCTTGA 0.788184 -176 AGGGATGAGTCCTTTCCCAAAGGCCTTCTT 1 123 0 CCTTTCCCAA 0.907938 -152 GGGAAAGGACTCATCCCTAGTTTAGCTGGA 1 135 1 TCATCCCTAG 0.790117 -140 AGCCATCCTAAAAAATAAGGTT 2 120 0 CCATCCTAAA 0.809679 -12 CCTGTCCCGTTCTTTCTCAAGAGCTTTTGT 5 258 1 TCTTTCTCAA 0.715395 -43 TAGTTTATTCTCTTCCCCAATAGGAGAAAG 6 48 1 TCTTCCCCAA 0.962653 -77 TTCTTCTAATTCATCCTTTATTCTTTCCAA 7 66 1 TCATCCTTTA 0.497242 -84 CATCCTTTATTCTTTCCAAAGAACTTCTGT 7 77 1 TCTTTCCAAA 0.737594 -73 GGCATATCATCCTTCCCAAGTCACAGAAGT 7 99 0 CCTTCCCAAG 0.875691 -51 TTGTTTGAAGCCATCCCTTACTGAATAAGT 8 26 1 CCATCCCTTA 0.7951 -149 AAGACGATACCCCTCCCGAATTATAGTTCC 9 72 0 CCCTCCCGAA 0.739131 -106 CCTCTCTTTTCCTTTCCTAGAAAGGCTTGG 10 111 1 CCTTTCCTAG 0.7831 -98 AGGAGAATCCTCTTCCCTCAGATAATCATC 10 142 1 TCTTCCCTCA 0.941586 -67 TGAAAGGCTTCCATCCCTAATT 12 3 0 CCATCCCTAA 0.957189 -219 CCATAAAGAGCCCTCCTCAAACATCATGAT 12 84 0 CCCTCCTCAA 0.849045 -138 TGGTTCCTGCCCTTCCATAAAGAGCCCTCC 12 98 0 CCTTCCATAA 0.800847 -124 AGTACAAAAATCTTCCTACATTCGTTTCAT 12 171 1 TCTTCCTACA 0.754122 -51 TAAAAGGGCTTCTTCCTTCATGATCTTTGA 13 38 1 TCTTCCTTCA 0.880049 -47 TCATAATCAATCTTTCTCAATCAAAGATCA 13 58 0 TCTTTCTCAA 0.715395 -27 ACTTCCCTCATAATCAATCT 13 75 0 ACTTCCCTCA 0.694012 -10 ********** Masking position 4 Map Score: 14.4211 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 484 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 GTCCTTTCCCAAAGGCCTTCTTAAGACCTTC 1 114 0 AAAGGCTTCT 0.899978 -161 GGCCTTTGGGAAAGGACTCATCCCTAGTTTA 1 128 1 AAAGGCTCAT 0.562952 -147 ATTTTGTGGAAAAGGGCTGTTTTAACAACTG 1 184 1 AAAGGCTGTT 0.832102 -91 CTCTCCAAATCAAAAACTTCTAGTATTCTTT 1 248 0 CAAAACTTCT 0.704104 -27 CCTCGTGCGACAAAAACTTTTTCTAACCCTT 5 136 1 CAAAACTTTT 0.596088 -165 AAAGCGGAAAAAAAGTCCGCTAAAGATTTCT 5 189 0 AAAAGCCGCT 0.727072 -112 GGTTGTTAGAGAAAGTCTTTTTTCCTGTCCC 5 235 1 GAAAGCTTTT 0.657707 -66 CGTTCTTTCTCAAGAGCTTTTGTTCGGATTG 5 265 1 CAAGACTTTT 0.806367 -36 GGATTGCGTAAAAGGACTCCT 5 290 1 AAAGGCTCCT 0.936013 -11 GAATTAGAAGAAACGTCCGTTAGCCCTCGTC 7 47 0 AAACGCCGTT 0.724413 -103 TATTCTTTCCAAAGAACTTCTGTGACTTGGG 7 84 1 AAAGACTTCT 0.86069 -66 CCGGGCAAAAGAACATCCCTTACTTATTCAG 8 46 0 GAACACCCTT 0.567629 -129 TGTCTTCTCGCAACATCCCCTTGTTTGCAAG 9 99 0 CAACACCCCT 0.757495 -79 TAAAAAGGCCCAAAGACTGTTAAAGAGGTGA 9 153 1 CAAAGCTGTT 0.70392 -25 GTATTTGTCTGAAGGACCTCTCTTTTCCTTT 10 95 1 GAAGGCCTCT 0.882031 -114 CTCCTCATATGAACGCCTCCTTATTCGCTGT 12 134 0 GAACGCTCCT 0.859591 -88 TTTTCCGCTAAAAGGGCTTCTTCCTTCATGA 13 30 1 AAAGGCTTCT 0.899978 -55 TGTATAGAACCAAGATCCTTTTTGGTATGTA 14 61 1 CAAGACCTTT 0.759178 -92 GCAAAAACAAAAACAACTCTTCTGTTGTTTG 14 99 1 AAACACTCTT 0.702038 -54 ***** ***** Masking position 11 Map Score: 13.4749 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 486 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 AAGGTGGCGAGGATAGTAACCTTATTTTTT 2 103 1 GGATAGTAAC 0.899997 -29 CCTTCCGATCAGAACGAAACACTCATCCAC 3 125 0 AGAACGAAAC 0.888198 -27 GAGTAGGATAAGAACGTAAGTTCTATAAGT 5 76 0 AGAACGTAAG 0.874831 -225 CTATCGTAGGAAAAAGCAACCTCGTGCGAC 5 117 1 AAAAAGCAAC 0.737766 -184 CCCCAATAGGAGAAAGCAACCGTGTAGCTG 6 62 1 AGAAAGCAAC 0.969881 -63 TCTTTTGCCCGGAAAGCAACCCAAAAAACG 8 65 1 GGAAAGCAAC 0.980899 -110 TGACCTAGGCAGAAAGGAACGAGTGTTTAG 8 119 0 AGAAAGGAAC 0.901436 -56 CGCAAGCATGGGAACGTAACAGAGATTGAT 8 151 1 GGAACGTAAC 0.976548 -24 AGAAAAAATAGGAACGTAAGAGTG 10 5 0 GGAACGTAAG 0.917665 -204 TGAGTGTTTAGGATTGCAACGATCCATATG 10 173 0 GGATTGCAAC 0.778844 -36 ********** Masking position 3 Map Score: 7.67411 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 56 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 AAGGTCTTAAGAAGGCCTTTGGGAAAGGACTC 1 115 1 GAGGCCTTTG 0.982891 -160 AGGAGTCCTTTTACGCAATCCGA 5 288 0 GGGTCCTTTA 0.892063 -13 CCAAGAGAGGGATGCTCTTTAAAGTACGCAGC 6 88 0 GAGCTCTTTA 0.917338 -37 TGACGGTCCTTCGAGCCAAGAGA 6 112 0 GAGGTCCTTG 0.920589 -13 CCAAGTCACAGAAGTTCTTTGGAAAGAATAAA 7 82 0 GAGTTCTTTG 0.968569 -68 ATAAGTAAGGGATGTTCTTTTGCCCGGAAAGC 8 50 1 GAGTTCTTTG 0.968569 -125 GTCTTCTAAAGGCGTTTTTTGGGTTGCTTTCC 8 75 0 GGGTTTTTTG 0.745525 -100 AAGGAAAAGAGAGGTCCTTCAGACAAATACAT 10 93 0 GAGTCCTTCG 0.957438 -116 ATTAGGGATGGAAGCCTTTCAGTTGAGGGATA 12 12 1 GAGCCTTTCG 0.845241 -210 GATGTTTGAGGAGGGCTCTTTATGGAAGGGCA 12 89 1 GAGGCTCTTA 0.667401 -133 CATGAAGGAAGAAGCCCTTTTAGCGGAAAATG 13 28 0 GAGCCCTTTA 0.954766 -57 ** ******* * Masking position 9 Map Score: 6.82628 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 126 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 CTATGCACGTTTCCCTGTCACCAGTTGTTAA 1 205 0 TTCCTGTCAC 0.976609 -70 ATTTGGCTCTCCAAATCAAAAAC 1 262 0 TTGCTCTCCA 0.946302 -13 CAATAAAATATTCACTGTCAAGAGCTATCCA 2 29 0 TTCCTGTCAA 0.954332 -103 AAAAACCCGATTGACTCTCAAGATTTTGTAT 4 26 0 TTGCTCTCAA 0.907621 -83 GAAAGTCTTTTTTCCTGTCCCGTTCTTTCTC 5 245 1 TTTCTGTCCC 0.911117 -56 TCCTGTCCCGTTCTTTCTCAAGAGCTTTTGT 5 257 1 TTCTTCTCAA 0.746262 -44 AGAGAAAAAATTCTCTCTCCC 11 1 0 TTCCTCTCCC 0.985133 -25 CGCCTCCTTATTCGCTGTCCCTCATGGTTCC 12 121 0 TTCCTGTCCC 0.985132 -101 *** ******* Masking position 6 Map Score: 7.26891 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 7 CCGATCAGAACGAAACACTCATCCACGCTC 3 121 0 CGAAACACTC 0.979737 -31 CCTTTTTTCTCTTAACTCTCTATCTAAGAA 5 163 1 CTTAACTCTC 0.908388 -138 CTATCTACTCCTAAACACTCGTTCCTTTCT 8 109 1 CTAAACACTC 0.988014 -66 CGTTGCAATCCTAAACACTCATTGAAGAGG 10 182 1 CTAAACACTC 0.988014 -27 AAACACAACACTCTCTCCGGTTT 14 140 0 CACAACACTC 0.950338 -13 ********** Masking position 5 Map Score: 3.2534 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 CCCTACTTTAAAGCAACGAATTCTTTTAATG 5 27 1 AAGAACGAAT 0.975508 -274 CCTAGGCAGAAAGGAACGAGTGTTTAGGAGT 8 115 0 AAGAACGAGT 0.970614 -60 AAAAAGAAATGATTGACCTTTTAT 9 4 1 AAGAATGATT 0.854288 -174 ACATCATATAATGAAACGAATGTAGGAAGAT 12 180 0 ATGAACGAAT 0.955264 -42 ACATCCCGATACGGAATGAATACATCATATA 12 201 0 ACGAATGAAT 0.89679 -21 ACGTAGACCTAACCAACGAGTTCCTAGACGA 14 15 1 AACAACGAGT 0.863938 -138 CCTTTTTGGTATGTAATGAATTGCAAAAACA 14 77 1 ATGAATGAAT 0.911795 -76 *** ******* Masking position 6 Map Score: 1.42808 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 52 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 GCTAGGGTTATCTTATATAG 1 1 0 TCTTATATAG 0.803821 -274 TGGTACAGCTTCTTGTTTTGCTGAAAATAA 1 47 0 TCTTGTTTTG 0.829567 -228 AGCAACGAATTCTTTTAATGAGTCTTCGTA 5 38 1 TCTTTTAATG 0.798644 -263 TTTTAATGAGTCTTCGTATGCTTACCACTT 5 50 1 TCTTCGTATG 0.776234 -251 CTTATCCTACTCTTTGTTTGGATCTATCGT 5 94 1 TCTTTGTTTG 0.80831 -207 GCTAAAGATTTCTTAGATAGAGAGTTAAGA 5 172 0 TCTTAGATAG 0.793041 -129 ACGGTTGCTTTCTCCTATTGGGGAAGAGAA 6 55 0 TCTCCTATTG 0.794789 -70 TAGATAGGTGTCTTCTAAAGGCGTTTTTTG 8 86 0 TCTTCTAAAG 0.828471 -89 TCCTTCATGATCTTTGATTGAGAAAGATTG 13 51 1 TCTTTGATTG 0.90303 -34 CTAACAAATTTCTTGTATAGAACCAAGATC 14 48 1 TCTTGTATAG 0.863721 -105 CAAAAACAACTCTTCTGTTGTTTGATGATT 14 106 1 TCTTCTGTTG 0.845262 -47 ********** Masking position 3 Map Score: 2.7296 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 204 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 TCTTAAAGTCTATAGTACTTTCGAGTTTAT 4 71 1 TATAGTACTT 0.945998 -38 GCTTACCACTTATAGAACTTACGTTCTTAT 5 69 1 TATAGAACTT 0.924388 -232 GCCCTCGTCCTATAGTACCTGCACTGATGG 7 26 0 TATAGTACCT 0.97529 -124 CCTCCCGAATTATAGTTCCTAGGAGGAAAA 9 61 0 TATAGTTCCT 0.923057 -117 AAATTTCTTGTATAGAACCAAGATCCTTTT 14 53 1 TATAGAACCA 0.893303 -100 ********** Masking position 4 Map Score: 0.846156 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 AGCTAGCCTGTAGAAAATAGAGAAGGTGGC 2 81 1 TAGAAAATAG 0.951741 -51 AGCCATCCTAAAAAATAAGGTTACTATC 2 114 0 TAAAAAATAA 0.681314 -18 TTGCTTAACTTAGAAAGTGGGATAGGCACA 3 24 0 TAGAAAGTGG 0.784773 -128 TTTGTATTCTTAAAAAATAGTT 4 3 0 TAAAAAATAG 0.925189 -106 GGATCTATCGTAGGAAAAAGCAACCTCGTG 5 113 1 TAGGAAAAAG 0.737485 -188 AGAGAGTTAAGAGAAAAAAGGGTTAGAAAA 5 154 0 GAGAAAAAAG 0.852772 -147 CAGGAAATCTTAGAAAAAAGCGGAAAAAAA 5 206 0 TAGAAAAAAG 0.930895 -95 GATAAAAAATGATAATTTTTAC 7 138 0 TAAAAAATGA 0.478964 -12 AGGTAATACGTAAAAAGAAGAATAAAAGGT 9 26 0 TAAAAAGAAG 0.784117 -152 TAGCAGGAGAGAAAAAATAGGAACGTAAGA 10 14 0 GAAAAAATAG 0.841712 -195 ********** Masking position 5 Map Score: 3.02375 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 257 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: 4.35095e-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 13 AAAGTATTTTGTGGAAAAGGGCTGTTTTAAC 1 179 1 GTGGAAAGGG 0.95043 -96 TTGGTAGAGCGTGGATGAGTGTTTCGTTCTG 3 115 1 GTGGAGAGTG 0.95043 -37 GCAGGTACTATAGGACGAGGGCTAACGGACG 7 34 1 TAGGAGAGGG 0.98143 -116 TAATTTTTACTTATAAGAGGGCATATCATCC 7 117 0 TTATAGAGGG 0.698466 -33 AAATCTCAATGAGGAGAAGTGGTAGCAGGAG 10 35 0 GAGGAAAGTG 0.814315 -174 CATCATGATGTTTGAGGAGGGCTCTTTATGG 12 83 1 TTTGAGAGGG 0.96239 -139 GAGGCGTTCATATGAGGAGGGAGATAGTACA 12 146 1 TATGAGAGGG 0.96239 -76 GAGAAAGATTGATTATGAGGGAAGT 13 70 1 GATTAGAGGG 0.902756 -15 ***** ***** Masking position 5 Map Score: 3.83913 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 108 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 14 ********** No masking Map Score: 4.35095e-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 15 ********** No masking Map Score: 4.35095e-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