AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_ctra_reg_300.orf -o110_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 RCT00127 206 Chlamydia_trachomatis #2 RCT00187 300 Chlamydia_trachomatis #3 RCT00189 215 Chlamydia_trachomatis #4 RCT00190 82 Chlamydia_trachomatis #5 RCT00362 68 Chlamydia_trachomatis #6 RCT00363 300 Chlamydia_trachomatis Motif number 1 CACACCTGTTAAGATTAGAGCTCCTAATAA 2 50 0 AAGATTAGAG 0.924887 -251 GATTGAGTGACAGAGAAGAGAGGGCGTTTA 2 169 0 CAGAGAAGAG 0.991133 -132 AGATATGCAGAAGAGTTGAGGCTTTAGATT 2 195 0 AAGAGTTGAG 0.923844 -106 AATGTAGCGCCAAGTATGAGACGAACTAGA 4 51 0 CAAGTATGAG 0.63785 -32 ATTCTTAAAAAAAATAAGAAT 5 2 0 AAAATAAGAA 0.683605 -67 GAAACTACTCAAAGGAAGAGCTGAATATGC 6 60 1 AAAGGAAGAG 0.969268 -241 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 6 179 0 AAGAGAAGAG 0.993671 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 6 190 1 AAGAGAAGAG 0.993671 -111 ATCATACACACAGGGAAGAGAAAAGAAATA 6 237 0 CAGGGAAGAG 0.987591 -64 TTCATGAGTTAAGAGAAGAAACAAGGAAAA 6 273 1 AAGAGAAGAA 0.964462 -28 ********** Masking position 2 Map Score: 15.1701 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 305 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 TTTTTTTCGAAACAGAAGTCGTATAAAATTTTTT 1 83 1 AAAGAAGCTT 0.892964 -124 GATTTTAATTAGGAAAGGCTTTTTTTATAAGAAC 1 125 1 AGAAAGGTTT 0.963269 -82 AGCTTGCTGCAATAGAGGGTATAGTCGTAATCAC 2 77 0 AAAGAGGTTG 0.955289 -224 AGTGACAGAGAAGAGAGGGCGTTTAAAGGCTGCG 2 160 0 AAAGAGGCTT 0.990643 -141 TATGCAGAAGAGTTGAGGCTTTAGATTGAGTGAC 2 188 0 AGTGAGGTTG 0.837752 -113 CCGCATTTTAAAGAGAGAATCTTTTCTACGCACG 3 26 0 AAAGAGATTT 0.895577 -190 CTTTAAAATGCGGAGAGGTCTTGTCTAGAGAGTG 3 47 1 CGAGAGGCTT 0.976719 -169 TATCACTCTTGGCAAAGGCCTTTTATGTTTTCAA 3 87 1 GGAAAGGCTT 0.912305 -129 TAATTTAATAAAGGATTTCTAAAACAAACT 4 7 1 AAAAAGGTTT 0.932378 -76 TCTCTTGAAGAGAAGAGAACGTTTAATGATGCTA 6 172 0 AGAGAGACTT 0.968742 -129 TCTCTTCAAGAGAAGAGGGCGTTTTTTTCATTGA 6 193 1 AGAGAGGCTT 0.995025 -108 ** ***** * * * Masking position 6 Map Score: 10.9123 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 ATACGACTTCTGTTTCGAAAAAAAATAAAAAC 1 75 0 TTTTCGAAAA 0.64063 -132 CGTATAAAATTTTTTCGATAAAAGATTTTAAT 1 102 1 TTTTCGATAA 0.740392 -105 TAAGAACCTTTCGTTCAATATAGTTACATACA 1 152 1 TGTTCAATTA 0.781189 -55 TCTGCATATCTCTTGCGATTAACGCCTTGCTT 2 214 1 TTTGCGATAA 0.973905 -87 TTGTATATTGTATTGCGATCTAATCACAGATA 3 126 0 TTTGCGATTA 0.961683 -90 AACAAACTCATGTTTCGATCTAGTTCGTCTCA 4 33 1 TTTTCGATTA 0.966762 -50 AATAGAAAGATTTTTCAATGAAAAAAACGCCC 6 209 0 TTTTCAATAA 0.937571 -92 * ******* ** Masking position 8 Map Score: 4.96785 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 26 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 AAAACTCGTGTACATTTTATATGGCCTCCAAA 1 48 0 TCATTTTATT 0.633678 -159 AATTAGGAAAGGCTTTTTTTATAAGAACCTTT 1 131 1 GCTTTTTTTT 0.914935 -76 TGCAGCAAGCTACTTTCTTTCTCTGGGAGTTA 2 100 1 TCTTTCTTTT 0.961195 -201 CTCTGGGAGTTACTTTGGTTATCGTCGGGGCA 2 120 1 TCTTTGGTTT 0.796199 -181 TCCAAAATGTTTCCCTCTTTTTTAAGTGTTCG 2 277 1 TCCCTCTTTT 0.813946 -24 TCTTGGCAAAGGCCTTTTATGTTTTCAACTTG 3 93 1 GCCTTTTATT 0.793483 -123 CATAGTAGATTCCTTTGTATATTGTATTGCGA 3 140 0 TCTTTGTATT 0.940573 -76 AACAACAGCCGCCTCTTTATGTAGCTGAGCAT 3 169 0 GCTCTTTATT 0.684674 -47 TTGTTTAATTTGCTTTCTTTATGGGTAGTA 3 196 1 TCTTTCTTTT 0.961195 -20 ATTCTTATTTTTTTTAAGAATCA 5 2 1 TCTTATTTTT 0.671852 -67 ACTTGTAGTTTGCTTTGTTATTGTAGGAAACT 6 34 1 TCTTTGTTAT 0.724966 -267 TCATTGAAAAATCTTTCTATTTCTTTTCTCTT 6 220 1 ACTTTCTATT 0.690121 -81 TAGATTTGTTTTCCTTGTTTCTTCTCTTAACT 6 279 0 TCCTTGTTTT 0.932648 -22 * ******** * Masking position 12 Map Score: 5.80109 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 330 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 AATTAGGAAAGGCTTTTTTTATAAGAACCT 1 131 1 GGCTTTTTTT 0.927602 -76 TCTTTCTCTGGGAGTTACTTTGGTTATCGT 2 115 1 GGAGTTACTT 0.849892 -186 GAAGAGTTGAGGCTTTAGATTGAGTGACAG 2 186 0 GGCTTTAGAT 0.85233 -115 TCTTGGCAAAGGCCTTTTATGTTTTCAACT 3 93 1 GGCCTTTTAT 0.892131 -123 TCTCATACTTGGCGCTACATTCGTACAAAC 4 60 1 GGCGCTACAT 0.956615 -23 TTATACAAGGCGTTATGTGTTTAACTTG 6 9 1 GGCGTTATGT 0.971382 -292 ATGCTGATGAGGCGCTATTTCAAGCTTTTC 6 86 1 GGCGCTATTT 0.977099 -215 AAGAGAAGAGGGCGTTTTTTTCATTGAAAA 6 200 1 GGCGTTTTTT 0.979153 -101 ********** Masking position 6 Map Score: 4.52737 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 68 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 CCTCTATTGCAGCAAGCTACTTTCTTTCTC 2 93 1 AGCAAGCTAC 0.988849 -208 CAATATACAAAGGAATCTACTATGCTCAGC 3 148 1 AGGAATCTAC 0.983562 -68 ACAATAACAAAGCAAACTACAAGTTAAACA 6 28 0 AGCAAACTAC 0.990611 -273 TTGTTATTGTAGGAAACTACTCAAAGGAAG 6 48 1 AGGAAACTAC 0.990611 -253 ********** Masking position 5 Map Score: 4.13963 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 TCTTTTATCGAAAAAATTTTATACGACTTC 1 97 0 AAAAAATTTT 0.824288 -110 TTTTTTCGATAAAAGATTTTAATTAGGAAA 1 111 1 AAAAGATTTT 0.880906 -96 AAAAAAGAGGGAAACATTTTGGAAGGAGAG 2 270 0 GAAACATTTT 0.953952 -31 GCACGGAGTAAAAACATCTT 3 1 0 AAAACATCTT 0.907542 -215 CCGTGCGTAGAAAAGATTCTCTCTTTAAAA 3 25 1 AAAAGATTCT 0.932999 -191 AAAAGAAATAGAAAGATTTTTCAATGAAAA 6 217 0 GAAAGATTTT 0.966174 -84 ********** Masking position 6 Map Score: 3.38979 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 87 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 TATAAAATGTACACGAGTTTTTATTTTTTT 1 59 1 ACACGAGTTT 0.967331 -148 GAGGATCGTATCATGAGATTGTTAATCAAG 2 243 0 TCATGAGATT 0.952773 -58 CTAGATCGAAACATGAGTTTGTTTTAGAAA 4 26 0 ACATGAGTTT 0.980746 -57 GATTTGCTGTTCATGAGTTAAGAGAAGAAA 6 264 1 TCATGAGTTA 0.952768 -37 ********** Masking position 6 Map Score: 0.624845 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 3 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 TTACAAGATAGTTTATTAGGATGAT 1 5 0 GTTATTAGGA 0.948396 -202 GATAAAAGATTTTAATTAGGAAAGGCTTTTT 1 118 1 TTTATTAGGA 0.980492 -89 TCCCCTATCCTGTCATTAGTATCACAAGAAA 1 184 0 TGTATTAGTA 0.893547 -23 TATTTTTGCATATTATTAGGAGCTCTAATCT 2 38 1 TATATTAGGA 0.952061 -263 TCTTAACAGGTGTGATTACGACTATACCCTC 2 66 1 TGTATTACGA 0.965939 -235 TATTTCAAGCTTTTCTTACGACGCTGATAGA 6 101 1 TTTCTTACGA 0.905714 -200 *** ******* Masking position 6 Map Score: 0.580588 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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: -2.74737e-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 11 ********** No masking Map Score: -2.74737e-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 12 ********** No masking Map Score: -2.74737e-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