AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_ctra_reg_300.orf -o020_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 RCT00053 300 Chlamydia_trachomatis #2 RCT00234 300 Chlamydia_trachomatis #3 RCT00380 245 Chlamydia_trachomatis #4 RCT00382 165 Chlamydia_trachomatis #5 RCT00385 300 Chlamydia_trachomatis #6 RCT00530 300 Chlamydia_trachomatis Motif number 1 TTTTTTTGAAAAATAAAAATTTTGCTATGGGAA 1 239 1 AAAAAATTTT 0.610477 -62 TGATACTTTTAGAAAATTCCCATAGCAAAATTT 1 255 0 AGAAACCCAT 0.811577 -46 GGGGTTTTCTAGAGAGTTCCTTTGTTGCATTTT 2 19 0 AGAAGCCTTT 0.914898 -282 GGAACTCTCTAGAAAACCCCCTTATAAGGCCTT 2 32 1 AGAAACCCTT 0.981691 -269 CTATGCTACAAAAAAAAACTTTTCGGCACTACC 2 126 0 AAAAACTTTT 0.943356 -175 AATGTCTTTCAAATAAATCTTTTGAATTTCACT 2 241 0 AAAAACTTTT 0.943158 -60 AAACGAAGAGAGAAAACCCTCTTCGTTAAAAGA 3 14 0 AGAAACTCTT 0.982058 -232 TTGAAACCACAGAAAAGACGCTTAAACCTTAAA 3 49 0 AGAAACGCTT 0.911578 -197 TTTTACAGATAAAAAATGCCTTTTGAGGGTTTA 3 149 0 AAAAACCTTT 0.942253 -97 TCTTGTGTTGAAAAGAACCTCTTCTTAGAAAGG 5 120 1 AAAGACTCTT 0.773246 -181 GACCGCCCGTAGAGAAAACCTTTCTAAGAAGAG 5 138 0 AGAAACCTTT 0.967439 -163 TAGATACACGAAAAAGCCCTCTCCGGATCTGAT 5 218 0 AAAAGCTCTC 0.800526 -83 TAGGTCGTGACAACAATACTTTTTAGCAATCTT 5 258 0 CAAAACTTTT 0.680757 -43 TGAGCATTCGAAATAACACTCTTACGTTCCTAT 6 87 1 AAAAACTCTT 0.968092 -214 GGAAAGGAAAAGAGAGGTCCTTCAGACAAATAC 6 187 0 AGAAGCCTTC 0.797181 -114 AGGCTTGGAAGGAGAATCCTCTTCCCTCAGATA 6 225 1 GGAAACTCTT 0.874095 -76 CTCTTCCCTCAGATAATCATCTCATATGGATCG 6 243 1 AGAAAATCTC 0.649842 -58 *** ** ***** Masking position 3 Map Score: 17.1215 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 615 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 ATGCAGTTACCCTTGGTAGGAAGCAAGTAAAT 1 30 0 CCTTGTGGAA 0.990054 -271 GCTCTGCTAGCTTTTGTAAGAAGTCAGGAGGC 1 170 1 CTTTTTAGAA 0.826952 -131 CTAGAGAGTTCCTTTGTTGCATTTTAACAGAT 2 12 0 CCTTTTGCAT 0.827087 -289 ATTTCATTTTCCTTGTTCAGAAGGCCTTATAA 2 53 0 CCTTGTAGAA 0.987232 -248 TTCGGGATACCCTCGTTTGGAAGGCTACTTGG 4 54 1 CCTCGTGGAA 0.979862 -112 GTAGAGAAAACCTTTCTAAGAAGAGGTTCTTT 5 131 0 CCTTTTAGAA 0.979898 -170 CCGCTGTTTGCCTTGATCAGATCCGGAGAGGG 5 203 1 CCTTGTAGAT 0.975937 -98 TACCACTTCTCCTCATTGAGATTTTATCCACC 6 134 1 CCTCATAGAT 0.791621 -167 TCCTTCCAAGCCTTTCTAGGAAAGGAAAAGAG 6 206 0 CCTTTTGGAA 0.984315 -95 ***** * **** Masking position 7 Map Score: 8.92947 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 80 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 AAATTGGCTCTCAGGGGGTTTCC 1 4 0 TCAGGGGGTT 0.941379 -297 TCTATCGATTGAAGGTGATACTTTTAGAAA 1 273 0 GAAGGTGATA 0.675129 -28 GAAGGCCTTATAAGGGGGTTTTCTAGAGAG 2 36 0 TAAGGGGGTT 0.976658 -265 GGATAGAGATGAAGTTGGTTTGAAGTTTTG 2 87 0 GAAGTTGGTT 0.852382 -214 ATCTTTTAACGAAGAGGGTTTTCTCTCTTC 3 13 1 GAAGAGGGTT 0.979839 -233 ACACTCACCTGAAGGCGGTTAAGCACTCCC 3 102 0 GAAGGCGGTT 0.963117 -144 CTCAATATGAGAAGAAGATTATCAACTGGC 3 182 0 GAAGAAGATT 0.829673 -64 AGTTCAGAAATAAGGAGATTC 3 235 1 TAAGGAGATT 0.807455 -11 CATAGTTTTTGCAGGTTGTTCGTTTAGGAA 4 127 1 GCAGGTTGTT 0.724682 -39 AATAGGAACGTAAGAGTGTTATTTCGAATG 6 91 0 TAAGAGTGTT 0.733398 -210 TTATCTGAGGGAAGAGGATTCTCCTTCCAA 6 229 0 GAAGAGGATT 0.946967 -72 ********** Masking position 3 Map Score: 8.47154 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 169 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 ATAAACAAATAGATCAGGAGAGATTTTGGCTA 1 95 1 AACAGGAGAG 0.892755 -206 TTTTCTGGGTAGTGCCGAAAAGTTTTTTTTTG 2 119 1 ATCCGAAAAG 0.604085 -182 GCGCGGAAAAGTAACCGGAAAGGTCCGGCCTT 2 192 0 GACCGGAAAG 0.968265 -109 AAACCTTAAAGAAAACGAAGAGAGAAAACCCT 3 27 0 GAACGAAGAG 0.973636 -219 GTTTAGTGTAACATAGGGAGTGCTTAACCGCC 3 87 1 AAAGGGAGTG 0.810308 -159 CTTGGGTAAAGAGGACGAAGAGTCTGTCTCAG 4 81 1 GGACGAAGAG 0.885083 -85 TGCCTTGATCAGATCCGGAGAGGGCTTTTTCG 5 211 1 AACCGGAGAG 0.968269 -90 TATTTCGAATGCTCAGGGAGAGAGCGGTACCC 6 70 0 GTAGGGAGAG 0.936169 -231 AGAAAAAATAGGAACGTAAGAGTGTTATTTCG 6 95 0 GACGTAAGAG 0.809207 -206 AGGAGAAGTGGTAGCAGGAGAGAAAAAATAGG 6 115 0 GACAGGAGAG 0.962699 -186 AGCCTTTCTAGGAAAGGAAAAGAGAGGTCCTT 6 198 0 GAAGGAAAAG 0.922552 -103 AACACTCATTGAAGAGGAAATGTT 6 287 1 GAAGGAAATG 0.727439 -14 * * ******** Masking position 9 Map Score: 6.64424 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 347 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 GCAAAGTTTGCTTTTTTTGAAAAATAAAAATT 1 228 1 CTTTTTGAAA 0.977286 -73 AAGTTGGTTTGAAGTTTTGAAATTTCATTTTC 2 74 0 GATTTTGAAA 0.959416 -227 TTACACTAAACATTTTTTGAAACCACAGAAAA 3 66 0 CTTTTTGAAA 0.977286 -180 TTCAAGTTTTGAAACTTGATTTTT 4 3 1 CATTTTGAAA 0.982464 -163 AGATATTAGGCGACTTTTGAAAAAAAATCACC 5 37 0 CATTTTGAAA 0.982464 -264 AATCCTGTGTCTTGTGTTGAAAAGAACCTCTT 5 111 1 CTTGTTGAAA 0.940235 -190 ATACTTTTTAGCAATCTTGAAAAACTAGATAC 5 244 0 GATCTTGAAA 0.896309 -57 * * ******** Masking position 10 Map Score: 7.1956 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 AGACAGAGCAAAAAGTGAGCAGGCATAAACAA 1 71 1 AAAGTAGCAG 0.988052 -230 GACTTCTTACAAAAGCTAGCAGAGCTTGGCTT 1 163 0 AAAGCAGCAG 0.979092 -138 AGCTTTTGTAAGAAGTCAGGAGGCTAGGGTAT 1 178 1 AAAGTAGGAG 0.966951 -123 GCCGGCGCGGAAAAGTAACCGGAAAGGTCCGG 2 196 0 AAAGTACCGG 0.966424 -105 CTTCGAGTTCAGAAATAAGGAGATTC 3 230 1 AAAATAGGAG 0.869994 -16 ACTTTTGAAAAAAAATCACCACAAATCACAAT 5 25 0 AAAATACCAC 0.804427 -276 TTTTTTGATTATAAGTAACCGCTGTTTGCCTT 5 185 1 AAAGTACCGC 0.910581 -116 GGTACCCACGATAAGCAAGCAGAATCCCGACT 6 45 0 AAAGCAGCAG 0.979092 -256 * **** ***** Masking position 8 Map Score: 4.94661 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 7 TAACTGCATCTTTTGCTCAGACAGAGCAAA 1 53 1 TTTTGCTCAG 0.96132 -248 CCTGCTCACTTTTTGCTCTGTCTGAGCAAA 1 64 0 TTTTGCTCTG 0.961326 -237 CAGGAGAGATTTTGGCTAATAAAATACTCA 1 109 1 TTTGGCTAAT 0.793517 -192 AAAATAAAAATTTTGCTATGGGAATTTTCT 1 248 1 TTTTGCTATG 0.940496 -53 TGAATTTCACTCTGGCTATGCAAGGCCGGC 2 222 0 TCTGGCTATG 0.953719 -79 GGACGAAGAGTCTGTCTCAGCCCTTTAGGG 4 93 1 TCTGTCTCAG 0.833692 -73 ********** Masking position 7 Map Score: 0.747058 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 103 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 8 TCTGTCTGAGCAAAAGATGCAGTTACCCTTG 1 47 0 CAAAAGAGCA 0.956289 -254 TTTTATTTTTCAAAAAAAGCAAACTTTGCTT 1 226 0 CAAAAAAGCA 0.895307 -75 TTATTAAACCCTCAAAAGGCATTTTTTATCT 3 145 1 CTCAAAAGCA 0.90492 -101 GTCCTCTTTACCCAAGTAGCCTTCCAAACGA 4 66 0 CCCAAGTGCC 0.925947 -100 AAAAAATCACCACAAATCACAATCAAGAATT 5 17 0 CACAAATACA 0.84204 -284 GATTTTTTTTCAAAAGTCGCCTAATATCTGC 5 40 1 CAAAAGTGCC 0.930397 -261 CTGCAGGACGCTCAAGATACCACGGTTTTTA 5 67 1 CTCAAGAACC 0.903183 -234 TTCTTTTCAACACAAGACACAGGATTTTATC 5 106 0 CACAAGAACA 0.956289 -195 ******* *** Masking position 5 Map Score: 1.9444 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 90 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 9 CCCAGAAAAATGGATAGAGATGAAGTTGGT 2 98 0 TGGATAGAGA 0.945049 -203 AGATTCTCTTGGATAAAGGGTTCCTGAAA 2 282 0 TGGATAAAGG 0.969778 -19 GAAGGCTACTTGGGTAAAGAGGACGAAGAG 4 73 1 TGGGTAAAGA 0.945049 -93 TTTATTTTAATGGATAAAATCCTGTGTCTT 5 94 1 TGGATAAAAT 0.944271 -207 TACATCTGGGTGGATAAAATCTCAATGAGG 6 144 0 TGGATAAAAT 0.944271 -157 ********** Masking position 5 Map Score: 0.466812 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 24 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 AGCTTGGCTTATCAGTTGAACAAATACTTT 1 143 0 ATCAGTTGAA 0.748316 -158 TATCTGTTAAAATGCAACAAA 2 2 1 ATCTGTTAAA 0.957903 -299 TTTCAAATAAATCTTTTGAATTTCACTCTG 2 238 0 ATCTTTTGAA 0.860716 -63 AGATCTTTTAACGAAGAGGGTT 3 3 1 ATCTTTTAAC 0.860167 -243 TAACATGAAAATCTGTACACTCACCTGAAG 3 118 0 ATCTGTACAC 0.877487 -128 GGCATTTTTTATCTGTAAAAGCCAGTTGAT 3 162 1 ATCTGTAAAA 0.877908 -84 GGCTTTAGTATTCTGTTAACTCAATATGAG 3 201 0 TTCTGTTAAC 0.855723 -45 TAAGAAGAGGTTCTTTTCAACACAAGACAC 5 117 0 TTCTTTTCAA 0.739962 -184 CCCTCTCCGGATCTGATCAAGGCAAACAGC 5 205 0 ATCTGATCAA 0.812443 -96 ********** Masking position 2 Map Score: 2.20168 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 118 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 AACCCCCTTATAAGGCCTTCTGAACAAGGA 2 46 1 TAAGGCCTTC 0.604174 -255 ACCGGAAAGGTCCGGCCTTCGCAAATATAA 2 181 0 TCCGGCCTTC 0.981391 -120 ACTTTTCCGCGCCGGCCTTGCATAGCCAGA 2 212 1 GCCGGCCTTG 0.953863 -89 AACAGAATACTAAAGCCTTCGAGTTCAGAA 3 214 1 TAAAGCCTTC 0.862411 -32 TGTTTTATATGCGATCCTTCGGGATACCCT 4 37 1 GCGATCCTTC 0.9221 -129 AAGGAAAAGAGAGGTCCTTCAGACAAATAC 6 187 0 GAGGTCCTTC 0.902661 -114 ********** Masking position 8 Map Score: 0.405256 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 45 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: -2.68342e-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 13 ********** No masking Map Score: -2.68342e-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 14 ********** No masking Map Score: -2.68342e-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