AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i341_weak2_ctra_reg_300.orf -o341_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 RCT00329 300 Chlamydia_trachomatis #2 RCT00330 61 Chlamydia_trachomatis #3 RCT00331 53 Chlamydia_trachomatis #4 RCT00675 166 Chlamydia_trachomatis #5 RCT00676 300 Chlamydia_trachomatis Motif number 1 GTTTCTAGTTAAAAAGTTTTATAAATAAGA 1 23 0 AAAAAGTTTT 0.865143 -278 TATGAGTGAAAAGAAGCTCGTCGGTGATAA 1 62 0 AAGAAGCTCG 0.984063 -239 TAAACACAAGAAAAAGCTCGTTATGAGTGA 1 83 0 AAAAAGCTCG 0.970771 -218 CTTGCAAGGTAAGAGGTTTTGGAATGTAGG 1 210 0 AAGAGGTTTT 0.892342 -91 AAGCAAGAGGAAGTCGCTTGTTAGGGCATA 1 237 1 AAGTCGCTTG 0.844654 -64 CTTATGAGCTAAGAAGCTTTCGGGTTGTTT 2 26 0 AAGAAGCTTT 0.988786 -36 CTTAGAGTACAAGAAGTTTGCCGGTGTAG 3 10 0 AAGAAGTTTG 0.968013 -44 CTTGTACTCTAAGAAGGTCTTTGTTATCCT 3 27 1 AAGAAGGTCT 0.922779 -27 TGATCGCAGGAAAACGCTTGACCCAAGAGA 4 14 1 AAAACGCTTG 0.959143 -153 ATTGGACTGCAAACAGCTTTAAAAAGGGGA 5 55 0 AAACAGCTTT 0.889156 -246 AAAACTTTGGAAAAAGGTTTTTTGAGAAGG 5 109 0 AAAAAGGTTT 0.916231 -192 AGGTTTTACAAAAAAACTTTGGAAAAAGGT 5 121 0 AAAAAACTTT 0.758127 -180 GAAGCGGGTGATGAGGCTTGAACTCACGAC 5 249 0 ATGAGGCTTG 0.833215 -52 ********** Masking position 1 Map Score: 15.9258 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 687 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 AAAACTTTTTAACTAGAAACTCCTACCTGTTATC 1 33 1 AACAACTCCT 0.868743 -268 ACCTGTTATCACCGACGAGCTTCTTTTCACTCAT 1 57 1 ACCGACTTCT 0.994419 -244 CCATCCCTACATTCCAAAACCTCTTACCTTGCAA 1 205 1 ATTAACCTCT 0.664575 -96 GTTGGAAACAACCCGAAAGCTTCTTAGCTCATAA 2 21 1 ACCAACTTCT 0.987019 -41 CTACACCGGCAAACTTCTTGTACTCTAA 3 5 1 ACCAACTTCT 0.987019 -49 ACAAAAGGATAACAAAGACCTTCTTAGAGTACAA 3 28 0 AACGACTTCT 0.983163 -26 AAAACGCTTGACCCAAGAGACACTTAAACATAGA 4 24 1 ACCGAACACT 0.77789 -143 AATCAATGAAAATTTTGACCCTCTCTTCTTCCTC 5 15 1 AATGACCTCT 0.92145 -286 GTGGCGCTCTACCACTGAGCTACACCCGCGAGAA 5 200 0 ACCGACTACA 0.939942 -101 TGAGGCTTGAACTCACGACCTTCACGTTGGCAAC 5 234 0 ACTGACTTCA 0.933219 -67 *** ** ***** Masking position 8 Map Score: 8.56197 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 125 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 3 TATAAATAAGAGAGGATAAGAAG 1 2 0 AGAGGAAAAA 0.980359 -299 CCACAGTTTCAGAGAAAAATTATAACTTCCAC 1 119 0 AGAGAAAATA 0.657482 -182 GATATAAATAAGACGAGAATGAAAACAATTTC 1 161 0 AGACGAAAGA 0.940709 -140 CTTGCAAGCAAGAGGAAGTCGCTTGTTAGGGC 1 232 1 AGAGGAGTGC 0.831065 -69 TCTTCCTTAAAGAGGATATTGA 1 289 1 AGAGGAATGA 0.965216 -12 AGACCTTCTTAGAGTACAAGAAGTTTGCCGGT 3 15 0 AGAGTAAAAA 0.781731 -39 GGACAAAAGGATAACAAAGACCTTCTT 3 37 0 AAAGGAAAAA 0.852885 -17 TCTTGACCCTAGAAAAGAAAGACCCCATCTAA 4 91 0 AGAAAAAAGA 0.773871 -76 AAATGATTTGAGAGGAAGCACACAT 4 152 1 AGAGGAGCCA 0.896198 -15 GGGGAAAAATAGAGGAAGAAGAGAGGGTCAAA 5 28 0 AGAGGAGAGA 0.99398 -273 ACAGCTTTAAAAAGGGGAAAAATAGAGGAAGA 5 41 0 AAAGGGAAAA 0.727364 -260 AGGTTTTTTGAGAAGGTGAAGAGGTGGTAAAA 5 93 0 AGAAGGGAGA 0.937995 -208 TACACCCGCGAGAAGAAGAGCATTCTAGATAA 5 182 0 AGAAGAGACA 0.909196 -119 GGGAAAGAGAAGCGGGTGATGAGGCTTGAACT 5 255 0 AGCGGGGAGA 0.917247 -46 ****** ** ** Masking position 1 Map Score: 9.96509 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 598 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 CTTCTTATCCTCTCTTATTTAT 1 3 1 TCTTATCCTC 0.784542 -298 CTCATAACGAGCTTTTTCTTGTGTTTAGGC 1 86 1 GCTTTTTCTT 0.789802 -215 AAGAAATTGTTTTCATTCTCGTCTTATTTA 1 159 1 TTTCATTCTC 0.815794 -142 CCTTGAGAGATCTCTTCCTTAAAGAGGATA 1 277 1 TCTCTTCCTT 0.968934 -24 AATTAGATGGGGTCTTTCTTTTCTAGGGTC 4 89 1 GGTCTTTCTT 0.782485 -78 ATGTGTGCTTCCTCTCAAATCATT 4 153 0 GTGCTTCCTC 0.808376 -14 ATTTTGACCCTCTCTTCTTCCTCTATTTTT 5 26 1 TCTCTTCTTC 0.968934 -275 CTCTTCTTCCTCTATTTTTCCCCTTTTTAA 5 37 1 TCTATTTTTC 0.69498 -264 CAGTCCAATTTTTCTTTTTTTACCACCTCT 5 76 1 TTTCTTTTTT 0.706687 -225 TATCTAGAATGCTCTTCTTCTCGCGGGTGT 5 183 1 GCTCTTCTTC 0.966853 -118 ATCACCCGCTTCTCTTTCCCGGATAACTTA 5 267 1 TCTCTTTCCC 0.922559 -34 ********** Masking position 6 Map Score: 4.39035 Number of sites scoring better than the average of aligned sites = 1159 Number in coding regions = 1159 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 TCCCAAACCTGCTGTACTTATG 2 50 0 CCAAACCTGC 0.944757 -12 CTACACCGGCAAACTTCTTG 3 1 1 CTACACCGGC 0.993101 -53 CTAATTCAAAATACACCTACGCATCAAAAT 4 65 0 ATACACCTAC 0.879151 -102 TTTACCACCTCTTCACCTTCTCAAAAAACC 5 94 1 CTTCACCTTC 0.961837 -207 TACCACTGAGCTACACCCGCGAGAAGAAGA 5 195 0 CTACACCCGC 0.996239 -106 GTTCAAGCCTCATCACCCGCTTCTCTTTCC 5 256 1 CATCACCCGC 0.977352 -45 ********** Masking position 5 Map Score: 4.383 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 36 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 GAAACTCCTACCTGTTATCACCGACGAGCT 1 48 1 CCTGTTATCA 0.922741 -253 AACCTCTTACCTTGCAAGCAAGAGGAAGTC 1 222 1 CTTGCAAGCA 0.965312 -79 CAAGCGTTTTCCTGCGATCAAAA 4 4 0 CCTGCGATCA 0.981269 -163 CGTAAGCACACCTGTAACCAAATGATTTGA 4 133 1 CCTGTAACCA 0.970612 -34 GAAAAATTGGACTGCAAACAGCTTTAAAAA 5 60 0 ACTGCAAACA 0.910733 -241 TTTTGTAAAACCTACAAGCAAAGGATTGCG 5 138 1 CCTACAAGCA 0.965312 -163 ********** Masking position 7 Map Score: 2.32971 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 76 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 TCGCAGGAAAACGCTTGACCCAAGAGACAC 4 17 1 ACGCTTGACC 0.993383 -150 GACCCAAGAGACACTTAAACATAGAATTCA 4 33 1 ACACTTAAAC 0.860116 -134 CGTTATGGCTACTCTTGACCCTAGAAAAGA 4 105 0 ACTCTTGACC 0.989788 -62 TTTTTTACCACCTCTTCACCTTCTCAAAAA 5 91 1 CCTCTTCACC 0.942232 -210 GCGGGTGATGAGGCTTGAACTCACGACCTT 5 246 0 AGGCTTGAAC 0.949809 -55 ********** Masking position 5 Map Score: 1.10827 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 22 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: 3.79592e-14 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: 3.79592e-14 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: 3.79592e-14 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