AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_ctra_reg_300.orf -o224_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 TCTAACTAAAGTCTTTTCCTAGAAATATAGATA 1 31 0 GCTTTTTAGA 0.974545 -251 AAAAAGTTGCGTCTTTTCATACAATTGCACATG 1 95 0 GCTTTTTACA 0.916067 -187 ACTTTTTAATGCCTTTGTGCAGAGGTTTTTTTC 1 121 1 GCTTTGCAGA 0.973517 -161 GTTTTCTTCGGGCTTTTTTCACTATGTCTTTTC 2 32 1 GCTTTTCACT 0.940343 -95 TTTTCACTATGTCTTTTCTCCCTCTCTCTTTAG 2 47 1 GCTTTTCCCT 0.934797 -80 TTTGTAAAGTATCTTTTTATAGTGAAGGACTCT 3 129 1 ACTTTTTAGT 0.638939 -172 AGTCTCGGAAGACTTTTTGTCGTTTTCGTAAAA 3 170 1 GCTTTTTCGT 0.963559 -131 TCTATTAAGAGACTTTTTTACGAAAACGACAAA 3 185 0 GCTTTTACGA 0.895733 -116 GATTTGGCGAGACTTTAGACCGAATGTGTCGCT 3 233 1 GCTTTACCGA 0.893791 -68 GCTAATAGACGACTTTTAAGAGTCTTTATATAA 3 263 1 GCTTTTGAGT 0.951367 -38 TAGTAAAGCCTTTTGGGAGATTCCTGATTT 5 8 1 GCTTTTGAGA 0.962634 -100 GAAGTTCATTGCTTTTTTTTAGAACTTTAACAT 6 11 1 GTTTTTTAGA 0.8164 -276 GGTCCTCGTCGTTTTTGCTCAGATGGTGGAATG 6 114 1 GTTTTGCAGA 0.810228 -173 AAATCCCTTGGGCTTTGGCCCGTGCAAGTTCGA 6 165 1 GCTTTGCCGT 0.962104 -122 * ***** **** Masking position 6 Map Score: 14.1313 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 104 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 ATTTCTAGGAAAAGACTTTAGTTAGAAAAAAAAGAGA 1 38 1 AAATTTAAAA 0.777135 -244 TCTATATAAAAGACTATTTAAAGAAAAAAACCTCTGC 1 139 0 AGATTTAAAA 0.972655 -143 ATAGAGAAAAAGAAGGATTAGAGATAGGGGAATCCCT 1 171 1 AGAATTAAAG 0.944778 -111 CACTATAAAAAGATACTTTACAAACAGATACACTTAG 3 116 0 AGATTTAAAG 0.99087 -185 AAGTCTTCCGAGACTCTTAAACAAGAGTCCTTCACTA 3 148 0 AGATTAAAAG 0.971668 -153 CTAATACCTCAGACTATCTATTAAGAGACTTTTTTAC 3 197 0 AGATCTAAAG 0.96206 -104 ACGACTTTTAAGAGTCTTTATATAAAGAACGGAGAAG 3 271 1 AGATTTAAAG 0.99087 -30 GCTTTTTTTTAGAACTTTAACATACAATCCATTGTAG 6 21 1 AGATTAAAAA 0.918301 -266 CTAGAACTTTTAGGTAAAGTTT 12 3 1 AGATTTAAAG 0.99087 -20 *** **** * ** Masking position 10 Map Score: 9.14636 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 3 GAAGAAAACCTTTGTCTTCGGACTCACCCA 2 6 0 TTTGCCGGAC 0.987214 -121 GGATTAGGCGGAGGATCCGAGGCATGGG 3 4 1 TTAGCAGGAC 0.98004 -297 AAACAAGGAATTAGCCGTCAGACACCCATGCCTCG 3 28 0 TTAGCCAGAC 0.98004 -273 CTTGTTTTCATTTGTCAGAAGAAACGAAGCTTACA 3 56 1 TTTGCAAGAC 0.987709 -245 AAAAGGTATTATTGTCTCAAGAACCAGAGAAAAAA 6 217 0 ATTGCAAGAC 0.935071 -70 AATAACAATTTTTGACCTAAGATGCTTATATTACT 11 13 1 TTTGCAAGAC 0.987709 -43 GCCGCCTTTGTTTGCTTTAAGGAGCCGCGTTTTCT 19 161 1 TTTGTAAGGC 0.835573 -140 AAAAGTGTAATTAGGCACCGGGGGCGGTCTGTGAA 19 243 1 TTAGCCGGGC 0.964606 -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 0.919615 -232 AGACTATTTAAAGAAAAAAACCTCTGCACA 1 136 0 AAGAAAAAAA 0.902778 -146 GTCTTTTATATAGAGAAAAAGAAGGATTAG 1 162 1 TAGAGAAAAA 0.964038 -120 AGAAAAGACATAGTGAAAAAAGCCCGAAGA 2 36 0 TAGTGAAAAA 0.790446 -91 CATTTGTCAGAAGAAACGAAGCTTACAGTG 3 64 1 AAGAAACGAA 0.877495 -237 TCTCAAGAACCAGAGAAAAAAGATGTGCTC 6 208 0 CAGAGAAAAA 0.907425 -79 TGCAACACGCTAGAAAAAAATTTAGGGTTG 8 20 1 TAGAAAAAAA 0.919615 -46 GCAACGGTTATGAGACGAAGTACGACCAA 8 47 0 ATGAGACGAA 0.702535 -19 AGGGTAAAGTAGAGTCGAACT 13 10 1 TAGAGTCGAA 0.744227 -12 TAAAGAAGGAAGAGAAGAATAAC 18 10 1 AAGAGAAGAA 0.959306 -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 TTCGCTTAGATAAAGGAGTGGATTT 2 112 1 TAAAGAGTGG 0.939346 -15 AGTATCTTTTTATAGTGAAGGACTCTTGTTT 3 136 1 TATAGGAAGG 0.923165 -165 TTTTACACAATAAAGGAAAGGGTTACTAACG 5 41 0 TAAAGAAAGG 0.963861 -67 TTTGCACAAATATAGAAAATGACAAGACGCG 5 72 1 TATAGAAATG 0.748639 -36 GAACTTCTTGTAAAGCTGTGGCGAGGACTCT 6 79 1 TAAAGTGTGG 0.922443 -208 CTTTTTGATTTATAGATGAGGAGAGCTATTT 6 247 1 TATAGTGAGG 0.970139 -40 TTATAGCTAAGGAGTTTGGG 9 2 1 TATAGTAAGG 0.953451 -19 AGGGTAAAGTAGAGTCGAACT 13 5 1 TAAAGAGAGT 0.8253 -17 ***** ***** Masking position 4 Map Score: 3.64832 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 98 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 AAATTCTCTCGACTGTTTGTT 1 2 1 AATTCTCTCG 0.507568 -280 TTTCTAGGAAAAGACTTTAGTTAGAAAAAA 1 39 1 AAGACTTTAG 0.715194 -243 AAAAAGAGATAAAACTCTCAACACTACAGC 1 66 1 AAAACTCTCA 0.740573 -216 AAGCCCGAAGAAAACCTTTGTCTTCGGACT 2 17 0 AAAACCTTTG 0.502171 -110 TTTATAGTGAAGGACTCTTGTTTAAGAGTC 3 144 1 AGGACTCTTG 0.914051 -157 AAAGTCTTCCGAGACTCTTAAACAAGAGTC 3 156 0 GAGACTCTTA 0.740651 -145 TTTCGTAAAAAAGTCTCTTAATAGATAGTC 3 193 1 AAGTCTCTTA 0.920444 -108 TCTTTATATAAAGACTCTTAAAAGTCGTCT 3 269 0 AAGACTCTTA 0.947662 -32 AAAAACGACGAGGACCCTAAAGAGTCCTCG 6 100 0 AGGACCCTAA 0.712362 -187 AAGGGATTTTAAGTCCCTAGTGTCTACCAT 6 144 0 AAGTCCCTAG 0.90303 -143 TAGGGACTTAAAATCCCTTGGGCTTTGGCC 6 155 1 AAATCCCTTG 0.835914 -132 TGCTCAGAACAAGACTCGAACTTGCACGGG 6 183 0 AAGACTCGAA 0.627393 -104 GCGTCAAGAAAAATCTCTTGTGTGGATGTC 19 106 1 AAATCTCTTG 0.87402 -195 ********** Masking position 5 Map Score: 3.96686 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 364 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 AGAAAACCTTTGTCTTCGGACTCACCCA 2 7 0 TGTCTTGACT 0.943285 -120 AGACAAAGGTTTTCTTCGGGCTTTTTTCACTA 2 24 1 TTTCTTGGCT 0.974392 -103 GAGGCATGGGTGTCTGACGGCTAATTCCTTGT 3 29 1 TGTCTGGGCT 0.923419 -272 GTAAGCTTCGTTTCTTCTGACAAATGAAAACA 3 58 0 TTTCTTGACA 0.953969 -243 GCCTTTCTTAACACTCGCGTCTTGT 5 93 0 TTTCTTCACT 0.959447 -15 TTCGAGTCTTGTTCTGAGCACATCTTTTTTCT 6 193 1 GTTCTGCACA 0.826718 -94 TTTTTCTCTGGTTCTTGAGACAATAATACCTT 6 218 1 GTTCTTGACA 0.930657 -69 ACAAGAGATTTTTCTTGACGCTAAGAAATCCC 19 95 0 TTTCTTCGCT 0.959014 -206 ****** **** Masking position 5 Map Score: 3.24479 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 46 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 GATGTCAAAATACGATTTCTTGATTTGGAT 1 228 1 TACGATTTCT 0.900577 -54 TAACTACTATTGCGAATACTTAT 1 269 1 TGCGAATACT 0.7326 -13 CCTTTATCTAAGCGAATTCTAAAAAAATAA 2 98 0 AGCGAATTCT 0.947757 -29 TCTATATTTGTGCAAATTTTACACAATAAA 5 58 0 TGCAAATTTT 0.735278 -50 TGATGCTAATTTTTCGAAAACAC 7 4 1 TGCTAATTTT 0.611675 -40 AAAATAACAATTTTTGACCTAAGAT 11 6 1 AACAATTTTT 0.494189 -50 TAAAACCTAGAACGATTTTTCAGGCTTTGT 19 47 1 AACGATTTTT 0.850251 -254 GCTTTGTTTTTGCGATTTTTGGTGTGGGAT 19 70 1 TGCGATTTTT 0.964601 -231 ATTTTTGGTGTGGGATTTCTTAGCGTCAAG 19 84 1 TGGGATTTCT 0.825637 -217 CATCCACACAAGAGATTTTTCTTGACGCTA 19 104 0 AGAGATTTTT 0.664972 -197 ATCCTGCAAGAGCGATTTCCACGACAAAGA 19 193 0 AGCGATTTCC 0.852826 -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 9 ********** 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 10 CAGCGGCTGAAGTCAAGAGGGATTCCCCTAT 1 194 0 AGTCAGAGGG 0.928322 -88 AATCATTCTAAAGAGAGAGGGAGAAAAGACA 2 56 0 AAGAGGAGGG 0.864644 -71 GGAGGATCCGAGGCATGGGTGTCTGACGGCT 3 20 1 AGGCAGGGTG 0.960231 -281 TACACAATAAAGGAAAGGGTTACTAACGAAA 5 38 0 AGGAAGGGTT 0.677003 -70 GAAAATGACAAGACGCGAGTGTTAAGAAAGG 5 86 1 AGACGGAGTG 0.917696 -22 TAGCTTTTCCAGTCGTGCGTGCTAGAACTTC 6 55 1 AGTCGGCGTG 0.747571 -232 GTGGAATGGTAGACACTAGGGACTTAAAATC 6 139 1 AGACATAGGG 0.691253 -148 TTATAGCTAAGGAGTTTGGG 9 10 1 AGGAGTTGGG 0.733905 -11 TAATTTTTAGGAGAGAGTGTT 10 9 1 AGGAGGAGTG 0.975786 -13 GTCATAAGGAGACAGGTT 17 7 1 AGGAGCAGGT 0.767854 -12 TCGCTCTTGCAGGATGGAGGGCATGGCCGTT 19 208 1 AGGATGAGGG 0.920305 -93 AAGTGTAATTAGGCACCGGGGGCGGTCTGTG 19 245 1 AGGCACGGGG 0.934485 -56 ***** ***** Masking position 1 Map Score: 3.66668 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 242 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: 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 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