AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_ctra_reg_100.orf -o224_ctra_100.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 RCT00037 281 Chlamydia_trachomatis #2 RCT00184 126 Chlamydia_trachomatis #3 RCT00476 19 Chlamydia_trachomatis #4 RCT00477 107 Chlamydia_trachomatis Motif number 1 TCCTAGAAATATAGATAACAAACAGTCGAGAG 1 16 0 AAGTAACAAA 0.847163 -266 TGTTATCTATATTTCTAGGAAAAGACTTTAGT 1 28 1 ATTTAGGAAA 0.937163 -254 GGAAAAGACTTTAGTTAGAAAAAAAAGAGATA 1 45 1 TAGTAGAAAA 0.859434 -237 GTTAGAAAAAAAAGAGATAAAACTCTCAACAC 1 58 1 AAGGATAAAA 0.922502 -224 CAGCATGTGCAATTGTATGAAAAGACGCAACT 1 92 1 ATTTATGAAA 0.783457 -190 ATAAAAGACTATTTAAAGAAAAAAACCTCTGC 1 139 0 ATTAAGAAAA 0.818692 -143 ATAGTCTTTTATATAGAGAAAAAGAAGGATTA 1 159 1 AATGAGAAAA 0.970153 -123 GAGAAAAGACATAGTGAAAAAAGCCCGAAGAA 2 35 0 AAGGAAAAAA 0.95691 -92 TTCTAAAGAGAGAGGGAGAAAAGACATAGTGA 2 50 0 AAGGAGAAAA 0.981147 -77 TATCTAAGCGAATTCTAAAAAAATAATAAAAT 2 92 0 ATTTAAAAAA 0.913406 -35 AAATTTGCACAAATATAGAAAATGACAAGACG 4 69 1 AATTAGAAAA 0.972032 -39 ACAAGACGCGAGTGTTAAGAAAGGC 4 93 1 ATGTAAGAAA 0.915279 -15 * ** ******* Masking position 7 Map Score: 12.8467 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 328 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 AAATTCTCTCGACTGTTTGTT 1 1 1 AAATCTCTCG 0.928499 -281 TTTTCTAACTAAAGTCTTTTCCTAGAAATAT 1 36 0 AAATCTTTTC 0.95837 -246 TTGAGAGTTTTATCTCTTTTTTTTCTAACTA 1 56 0 TATTCTTTTT 0.679057 -226 GCAACTTTTTAATGCCTTTGTGCAGAGGTTT 1 118 1 AATCCTTTGT 0.934087 -164 TTTAAAGAAAAAAACCTCTGCACAAAGGCAT 1 129 0 AAACCTCTGC 0.982907 -153 GAGATAGGGGAATCCCTCTTGACTTCAGCCG 1 191 1 AATCCTCTTG 0.955079 -91 AAGCCCGAAGAAAACCTTTGTCTTCGGACTC 2 16 0 AAACCTTTGT 0.960048 -111 CTTTTTTCACTATGTCTTTTCTCCCTCTCTC 2 44 1 TATTCTTTTC 0.844063 -83 AAATCCACTCCTTTATCTAAG 2 116 0 AAACCACTCC 0.879615 -11 TAGTAAAGCCTTTTGGGAGATTCCT 4 5 1 AAACCTTTTG 0.97471 -103 ATTTCGTTAGTAACCCTTTCCTTTATTGTGT 4 37 1 TAACCTTTCC 0.960773 -71 *** ******* Masking position 2 Map Score: 10.814 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 653 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 AAATTCTCTCGACTGTTTGTTATCT 1 6 1 CTCTCGACTG 0.900371 -276 AGAGTTTTATCTCTTTTTTTTCTAACTAAA 1 54 0 CTCTTTTTTT 0.944973 -228 TGTGCAGAGGTTTTTTTCTTTAAATAGTCT 1 136 1 TTTTTTTCTT 0.662481 -146 TATCTCTAATCCTTCTTTTTCTCTATATAA 1 167 0 CCTTCTTTTT 0.788928 -115 AGGGGAATCCCTCTTGACTTCAGCCGCTGG 1 196 1 CTCTTGACTT 0.975611 -86 AAAATACGATTTCTTGATTTGGATTAGCGA 1 234 1 TTCTTGATTT 0.746903 -48 CCGAAGAAAACCTTTGTCTTCGGACTCACC 2 13 0 CCTTTGTCTT 0.928016 -114 TCTTTTCTCCCTCTCTCTTTAGAATGATTC 2 58 1 CTCTCTCTTT 0.926034 -69 TCGTTAGTAACCCTTTCCTTTATTGTGTAA 4 40 1 CCCTTTCCTT 0.95069 -68 TTTCTTAACACTCGCGTCTTGTCATTTTCT 4 85 0 CTCGCGTCTT 0.93548 -23 ********** Masking position 9 Map Score: 5.71975 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 767 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 GAAAAAAACCTCTGCACAAAGGCATTAAAA 1 124 0 TCTGCACAAA 0.961466 -158 CTTCGGGCTTTTTTCACTATGTCTTTTCTC 2 37 1 TTTTCACTAT 0.92154 -90 TTGTGCAAATTTTACACAATAAAGGAAAGG 4 51 0 TTTACACAAT 0.966595 -57 TTGTGTAAAATTTGCACAAATATAGAAAAT 4 62 1 TTTGCACAAA 0.817407 -46 ********** Masking position 6 Map Score: 1.00529 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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 GTGTTGAGAGTTTTATCTCTTTTTTTTCTA 1 60 0 TTTTATCTCT 0.706202 -222 TCTAATCCTTCTTTTTCTCTATATAAAAGA 1 163 0 CTTTTTCTCT 0.919829 -119 AGAGGGATTCCCCTATCTCTAATCCTTCTT 1 180 0 CCCTATCTCT 0.992969 -102 CCCGAAGAAAACCTTTGTCTTCGGACTCAC 2 14 0 ACCTTTGTCT 0.923099 -113 GGGCTTTTTTCACTATGTCTTTTCTCCCTC 2 41 1 CACTATGTCT 0.902139 -86 TGTCTTTTCTCCCTCTCTCTTTAGAATGAT 2 56 1 CCCTCTCTCT 0.988072 -71 AAATCCACTCCTTTATCTAAGCGAATTC 2 109 0 TCCTTTATCT 0.885848 -18 TCGTTAGTAACCCTTTCCTTTATTGTGTAA 4 40 1 CCCTTTCCTT 0.845057 -68 ********** Masking position 6 Map Score: 4.91432 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 427 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 ********** No masking Map Score: 1.3033e-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 7 ********** No masking Map Score: 1.3033e-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 8 ********** No masking Map Score: 1.3033e-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