AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_mixed15_ctra_reg_300.orf -o300_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 RCT00313 295 Chlamydia_trachomatis #2 RCT00316 275 Chlamydia_trachomatis #3 RCT00598 55 Chlamydia_trachomatis #4 RCT00599 52 Chlamydia_trachomatis #5 RCT00600 178 Chlamydia_trachomatis Motif number 1 TTGTCTTACTTTTTTCTGTGAATTTGCTTAA 1 37 0 TTTTCTGTGA 0.982864 -259 ACCTGTGCATGTATTTTGTAAGATAGATCAA 1 161 0 GTTTTTGTAA 0.953611 -135 TGTGAGTTTCTTTGTCTGTAAACATGAGATT 1 201 0 TTGTCTGTAA 0.902828 -95 GTTGGAAATGGTTTTCTGTGAGTTTCTTTGT 1 217 0 GTTTCTGTGA 0.992615 -79 AAAGCAATTTGTTTTCGGTAATTGGAAA 1 278 1 GTTTCGGTAA 0.978208 -18 GTCCTCAAGCGCCTTCTGTAAAACCAGAAGG 2 70 0 GCTTCTGTAA 0.956086 -206 ATGAGGAAATGTTTTCTCTTATTCAAGAAGG 2 132 1 GTTTCTCTTA 0.873207 -144 TAGACTACACTTGTTCTGTGATAAACAGCTC 5 55 0 TTTTCTGTGA 0.982864 -124 AGATATCGGTTTTTTTTCTGAGGCTCTTTGA 5 105 1 TTTTTTCTGA 0.751251 -74 TATTTTTGTTGTATTAGGTAATCTAATAGTT 5 142 1 GTTTAGGTAA 0.833684 -37 ** ******** Masking position 5 Map Score: 10.822 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 165 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 AAAACCAACTATTTAAGCAAATTCACAGAA 1 25 1 ATTTAAGCAA 0.903286 -271 AGATTAGCATATCCAAGAGATTTATATCAA 1 70 1 ATCCAAGAGA 0.890722 -226 AGAGATTTATATCAAAGCAATAGAAAATAA 1 85 1 ATCAAAGCAA 0.988572 -211 TGTAAGATAGATCAAAGCGTAATACTCGAT 1 146 0 ATCAAAGCGT 0.962012 -150 ACTCTGAGCCATCAAAGCAATTTGTTTTCG 1 265 1 ATCAAAGCAA 0.988572 -31 ATCTAAGCAACTGCCTTCTT 3 46 0 ATCTAAGCAA 0.983706 -10 TAAGCTCCTGATACAAGCATAGCTAGGTAT 4 30 0 ATACAAGCAT 0.862658 -23 ********** Masking position 5 Map Score: 7.79662 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 59 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 AAATCTCTTGGATATGCTAATCTTCTTGTC 1 63 0 GATATGCTAA 0.797421 -233 CGTAATACTCGATTTCTTGCAAGGAAGGCT 1 129 0 GATTTCTTGC 0.951714 -167 GTAAACATGAGATTTGCTGAATAACCTGTG 1 185 0 GATTTGCTGA 0.956911 -111 CGGGTACCGAGATTTCCTGCATGACCGG 2 9 0 GATTTCCTGC 0.983644 -267 AGATAGCCAAGATAGCTTCCACGGAATGAC 2 102 0 GATAGCTTCC 0.816756 -174 TAAGAGAAAACATTTCCTCATAGATAGCCA 2 123 0 CATTTCCTCA 0.889691 -153 TGCTTAATGGGATTGCCTGAAGTATCTACT 2 232 0 GATTGCCTGA 0.976352 -44 AAAAAAAACCGATATCTTCAGACTTTTTTT 5 92 0 GATATCTTCA 0.905152 -87 TGAACTATTAGATTACCTAATACAACAAAA 5 145 0 GATTACCTAA 0.83646 -34 ********** Masking position 3 Map Score: 6.26959 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 240 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 GAAATCGAGTATTACGCTTTGATCTATCTTA 1 143 1 ATTACGCTTG 0.919023 -153 AGATTTGCTGAATAACCTGTGCATGTATTTT 1 175 0 AATAACCTTG 0.981253 -121 GAAACAACCTTTGTCAAACAAAG 3 3 1 AACAACCTTG 0.991688 -53 TCTTTTTCTCATCAACCTTTGTTTGACAAAG 3 19 0 ATCAACCTTG 0.988152 -37 TAGGTATTTAAACACCCTCTGGGGTT 4 6 0 AACACCCTTG 0.992294 -47 ******** ** Masking position 4 Map Score: 4.34802 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 11 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 CTAATCTTCTTGTCTTACTTTTTTCTGTGAA 1 46 0 TGCTTACTTT 0.957631 -250 TATTTTTATATGATTTATTTTCTATTGCTTT 1 98 0 TGTTTATTTT 0.865526 -198 CTTGCAAGGAAGGCTTATTTTTATATGATTT 1 113 0 AGCTTATTTT 0.924791 -183 TGGTTTTCTGTGAGTTTCTTTGTCTGTAAAC 1 209 0 TGGTTTCTTT 0.957277 -87 TCTAAGCAACTGCCTTCTTTTTCTCATCAAC 3 34 0 TGCTTCTTTT 0.951697 -22 CGATATCTTCAGACTTTTTTTCAAGTTTAGA 5 82 0 AGCTTTTTTT 0.941215 -97 TCTGAAGATATCGGTTTTTTTTCTGAGGCTC 5 100 1 TCGTTTTTTT 0.846416 -79 AATAGTTCAATGGGTTTATTTAT 5 166 1 TGGTTTATTT 0.891479 -13 ** ******** Masking position 6 Map Score: 3.58436 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 111 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 GCCTTCTGTAAAACCAGAAGGCGCTGTATAA 2 60 0 AACCAGAAGG 0.989623 -216 GTTTTCTCTTATTCAAGAAGGAGAAACCAAT 2 142 1 ATCAAGAAGG 0.94812 -134 GCTACAATTAAACCCCGATGGTTCTGTCGCA 2 202 1 AACCCGATGG 0.983159 -74 ACAGATTCCCCAGGGATAAAAGGAT 2 261 0 ATCCCCAGGG 0.978368 -15 AACCCCAGAGGGTGTTTAAATA 4 2 1 ACCCAGAGGG 0.991947 -51 ** ******** Masking position 8 Map Score: 0.28874 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 7 AGTTGGTTTTAGCCCCTTTGTTAT 1 5 0 AGCCCCTTTG 0.953309 -291 TAAAACCAGAAGGCGCTGTATAACGGTGTC 2 53 0 AGGCGCTGTA 0.974703 -223 GTTTTACAGAAGGCGCTTGAGGACTGTCAT 2 77 1 AGGCGCTTGA 0.980458 -199 TGCTTGTATCAGGAGCTTAGTT 4 41 1 AGGAGCTTAG 0.935959 -12 TTTTTTTCTGAGGCTCTTTGAAAAAACTAT 5 115 1 AGGCTCTTTG 0.9798 -64 ********** Masking position 7 Map Score: 0.0857871 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 69 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: 1.72905e-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 9 ********** No masking Map Score: 1.72905e-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 10 ********** No masking Map Score: 1.72905e-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