AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_ctra_reg_300.orf -o316_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 RCT00332 35 Chlamydia_trachomatis #5 RCT00677 300 Chlamydia_trachomatis #6 RCT00695 91 Chlamydia_trachomatis #7 RCT00696 23 Chlamydia_trachomatis #8 RCT00697 36 Chlamydia_trachomatis #9 RCT00698 41 Chlamydia_trachomatis Motif number 1 GTTTCTAGTTAAAAAGTTTTATAAATAAGA 1 23 0 AAAAAGTTTT 0.94117 -278 TATGAGTGAAAAGAAGCTCGTCGGTGATAA 1 62 0 AAGAAGCTCG 0.977514 -239 TAAACACAAGAAAAAGCTCGTTATGAGTGA 1 83 0 AAAAAGCTCG 0.964614 -218 CTTGCAAGGTAAGAGGTTTTGGAATGTAGG 1 210 0 AAGAGGTTTT 0.874471 -91 CTTATGAGCTAAGAAGCTTTCGGGTTGTTT 2 26 0 AAGAAGCTTT 0.988459 -36 CTTAGAGTACAAGAAGTTTGCCGGTGTAG 3 10 0 AAGAAGTTTG 0.959772 -44 CTTGTACTCTAAGAAGGTCTTTGTTATCCT 3 27 1 AAGAAGGTCT 0.962633 -27 AGGTTTTACAAAAAAACTTTGGAAAAAGGT 5 115 1 AAAAAACTTT 0.824105 -186 AAAACTTTGGAAAAAGGTTTTTTGAGAAGG 5 127 1 AAAAAGGTTT 0.954917 -174 ATTGGACTGCAAACAGCTTTAAAAAGGGGA 5 181 1 AAACAGCTTT 0.917652 -120 ********** Masking position 8 Map Score: 12.9859 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 537 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 TAAATAAGAGAGGATAAGAAG 1 1 0 AGATAAGAAG 0.971702 -300 AAGCTCGTCGGTGATAACAGGTAGGAGTTTC 1 48 0 GGATAACAGG 0.762834 -253 CTCGTTATGAGTGAAAAGAAGCTCGTCGGTG 1 66 0 GGAAAAGAAG 0.965582 -235 AAGCCTAAACACAAGAAAAAGCTCGTTATGA 1 87 0 AAAGAAAAAG 0.7626 -214 TCTTGCTTGCAAGGTAAGAGGTTTTGGAATG 1 214 0 AGGTAAGAGG 0.916987 -87 TACCTTGCAAGCAAGAGGAAGTCGCTTGTTA 1 229 1 GAAGAGGAAG 0.889714 -72 CTGTACTTATGAGCTAAGAAGCTTTCGGGTT 2 30 0 GGCTAAGAAG 0.968036 -32 AACTTCTTGTACTCTAAGAAGGTCTTTGTTA 3 22 1 ATCTAAGAAG 0.765214 -32 AGCTACACCCGCGAGAAGAAGAGCATTCTAG 5 49 1 GGAGAAGAAG 0.986259 -252 TTTTTTGAGAAGGTGAAGAGGTGGTAAAAAA 5 144 1 AGTGAAGAGG 0.791818 -157 GTGAAGAGGTGGTAAAAAAAGAAAAATTGGA 5 156 1 GTAAAAAAAG 0.664204 -145 ACTGCAAACAGCTTTAAAAAGGGGAAAAATA 5 186 1 GTTTAAAAAG 0.579904 -115 GGGGAAAAATAGAGGAAGAAGAGAGGGTCAA 5 206 1 AAGGAAGAAG 0.892174 -95 TGATTTAGCGGAAGTAAAAAGGTACAAGTAA 5 246 1 GAGTAAAAAG 0.841759 -55 CCTTCCCGCAAGGGAAGGAAGTCTTGCTGTT 6 51 0 AGGAAGGAAG 0.814812 -41 CCTTATAGTGAGATAGAAAGCTAGAGGAGC 8 10 1 GGATAGAAAG 0.897924 -27 * ********* Masking position 6 Map Score: 11.9906 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 732 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 ACCTCTTACCTTGCAAGCAAGAGGAAGTCG 1 223 1 TTGCAAGCAA 0.9394 -78 GCATATACTGTTGGAAACAACCCGAAAGCT 2 12 1 TTGGAAACAA 0.847098 -50 ATCGCTCATTGTAAGCAGGAAATAATTG 4 9 1 TTGTAAGCAG 0.947676 -27 TGAGCTACACCCGCGAGAAGAAGAGCATTC 5 47 1 CCGCGAGAAG 0.865154 -254 AAGCAAAGGATTGCGAAAAACTCCCCAGAT 5 83 0 TTGCGAAAAA 0.821628 -218 TTTGTAAAACCTACAAGCAAAGGATTGCGA 5 97 0 CTACAAGCAA 0.819571 -204 CTTGTAGGTTTTACAAAAAAACTTTGGAAA 5 110 1 TTACAAAAAA 0.534049 -191 CAAAAAAACTTTGGAAAAAGGTTTTTTGAG 5 123 1 TTGGAAAAAG 0.847348 -178 AAAAATTGGACTGCAAACAGCTTTAAAAAG 5 177 1 CTGCAAACAG 0.951436 -124 ATTATACAACTCGTAAGCAG 6 1 0 TCGTAAGCAG 0.896549 -91 GAAGGAATATCTGTAGGCAGAACAGCAAGA 6 31 1 CTGTAGGCAG 0.850218 -61 CTTCCTTCCCTTGCGGGAAGGACGCGAATA 6 61 1 TTGCGGGAAG 0.885828 -31 ********** Masking position 9 Map Score: 6.7615 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 606 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 4 TTAAAAAGTTTTATAAATAAGAGAGGATAAGA 1 13 0 TTAAAATAGA 0.931862 -288 ACAGTTTCAGAGAAAAATTATAACTTCCACTA 1 117 0 AGAAAATATA 0.862405 -184 GAAACTGTGGAGAGACATAAGAAATTGTTTTC 1 141 1 AGAACATAGA 0.937138 -160 TGTTGCAAAGATATAAATAAGACGAGAATGAA 1 170 0 ATAAAATAGA 0.956407 -131 TGGTAAAAAAAGAAAAATTGGACTGCAAACAG 5 165 1 AGAAAATGGA 0.969497 -136 GCAAACAGCTTTAAAAAGGGGAAAAATAGAGG 5 189 1 TTAAAAGGGA 0.814312 -112 GGGGAAAAATAGAGGAAGAAGAGAGGGTCAAA 5 206 1 AGAGAAGAGA 0.894088 -95 ATACTCAACCTGAAAAATCAGATAGCGAGAGA 9 11 1 TGAAAATAGA 0.972212 -31 *** **** *** Masking position 7 Map Score: 3.43037 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 165 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 TAACTAGAAACTCCTACCTGTTATCACCGAC 1 42 1 CTCCTACTGT 0.88249 -259 CATTCCAAAACCTCTTACCTTGCAAGCAAGA 1 214 1 CCTCTTCCTT 0.925486 -87 CAAGCGACTTCCTCTTGCTTGCAAGGTAAGA 1 226 0 CCTCTTCTTG 0.925484 -75 CAATCCTTTGCTTGTAGGTTTTACAAAAAAA 5 100 1 CTTGTAGTTT 0.881717 -201 CTCTCTTCTTCCTCTATTTTTCCCCTTTTTA 5 200 0 CCTCTATTTT 0.951834 -101 AGACCTGTTACTTGTACCTTTTTACTTCCGC 5 253 0 CTTGTACTTT 0.946426 -48 GTCTGTCAACCCCCTATGTTTTAGAGGAGAA 5 280 1 CCCCTAGTTT 0.968277 -21 CGTGCCGCTCCTCTAGCTTTCTATCTCACT 8 17 0 CCTCTACTTT 0.992232 -20 ****** **** Masking position 5 Map Score: 3.03316 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 187 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 ACGTTGCCAACGTGAAGGTCGTG 5 4 0 CGTGAAGGTC 0.96717 -297 ACGTTGGCAACGTGGCGCTCTACCACTGAG 5 21 1 CGTGGCGCTC 0.994011 -280 TCTTCTCGCGGGTGTAGCTCAGTGGTAGAG 5 38 0 GGTGTAGCTC 0.96717 -263 CGTGCCGCTCCTCTAGCTTT 8 27 0 CGTGCCGCTC 0.996737 -10 CCTTGCATCTCTCTCGCTATC 9 31 0 CTTGCATCTC 0.912197 -11 ********** Masking position 3 Map Score: 1.84095 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 36 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 7 CTTCTTTTCACTCATAACGAGCTTTTTCTTGT 1 76 1 CTATAAGAGC 0.537767 -225 AAAATTATAACTTCCACTAAGCCTAAACACAA 1 104 0 CTCCACAAGC 0.940502 -197 TGTCTCTCCACAGTTTCAGAGAAAAATTATAA 1 126 0 CATTTCGAGA 0.455126 -175 CAAAACCTCTTACCTTGCAAGCAAGAGGAAGT 1 219 1 TACTTGAAGC 0.635056 -82 TAAATGATTTCACCTTGAGAGATCTCTTCCTT 1 265 1 CACTTGGAGA 0.949207 -36 TGAGAGATCTCTTCCTTAAAGAGGATATTGA 1 280 1 CTCCTTAAGA 0.578251 -21 CTGTTGGAAACAACCCGAAAGCTTCTTAGCTC 2 19 1 CACCCGAAGC 0.962244 -43 ATCGCTCATTGTAAGCAGGAAATAAT 4 5 1 CTATTGAAGC 0.891507 -31 ACGTGGCGCTCTACCACTGAGCTACACCCGCG 5 30 1 CTCCACGAGC 0.950523 -271 CTTCATTATACAACTCGTAAGCAG 6 3 0 CACTCGAAGC 0.965541 -89 TATTCGCGTCCTTCCCGCAAGGGAAGGAAGTC 6 59 0 CTCCCGAAGG 0.808351 -33 AGGCCACCTACTAAGAGTATGAA 7 8 0 CACTACAAGA 0.903364 -16 CCTTATAGTGAGATAGAAAGCTA 8 2 1 CTATAGGAGA 0.864559 -35 CCTGAAAAATCAGATAGCGAGAGAGATGCAAG 9 19 1 CAATAGGAGA 0.864559 -23 ** **** **** Masking position 10 Map Score: 5.95336 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 558 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: -6.44162e-13 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: -6.44162e-13 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: -6.44162e-13 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