AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_ctra_reg_300.orf -o207_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 Purged sequences: RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCT00037 281 Chlamydia_trachomatis #2 RCT00184 126 Chlamydia_trachomatis #3 RCT00185 300 Chlamydia_trachomatis #4 RCT00476 19 Chlamydia_trachomatis #5 RCT00477 107 Chlamydia_trachomatis #6 RCT00478 286 Chlamydia_trachomatis #7 RCT00480 43 Chlamydia_trachomatis #8 RCT00481 65 Chlamydia_trachomatis #9 RCT00482 20 Chlamydia_trachomatis #10 RCT00483 21 Chlamydia_trachomatis #11 RCT00484 55 Chlamydia_trachomatis #12 RCT00485 22 Chlamydia_trachomatis #13 RCT00488 21 Chlamydia_trachomatis #14 RCT00489 27 Chlamydia_trachomatis #15 RCT00493 16 Chlamydia_trachomatis #16 RCT00495 32 Chlamydia_trachomatis #17 RCT00497 18 Chlamydia_trachomatis #18 RCT00499 23 Chlamydia_trachomatis #19 RCT00502 300 Chlamydia_trachomatis Motif number 1 TATCTATATTTCTAGGAAAAGACTTTAGTTAGA 1 31 1 TCTGAAAAGC 0.982334 -251 CATGTGCAATTGTATGAAAAGACGCAACTTTTT 1 95 1 TGTGAAAAGC 0.950282 -187 GAAAAAAACCTCTGCACAAAGGCATTAAAAAGT 1 121 0 TCTACAAAGC 0.968853 -161 GAGGTTTTTTTCTTTAAATAGTCTTTTATATAG 1 142 1 TCTAAATAGC 0.852588 -140 GAAAAGACATAGTGAAAAAAGCCCGAAGAAAAC 2 32 0 AGTAAAAAGC 0.934296 -95 CTAAAGAGAGAGGGAGAAAAGACATAGTGAAAA 2 47 0 AGGGAAAAGC 0.897524 -80 AGAGTCCTTCACTATAAAAAGATACTTTACAAA 3 129 0 ACTAAAAAGT 0.686194 -172 TTTTACGAAAACGACAAAAAGTCTTCCGAGACT 3 170 0 ACGAAAAAGC 0.968724 -131 TTTGTCGTTTTCGTAAAAAAGTCTCTTAATAGA 3 185 1 TCGAAAAAGC 0.980623 -116 AGCGACACATTCGGTCTAAAGTCTCGCCAAATC 3 233 0 TCGCTAAAGC 0.78593 -68 TTATATAAAGACTCTTAAAAGTCGTCTATTAGC 3 263 0 ACTTAAAAGC 0.867048 -38 AAATCAGGAATCTCCCAAAAGGCTTTACTA 5 8 0 TCTCAAAAGC 0.976924 -100 AAGACGCGAGTGTTAAGAAAGGC 5 95 1 TGTAGAAAGC 0.79954 -13 ATGTTAAAGTTCTAAAAAAAAGCAATGAACTTC 6 11 0 TCTAAAAAAC 0.870871 -276 CATTCCACCATCTGAGCAAAAACGACGAGGACC 6 114 0 TCTGCAAAAC 0.718565 -173 TCGAACTTGCACGGGCCAAAGCCCAAGGGATTT 6 165 0 ACGCCAAAGC 0.899269 -122 *** ****** * Masking position 8 Map Score: 14.7269 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 201 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 2 TCTCGACTGTTTGTTATCTATATTTCTAGGAAA 1 17 1 TTTTCTATAT 0.892746 -265 CTAACTAAAGTCTTTTCCTAGAAATATAGATAA 1 30 0 TCTTCTAGAA 0.885854 -252 TGTGCAGAGGTTTTTTTCTTTAAATAGTCTTTT 1 136 1 TTTTCTTTAA 0.810287 -146 CTAATCCTTCTTTTTCTCTATATAAAAGACTAT 1 159 0 TTTTCTATAT 0.892743 -123 TAAACAAGAGTCCTTCACTATAAAAAGATACTT 3 135 0 TCTTCTATAA 0.976309 -166 GCCCTTCTCCGTTCTTTATATAAAGACTCTT 3 280 0 CCTTTTATAT 0.512341 -21 TCGTTAGTAACCCTTTCCTTTATTGTGTAAAAT 5 40 1 CCTTCTTTAT 0.834742 -68 TCGCGTCTTGTCATTTTCTATATTTGTGCAAAT 5 71 0 TCTTCTATAT 0.959191 -37 TAAATAGCTCTCCTCATCTATAAATCAAAAAGG 6 246 0 TCTCCTATAA 0.922849 -41 CCCAAACTCCTTAGCTATAA 9 1 0 TCTTCTATAA 0.976307 -20 AACACTCTCTCCTAAAAATTA 10 5 0 CTTCCTAAAA 0.499663 -17 AAACTTTACCTAAAAGTTCTAG 12 8 0 ACTTCTAAAA 0.65055 -15 TTCGCCGCCTTTGTTTGCTTTAAGGAGCCGCGT 19 158 1 TTTTCTTTAA 0.810288 -143 GAGGGCATGGCCGTTTGCTAAAAGTGTAATTAG 19 224 1 CCTTCTAAAA 0.906674 -77 ** ** ****** Masking position 12 Map Score: 9.62093 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 224 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 GAAGAAAACCTTTGTCTTCGGACTCACCCA 2 6 0 TTTGCCGGAC 0.990782 -121 GGATTAGGCGGAGGATCCGAGGCATGGG 3 4 1 TTAGCAGGAC 0.985581 -297 AAACAAGGAATTAGCCGTCAGACACCCATGCCTCG 3 28 0 TTAGCCAGAC 0.98558 -273 CTTGTTTTCATTTGTCAGAAGAAACGAAGCTTACA 3 56 1 TTTGCAAGAC 0.99114 -245 AAAAGGTATTATTGTCTCAAGAACCAGAGAAAAAA 6 217 0 ATTGCAAGAC 0.95249 -70 AATAACAATTTTTGACCTAAGATGCTTATATTACT 11 13 1 TTTGCAAGAC 0.99114 -43 GCCGCCTTTGTTTGCTTTAAGGAGCCGCGTTTTCT 19 161 1 TTTGTAAGGC 0.876148 -140 AAAAGTGTAATTAGGCACCGGGGGCGGTCTGTGAA 19 243 1 TTAGCCGGGC 0.974319 -58 **** * **** * Masking position 2 Map Score: 6.63632 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 31 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 AGACTTTAGTTAGAAAAAAAAGAGATAAAA 1 50 1 TAGAAAAAAA 0.911438 -232 AGACTATTTAAAGAAAAAAACCTCTGCACA 1 136 0 AAGAAAAAAA 0.893086 -146 GTCTTTTATATAGAGAAAAAGAAGGATTAG 1 162 1 TAGAGAAAAA 0.960184 -120 AGAAAAGACATAGTGAAAAAAGCCCGAAGA 2 36 0 TAGTGAAAAA 0.77238 -91 CATTTGTCAGAAGAAACGAAGCTTACAGTG 3 64 1 AAGAAACGAA 0.865658 -237 TCTCAAGAACCAGAGAAAAAAGATGTGCTC 6 208 0 CAGAGAAAAA 0.898144 -79 TGCAACACGCTAGAAAAAAATTTAGGGTTG 8 20 1 TAGAAAAAAA 0.911438 -46 GCAACGGTTATGAGACGAAGTACGACCAA 8 47 0 ATGAGACGAA 0.679959 -19 AGGGTAAAGTAGAGTCGAACT 13 10 1 TAGAGTCGAA 0.72357 -12 TAAAGAAGGAAGAGAAGAATAAC 18 10 1 AAGAGAAGAA 0.954969 -14 ********** Masking position 9 Map Score: 6.39683 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 263 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 TTTCTAGGAAAAGACTTTAGTTAGAAAAAA 1 39 1 AAGACTTTAG 0.871181 -243 AAAAAGAGATAAAACTCTCAACACTACAGC 1 66 1 AAAACTCTCA 0.677935 -216 AAGCCCGAAGAAAACCTTTGTCTTCGGACT 2 17 0 AAAACCTTTG 0.713075 -110 TTTATAGTGAAGGACTCTTGTTTAAGAGTC 3 144 1 AGGACTCTTG 0.949464 -157 AAAGTCTTCCGAGACTCTTAAACAAGAGTC 3 156 0 GAGACTCTTA 0.88073 -145 TTTCGTAAAAAAGTCTCTTAATAGATAGTC 3 193 1 AAGTCTCTTA 0.914052 -108 TAGATTTGGCGAGACTTTAGACCGAATGTG 3 231 1 GAGACTTTAG 0.662505 -70 TCTTTATATAAAGACTCTTAAAAGTCGTCT 3 269 0 AAGACTCTTA 0.962179 -32 AAAAACGACGAGGACCCTAAAGAGTCCTCG 6 100 0 AGGACCCTAA 0.832225 -187 AAGGGATTTTAAGTCCCTAGTGTCTACCAT 6 144 0 AAGTCCCTAG 0.878512 -143 TAGGGACTTAAAATCCCTTGGGCTTTGGCC 6 155 1 AAATCCCTTG 0.800306 -132 TGCTCAGAACAAGACTCGAACTTGCACGGG 6 183 0 AAGACTCGAA 0.70338 -104 CTAGAACTTTTAGGTAAAGTTT 12 3 1 AGAACTTTTA 0.518022 -20 GCGTCAAGAAAAATCTCTTGTGTGGATGTC 19 106 1 AAATCTCTTG 0.858036 -195 ********** Masking position 5 Map Score: 5.9828 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 401 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 ATAGGGGAATCCCTCTTGACTTCAGCCGCTG 1 194 1 CCCTCTGACT 0.939321 -88 TGTCTTTTCTCCCTCTCTCTTTAGAATGATT 2 56 1 CCCTCCTCTT 0.894313 -71 AGCCGTCAGACACCCATGCCTCGGATCCTCC 3 20 0 CACCCTGCCT 0.975997 -281 TTTCGTTAGTAACCCTTTCCTTTATTGTGTA 5 38 1 AACCCTTCCT 0.815084 -70 CCTTTCTTAACACTCGCGTCTTGTCATTTTC 5 86 0 CACTCCGTCT 0.915367 -22 GAAGTTCTAGCACGCACGACTGGAAAAGCTA 6 55 0 CACGCCGACT 0.854406 -232 AACACTCTCTCCTAAAAATTA 10 9 0 CACTCCTCCT 0.983802 -13 AACCTGTCTCCTTATGAC 17 7 0 ACCTGCTCCT 0.817422 -12 AACGGCCATGCCCTCCATCCTGCAAGAGCGA 19 208 0 CCCTCATCCT 0.937436 -93 CACAGACCGCCCCCGGTGCCTAATTACACTT 19 245 0 CCCCGTGCCT 0.945472 -56 ***** ***** Masking position 11 Map Score: 3.53158 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 176 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 GATGTCAAAATACGATTTCTTGATTTGGAT 1 228 1 TACGATTTCT 0.90979 -54 TAACTACTATTGCGAATACTTAT 1 269 1 TGCGAATACT 0.753116 -13 CCTTTATCTAAGCGAATTCTAAAAAAATAA 2 98 0 AGCGAATTCT 0.952826 -29 TCTATATTTGTGCAAATTTTACACAATAAA 5 58 0 TGCAAATTTT 0.755657 -50 TGATGCTAATTTTTCGAAAACAC 7 4 1 TGCTAATTTT 0.636871 -40 AAAATAACAATTTTTGACCTAAGAT 11 6 1 AACAATTTTT 0.520816 -50 TAAAACCTAGAACGATTTTTCAGGCTTTGT 19 47 1 AACGATTTTT 0.863411 -254 GCTTTGTTTTTGCGATTTTTGGTGTGGGAT 19 70 1 TGCGATTTTT 0.968091 -231 ATTTTTGGTGTGGGATTTCTTAGCGTCAAG 19 84 1 TGGGATTTCT 0.840567 -217 CATCCACACAAGAGATTTTTCTTGACGCTA 19 104 0 AGAGATTTTT 0.688075 -197 ATCCTGCAAGAGCGATTTCCACGACAAAGA 19 193 0 AGCGATTTCC 0.865803 -108 ********** Masking position 5 Map Score: 3.43645 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 332 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 8 AAAGACTTTAGTTAGAAAAAAAAGAGATAA 1 48 1 GTTAGAAAAA 0.854033 -234 TGGGTGAGTCCGAAGACAAAGGTTTTC 2 8 1 GTCCGAAGAC 0.935872 -119 AGTGAAAAAAGCCCGAAGAAAACCTTTGTC 2 25 0 GCCCGAAGAA 0.982977 -102 GTTTTCATTTGTCAGAAGAAACGAAGCTTA 3 59 1 GTCAGAAGAA 0.97791 -242 AGGTATTATTGTCTCAAGAACCAGAGAAAA 6 219 0 GTCTCAAGAA 0.855695 -68 TATGCAACACGCTAGAAAAAAATTTAGGGT 8 18 1 GCTAGAAAAA 0.876016 -48 CAAAAACAAAGCCTGAAAAATCGTTCTAGG 19 52 0 GCCTGAAAAA 0.947574 -249 ********** Masking position 6 Map Score: 1.84448 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 97 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 AAGAAGGATTAGAGATAGGGGAATCCCTCT 1 180 1 AGAGATAGGG 0.978089 -102 ATCATTCTAAAGAGAGAGGGAGAAAAGACA 2 56 0 AGAGAGAGGG 0.97967 -71 TTATAGCTAAGGAGTTTGGG 9 11 1 GGAGTTTGGG 0.889387 -10 TAATTTTTAGGAGAGAGTGTT 10 10 1 GGAGAGAGTG 0.956639 -12 TGCAGATAGGTTATAAGGGTG 16 2 1 GCAGATAGGT 0.910993 -31 GTCATAAGGAGACAGGTT 17 8 1 GGAGACAGGT 0.963215 -11 ********** Masking position 3 Map Score: 0.714134 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 117 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 10 ********** No masking Map Score: 2.01384e-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 11 AATCTAATACCTCAGACTATCTATTAAGAGACT 3 204 0 CTCGAATCTA 0.904636 -97 GGTCTAAAGTCTCGCCAAATCTAATACCTCAGA 3 221 0 CTCCCATCTA 0.987736 -80 CTAAAGAGTCCTCGCCACAGCTTTACAAGAAGT 6 81 0 CTCCCAGCTT 0.969942 -206 GAGTCTTGTTCTGAGCACATCTTTTTTCTCTGG 6 196 1 CTGGCATCTT 0.971174 -91 AGTTAAATAGCTCTCCTCATCTATAAATCAAAA 6 249 0 CTCCCATCTA 0.987736 -38 AGCTATTTAACTCGGGGTATCTTTTTG 6 270 1 CTCGGATCTT 0.948206 -17 TCGTTACCGTCCTAATCTTTTAATTTG 14 9 0 CCGCCATCTT 0.931584 -19 *** ** ***** Masking position 9 Map Score: 1.32389 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 12 ********** No masking Map Score: 2.01384e-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: 2.01384e-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: 2.01384e-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