AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i046_1_2_4_4_ctra_reg_300.orf -o046_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 RCT00325 34 Chlamydia_trachomatis #2 RCT00326 28 Chlamydia_trachomatis #3 RCT00843 196 Chlamydia_trachomatis #4 RCT00327 300 Chlamydia_trachomatis Motif number 1 AAAAAATCTTTGTTAGTGGTGTTTCG 2 3 1 AAAACTTTAG 0.971115 -26 CTTTTGGGACAACAACTTTTCAAGAGTTTTGTTT 3 20 1 AACACTTAAG 0.96136 -177 AAGAAGGTTATACAACTTAAGTATCTCTTGAAGC 3 80 1 TACACTATAT 0.765229 -117 CGGGGATTGTAACACCACTTTTATTTAGGCTTCA 3 108 0 AACACCTTAT 0.982276 -89 CAACTAGTTCAAAATCCTTGGAAGAGCAAGGGTT 4 15 1 AAAACTTAAG 0.958271 -286 GATATACTACAAAATCGCAACAATTAGTGCATCT 4 82 1 AAAACCAAAT 0.940555 -219 TGCAATTGATAAAAACCCTGCTATACTTTCTCGT 4 119 0 AAAACCTTAT 0.980828 -182 TTCGATAAATAACAGTTTTTCTATTCAACTTCTC 4 158 0 AACATTTTAT 0.817169 -143 ACTTTACTAAAAAAGCTCATTTATAATTCGATAA 4 184 0 AAAACCATAT 0.95861 -117 TATAACCGTTAAAACCGTTTTAATTCAAAAATTA 4 243 0 AAAACTTAAT 0.969926 -58 **** * ** *** Masking position 4 Map Score: 10.3346 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 175 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 AACCTTCTTTGAATTATAAAAATTACCAAA 3 59 0 GAATTATAAA 0.976296 -138 AAGAGACCGGGGATTGTAACACCACTTTTA 3 119 0 GGATTGTAAC 0.978027 -78 AAGAGAAGTTGAATAGAAAAACTGTTATTT 4 156 1 GAATAGAAAA 0.818672 -145 GTTATTTATCGAATTATAAATGAGCTTTTT 4 179 1 GAATTATAAA 0.976296 -122 ATTAATTTTTGAATTAAAACGGTTTTAACG 4 241 1 GAATTAAAAC 0.97171 -60 TTTAGACAAAGGATTATAACCGTTAAAACC 4 261 0 GGATTATAAC 0.981701 -40 ********** Masking position 4 Map Score: 7.00425 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 AAAGAAGGATCTTTTTAGCTGAGAGGG 1 7 1 GGATCTTTTA 0.899678 -28 ACTTTTCAAGAGTTTTGTTTACTTGTTTGGT 3 34 1 AGTTTTTTTA 0.977844 -163 TTGTAACACCACTTTTATTTAGGCTTCAAGA 3 105 0 ACTTTTTTTA 0.977844 -92 ATACGTAATTGGTTTTATTTAATAACGCGCG 3 165 0 GGTTTTTTTA 0.961527 -32 GTTTAATATTACTTCTTCTTACCGATATACT 4 59 1 ACTTCTCTTA 0.919936 -242 TTTCTATTCAACTTCTCTTTGCTGCAATTGA 4 144 0 ACTTCTTTTG 0.919936 -157 GAATAGAAAAACTGTTATTTATCGAATTATA 4 166 1 ACTGTTTTTA 0.921399 -135 CTAAACTCCTAGATTGATTTAGACAAAGGAT 4 277 0 AGATTGTTTA 0.811015 -24 ****** **** Masking position 9 Map Score: 4.1224 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 109 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 ACAACAACTTTTCAAGAGTTTTGTTTACTT 3 28 1 TTCAAGAGTT 0.95751 -169 AAGAGTTTTGTTTACTTGTTTGGTAATTTT 3 41 1 TTTACTTGTT 0.769033 -156 TTATTTAGGCTTCAAGAGATACTTAAGTTG 3 92 0 TTCAAGAGAT 0.875669 -105 CCAAGGATTTTGAACTAGTTGCCCA 4 6 0 TGAACTAGTT 0.840839 -295 AAGGGTTGTGTGCACATGTTTAATATTACT 4 42 1 TGCACATGTT 0.953659 -259 TCGTGTTAGATGCACTAATTGTTGCGATTT 4 93 0 TGCACTAATT 0.90306 -208 CTGCTATACTTTCTCGTGTTAGATGCACTA 4 106 0 TTCTCGTGTT 0.849483 -195 TTCTCTTTGCTGCAATTGATAAAAACCCTG 4 133 0 TGCAATTGAT 0.860038 -168 ACCGTTTTAATTCAAAAATTAATTCGCTGT 4 234 0 TTCAAAAATT 0.663742 -67 ********** Masking position 1 Map Score: 2.86986 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 375 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 5 AAAGAAGGATCTTTTTAGCT 1 1 1 AAAGAAGGAT 0.958018 -34 TTTATAATTCAAAGAAGGTTATACAACTTA 3 69 1 AAAGAAGGTT 0.986839 -128 AGTTGAATAGAAAAACTGTTATTTATCGAA 4 162 1 AAAAACTGTT 0.934887 -139 CTTTTTTAGTAAAGTCGGTTTTGATTTGGC 4 203 1 AAAGTCGGTT 0.980892 -98 ATTTTTGAATTAAAACGGTTTTAACGGTTA 4 245 1 TAAAACGGTT 0.958018 -56 ********** Masking position 3 Map Score: 3.09575 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 70 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: -1.11312e-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: -1.11312e-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: -1.11312e-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