AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_mixed15_ctra_reg_100.orf -o300_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 RCT00316 275 Chlamydia_trachomatis #2 RCT00598 55 Chlamydia_trachomatis #3 RCT00599 52 Chlamydia_trachomatis #4 RCT00600 178 Chlamydia_trachomatis Motif number 1 TCTGTAAAACCAGAAGGCGCTGTATAACGGTG 1 55 0 CAGAAGCGTG 0.974315 -221 TCTGGTTTTACAGAAGGCGCTTGAGGACTGTC 1 73 1 CAGAAGCGTT 0.990918 -203 TCTTGAATAAGAGAAAACATTTCCTCATAGAT 1 128 0 GAGAAACATT 0.85157 -148 ATTCAAGAAGGAGAAACCAATTTGAACCATGT 1 152 1 GAGAAACATT 0.851536 -124 GGTTCTGTCGCAGTAGATACTTCAGGCAATCC 1 221 1 CAGTAGTATT 0.774902 -55 CCCCAGGGATAAAAGGATGCTTAATGGGATTG 1 247 0 AAAAGGTGTT 0.898623 -29 CTTTGTTTGACAAAGGTTGTTTC 2 2 0 CAAAGGTGTT 0.953233 -54 CTTTGTCAAACAAAGGTTGATGAGAAAAAGAA 2 19 1 CAAAGGTGTG 0.878686 -37 TGATGAGAAAAAGAAGGCAGTTGCTTAGAT 2 36 1 AAGAAGCATT 0.955429 -20 AACCCCAGAGGGTGTTTAAATACCTAG 3 6 1 CAGAGGTGTT 0.984739 -47 AAAAAGTCTGAAGATATCGGTTTTTTTTCTGA 4 94 1 AAGATACGTT 0.732626 -85 AGGCTCTTTGAAAAAACTATTTTTGTTGTATT 4 125 1 AAAAAATATT 0.566642 -54 ****** ** ** Masking position 2 Map Score: 9.86867 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 653 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 ACACCGTTATACAGCGCCTTCTGGTTTTAC 1 54 1 ACAGCGCCTT 0.963931 -222 TGACAGTCCTCAAGCGCCTTCTGTAAAACC 1 76 0 CAAGCGCCTT 0.977675 -200 ATCTACTGCGACAGAACCATCGGGGTTTAA 1 209 0 ACAGAACCAT 0.785263 -67 GAAACAACCTTTGTCAAACAA 2 2 1 AAACAACCTT 0.972981 -54 TTCTTTTTCTCATCAACCTTTGTTTGACAA 2 21 0 CATCAACCTT 0.863571 -35 ATCTAAGCAACTGCCTTCTTTTTCTCA 2 39 0 CAACTGCCTT 0.947336 -17 CTAGGTATTTAAACACCCTCTGGGGTT 3 8 0 AAACACCCTC 0.922897 -45 TAGTTTTTTCAAAGAGCCTCAGAAAAAAAA 4 114 0 AAAGAGCCTC 0.976695 -65 ********** Masking position 7 Map Score: 5.15297 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 214 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 ATACAGCGCCTTCTGGTTTTACAGAAGGCG 1 62 1 TTCTGGTTTT 0.907723 -214 CATGTCGAACAGCTGAGTTTTCAGCTACAA 1 179 1 AGCTGAGTTT 0.925652 -97 CGACAGAACCATCGGGGTTTAATTGTAGCT 1 201 0 ATCGGGGTTT 0.968221 -75 ATACAAGCATAGCTAGGTATTTAAACACCC 3 20 0 AGCTAGGTAT 0.902889 -33 TCTCTGCTTTATCTAGTTTTTGATCGAAAA 4 23 0 ATCTAGTTTT 0.955469 -156 GCAGAGAATGAGCTGTTTATCACAGAACAA 4 46 1 AGCTGTTTAT 0.921565 -133 GTCTGAAGATATCGGTTTTTTTTCTGAGGC 4 99 1 ATCGGTTTTT 0.937694 -80 TCTTTGAAAAAACTATTTTTGTTGTATTAG 4 129 1 AACTATTTTT 0.759471 -50 ********** Masking position 8 Map Score: 4.02179 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 190 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 CGGGTACCGAGATTTCCTGCATGACCGG 1 3 0 GATTCCTCAC 0.993828 -273 TAAGAGAAAACATTTCCTCATAGATAGCCAAGATAG 1 117 0 CATTCCTAAA 0.967893 -159 TGCTTAATGGGATTGCCTGAAGTATCTACTGCGACA 1 226 0 GATTCCTAAC 0.994546 -50 CAACTGCCTTCTTTTTCTCATCAACCTTTGTTTGAC 2 23 0 CTTTTCTAAC 0.942007 -33 ATAAACAGCTCATTCTCTGCTTTATCTAGTTTTTGA 4 30 0 CATTTCTCAC 0.982009 -149 TGAACTATTAGATTACCTAATACAACAAAAATAGTT 4 139 0 GATTCCTAAC 0.994659 -40 **** *** * * * Masking position 8 Map Score: 3.91274 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 TCTCGGTACCCGAAGCAAGTCATCTGGACA 1 27 1 CGAAGCAAGT 0.908994 -249 AATTAAACCCCGATGGTTCTGTCGCAGTAG 1 207 1 CGATGGTTCT 0.855473 -69 CTTTGTTTGACAAAGGTTGTTTC 2 4 0 CAAAGGTTGT 0.890584 -52 ATCTAAGCAACTGCCTTCTTTT 2 44 0 CTAAGCAACT 0.901238 -12 AAATACCTAGCTATGCTTGTATCAGGAGCT 3 28 1 CTATGCTTGT 0.975874 -25 AACTAAGCTCCTGATACAAGCA 3 41 0 CTAAGCTCCT 0.95438 -12 CAAGTTTAGACTACACTTGTTCTGTGATAA 4 62 0 CTACACTTGT 0.886355 -117 CAAGTGTAGTCTAAACTTGAAAAAAAGTCT 4 73 1 CTAAACTTGA 0.792636 -106 ********** Masking position 3 Map Score: 1.2303 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 236 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: 1.48747e-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 7 ********** No masking Map Score: 1.48747e-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 8 ********** No masking Map Score: 1.48747e-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