AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i139_NADH_Oxidoreductase_ctra_reg_300.orf -o139_ctra_300.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/amcguire/genomes/ctra.fna -g0.41 -x5 -e 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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCT00265 300 Chlamydia_trachomatis #2 RCT00604 21 Chlamydia_trachomatis #3 RCT00605 113 Chlamydia_trachomatis #4 RCT00710 142 Chlamydia_trachomatis #5 RCT00711 104 Chlamydia_trachomatis #6 RCT00712 250 Chlamydia_trachomatis #7 RCT00713 300 Chlamydia_trachomatis Motif number 1 CATCGCCGCCAACAAGATAGACAAATCTCT 1 65 1 AACAAGATAG 0.967122 -236 GTAAAGCTCCAGGAAGAGAGATTTGTCTAT 1 81 0 AGGAAGAGAG 0.955499 -220 TTCCGGACTAAAAAGGGGAGCCATC 3 6 0 AAAAGGGGAG 0.779341 -108 TACGCCGAATAACAAAAAAGAGCAATATTA 3 39 1 AACAAAAAAG 0.795503 -75 CATCACAAAAAACAAGAAAAATTTTATTAT 3 69 1 AACAAGAAAA 0.895346 -45 AACAAGAAAGCCTTATTCCT 5 1 1 AACAAGAAAG 0.973148 -104 AGGTTAACACAGGAAGATAGGGGGATCAAT 5 54 0 AGGAAGATAG 0.901604 -51 ATTAGGGTTAAAAAGGATAGGTTAACACAG 5 72 0 AAAAGGATAG 0.917416 -33 GCCCTCTATAAAAAAGAGAAAGCGCTAAAA 6 13 0 AAAAAGAGAA 0.910446 -238 GATCAATGAGAAGAGGAAAGAGGGCCCTGT 6 53 0 AAGAGGAAAG 0.918627 -198 GGATAACAAAAAAAAGAGAAGGGATCAATG 6 75 0 AAAAAGAGAA 0.910446 -176 CAGTTACGATAGCAGGAGAGCAACTTGAAT 6 191 0 AGCAGGAGAG 0.961808 -60 GAATCTTCTAACAAGAGAACAAGCTCCTT 7 10 1 AACAAGAGAA 0.942103 -291 TGTTTAGAAAAGAAAGAAAGGAGCTTGTTC 7 27 0 AGAAAGAAAG 0.931909 -274 ATTAAAACTGAAAAAAATAGTTTAAAACAA 7 261 1 AAAAAAATAG 0.66361 -40 ********** Masking position 4 Map Score: 21.3731 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 509 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 2 CAACAAGATAGACAAATCTCTCTTCCTGGA 1 74 1 GACAAATCTC 0.924231 -227 TTTGTTATTCGACAAATATTTCCGGTCCTT 1 121 0 GACAAATATT 0.9634 -180 TTTGTCGAATAACAAATATTAGAATCCTAT 1 135 1 AACAAATATT 0.867035 -166 TTTTTATTCGTAAAAATTTTAATAATTTGT 1 177 1 TAAAAATTTT 0.702355 -124 TTCAAAACGTAACAAATTATTAAAATTTTT 1 188 0 AACAAATTAT 0.681437 -113 AAAGGGAATCGACAAGTTTTTCGAGCATTG 1 249 0 GACAAGTTTT 0.868611 -52 TTGCTTTTACGACAAATTTTCCAAAGGGAA 1 271 0 GACAAATTTT 0.974601 -30 CAAAAAACAAGAAAAATTTTATTATTAAAT 3 74 1 GAAAAATTTT 0.95793 -40 TCCTTTGGAGGAAAAACCTTTCACTTTCTT 6 157 1 GAAAAACCTT 0.700683 -94 TCTGTTAATAGAAAAATTTTTTATAAAACT 7 110 0 GAAAAATTTT 0.95793 -191 ATTAACAGAGGAAAAATAACCTATTGATAA 7 131 1 GAAAAATAAC 0.673226 -170 GAAAAAATATCCTCTAGTTGT 7 290 0 AAAAAATATC 0.694349 -11 ********** Masking position 5 Map Score: 9.46224 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 179 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 CAAATGCAGCAAAGGACCGGAAATATTTGT 1 110 1 AAAGGACCGG 0.95811 -191 GGCTTTGCTGAAAGGAGCTCGTTT 4 5 0 AAAGGAGCTC 0.969814 -138 AAGCAAAGCCCAAGGACCTGGGCTTTGCTG 4 25 0 CAAGGACCTG 0.987818 -118 CTTTTATTTGCAAGGACTTGCCTTTGCGAG 6 113 0 CAAGGACTTG 0.917226 -138 TTTTTCCTCCAAAGGAGGTGTGAGGTTGTA 6 143 0 AAAGGAGGTG 0.969811 -108 GAAAAGAAAGAAAGGAGCTTGTTCTCTTGT 7 21 0 AAAGGAGCTT 0.974502 -280 CAGAGCGGTACAAGGAGATGTCAAATAAAG 7 162 1 CAAGGAGATG 0.95504 -139 TAAGGATCCTAAAGCAGCTTTATTTGACAT 7 179 0 AAAGCAGCTT 0.863504 -122 ********** Masking position 6 Map Score: 8.14329 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 211 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 4 ATATTCAACGTTTCTAAACACCTAGTACAA 1 11 1 TTTCTAAACA 0.904549 -290 ATATTAGAATCCTATAAACAACCGAGTTTT 1 150 1 CCTATAAACA 0.887827 -151 AACGTAACAAATTATTAAAATTTTTACGAA 1 183 0 ATTATTAAAA 0.651284 -118 TATAGGTTACTCTATAAAAAATCAACGGAG 4 78 0 TCTATAAAAA 0.952818 -65 AATTATAAAAATCCCTGGAAT 4 132 0 ATTATAAAAA 0.83988 -11 AAAAGTGCCCTCTATAAAAAAGAGAAAGCG 6 19 0 TCTATAAAAA 0.952818 -232 AGAGGGCACTTTTATCAACAGGGCCCTCTT 6 36 1 TTTATCAACA 0.851376 -215 TGCTATCGTAACTGTAAACATTTTGGCGTC 6 207 1 ACTGTAAACA 0.717597 -44 CTTTCTTTCTTTTCTAAACAAGGTTCAGCG 7 37 1 TTTCTAAACA 0.904549 -264 TTCAGCGCTTTCTATTAAAAGAAACCCTAT 7 60 1 TCTATTAAAA 0.878893 -241 AGCACATAGTTTTATAAAAAATTTTTCTAT 7 103 1 TTTATAAAAA 0.927123 -198 AAAAAATTTTTCTATTAACAGAGGAAAAAT 7 118 1 TCTATTAACA 0.931002 -183 AAATAACCTATTGATAAACAGAGCGGTACA 7 144 1 TTGATAAACA 0.812467 -157 ********** Masking position 7 Map Score: 13.0659 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 112 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 TATTTCCGGTCCTTTGCTGCATTTGTAAAGC 1 104 0 CCTTTGCGCA 0.985936 -197 TTGTCGATTCCCTTTGGAAAATTTGTCGTAA 1 264 1 CCTTTGGAAA 0.93889 -37 AAGGACCTGGGCTTTGCTGAAAGGAGCTCGT 4 13 0 GCTTTGCGAA 0.914881 -130 GGGGATCAATCCTTTTCCAGAAGGAACAGCA 5 33 0 CCTTTTCAGA 0.971545 -72 CAAGGACTTGCCTTTGCGAGAACGGAAAGGA 6 102 0 CCTTTGCAGA 0.990492 -149 CCTCACACCTCCTTTGGAGGAAAAACCTTTC 6 148 1 CCTTTGGGGA 0.976107 -103 CTCCTTTCTTTCTTTTCTAAACAAGGTTCAG 7 34 1 TCTTTTCAAA 0.648641 -267 CTATTCAGACCCTATGCAGCACATAGTTTTA 7 86 1 CCTATGCGCA 0.917021 -215 TTCATGCAACCATTTTCTAGAATCTAGGTAA 7 206 0 CATTTTCAGA 0.769972 -95 ******* *** Masking position 5 Map Score: 6.93679 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 142 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 CATTAGGAATAAGGCTTTCTTGTT 5 5 0 AAGGCTTTCT 0.944314 -100 TATTTTAGCGCTTTCTCTTTTTTATA 6 7 1 AGCGCTTTCT 0.988767 -244 TGTTGATAAAAGTGCCCTCTATAAAAAAGA 6 26 0 AGTGCCCTCT 0.972623 -225 TTTTATCAACAGGGCCCTCTTTCCTCTTCT 6 45 1 AGGGCCCTCT 0.988759 -206 AACAAGGTTCAGCGCTTTCTATTAAAAGAA 7 53 1 AGCGCTTTCT 0.988767 -248 ********** Masking position 8 Map Score: 4.7577 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 39 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 AGGTGTTTAGAAACGTTGAATAT 1 4 0 AAACGTTGAA 0.898064 -297 TCTCTTCCTGGAGCTTTACAAATGCAGCAA 1 92 1 GAGCTTTACA 0.897701 -209 TACACGTTCAAAACGTAACAAATTATTAAA 1 194 0 AAACGTAACA 0.815578 -107 GAAAGGTTGAGAACGTTACACGTTCAAAAC 1 210 0 GAACGTTACA 0.960299 -91 CCTTGTAATAAAACTTTAAAAAACTCCGTT 4 55 1 AAACTTTAAA 0.78063 -88 AAAAAAGAGAAAGCGCTAAAATA 6 4 0 AAGCGCTAAA 0.9432 -247 TTTTAATAGAAAGCGCTGAACCTTGTTTAG 7 50 0 AAGCGCTGAA 0.903877 -251 TTGATAAACAGAGCGGTACAAGGAGATGTC 7 154 1 GAGCGGTACA 0.933459 -147 ********** Masking position 2 Map Score: 1.58101 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 121 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 GGACTAAAAAGGGGAGCCATC 3 2 0 GGGGAGCCAT 0.973995 -112 GAATAACAAAAAAGAGCAATATTACATCAC 3 45 1 AAAGAGCAAT 0.777088 -69 AGGAAGATAGGGGGATCAATCCTTTTCCAG 5 44 0 GGGGATCAAT 0.984507 -61 AAAAAAGAGAAGGGATCAATGAGAAGAGGA 6 66 0 AGGGATCAAT 0.956666 -185 TACGATAGCAGGAGAGCAACTTGAATCCTA 6 187 0 GGAGAGCAAC 0.982218 -64 TTGAGGAGATGAACAGCCTCCACA 6 237 0 GGAGATGAAC 0.889641 -14 ********** Masking position 5 Map Score: 1.28563 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 83 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 ATATTCAACGTTTCTAAACA 1 1 1 ATATTCAACG 0.935494 -300 AATTTGTTACGTTTTGAACGTGTAACGTTC 1 200 1 GTTTTGAACG 0.837958 -101 CGTAAAAGCAAATTTCAACAC 1 290 1 AATTTCAACA 0.944626 -11 TACTCTATAAAAAATCAACGGAGTTTTTTA 4 71 0 AAAATCAACG 0.869715 -72 AAATCCCTGGAATTTCAACGAGACTGTAGC 4 115 0 AATTTCAACG 0.980577 -28 TGGTTGCATGAATTTGAACAAACAAACTAA 7 225 1 AATTTGAACA 0.899157 -76 ********** Masking position 5 Map Score: 0.981533 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 42 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 CTCGGTTGTTTATAGGATTCTAATATTTGT 1 146 0 TATAGGATTC 0.976754 -155 AGCGTCAAGTTATAGGTTACTCTATAAAAA 4 88 0 TATAGGTTAC 0.904127 -55 TTTCACTTTCTTTAGGATTCAAGTTGCTCT 6 175 1 TTTAGGATTC 0.976754 -76 ATAAAGCTGCTTTAGGATCCTTACCTAGAT 7 186 1 TTTAGGATCC 0.972464 -115 ********** Masking position 4 Map Score: 0.808072 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 TCTAATATTTGTTATTCGACAAATATTTCCG 1 127 0 GTTATTCGCA 0.98345 -174 AACCGAGTTTTTTATTCGTAAAAATTTTAAT 1 169 1 TTTATTCGAA 0.960678 -132 GCTCTTTTTTGTTATTCGGCGTATATTTCCG 3 31 0 GTTATTCGCG 0.963989 -83 AGGTTGTACTTTTATTTGCAAGGACTTGCCT 6 120 0 TTTATTTGAA 0.915564 -131 CTAAAGCAGCTTTATTTGACATCTCCTTGTA 7 170 0 TTTATTTGCA 0.960678 -131 ******** ** Masking position 6 Map Score: 0.308627 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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: 8.12451e-13 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 ********** No masking Map Score: 8.12451e-13 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 14 ********** No masking Map Score: 8.12451e-13 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