AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_ctra_reg_100.orf -o316_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 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 TCTTATTTATAAAACTTTTTAACTAGAAAC 1 23 1 AAAACTTTTT 0.940725 -278 TTATCACCGACGAGCTTCTTTTCACTCATA 1 62 1 CGAGCTTCTT 0.977187 -239 TCACTCATAACGAGCTTTTTCTTGTGTTTA 1 83 1 CGAGCTTTTT 0.964106 -218 CCTACATTCCAAAACCTCTTACCTTGCAAG 1 210 1 AAAACCTCTT 0.87285 -91 AAACAACCCGAAAGCTTCTTAGCTCATAAG 2 26 1 AAAGCTTCTT 0.988289 -36 CTACACCGGCAAACTTCTTGTACTCTAAG 3 10 1 CAAACTTCTT 0.959198 -44 AGGATAACAAAGACCTTCTTAGAGTACAAG 3 27 0 AGACCTTCTT 0.962098 -27 ACCTTTTTCCAAAGTTTTTTTGTAAAACCT 5 115 0 AAAGTTTTTT 0.821962 -186 CCTTCTCAAAAAACCTTTTTCCAAAGTTTT 5 127 0 AAACCTTTTT 0.954359 -174 TCCCCTTTTTAAAGCTGTTTGCAGTCCAAT 5 181 0 AAAGCTGTTT 0.916542 -120 ********** Masking position 3 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 0.976146 -300 AAGCTCGTCGGTGATAACAGGTAGGAGTTTC 1 48 0 GGATAACAGG 0.832587 -253 CTCGTTATGAGTGAAAAGAAGCTCGTCGGTG 1 66 0 GGAAAAGAAG 0.96534 -235 AAGCCTAAACACAAGAAAAAGCTCGTTATGA 1 87 0 AAAGAAAAAG 0.777019 -214 TCTTGCTTGCAAGGTAAGAGGTTTTGGAATG 1 214 0 AGGTAAGAGG 0.950787 -87 TACCTTGCAAGCAAGAGGAAGTCGCTTGTTA 1 229 1 GAAGAGGAAG 0.93677 -72 CTGTACTTATGAGCTAAGAAGCTTTCGGGTT 2 30 0 GGCTAAGAAG 0.952846 -32 AGCTACACCCGCGAGAAGAAGAGCATTCTAG 5 49 1 GGAGAAGAAG 0.9903 -252 TTTTTTGAGAAGGTGAAGAGGTGGTAAAAAA 5 144 1 AGTGAAGAGG 0.832446 -157 GGGGAAAAATAGAGGAAGAAGAGAGGGTCAA 5 206 1 AAGGAAGAAG 0.936559 -95 TGATTTAGCGGAAGTAAAAAGGTACAAGTAA 5 246 1 GAGTAAAAAG 0.818667 -55 CCTTCCCGCAAGGGAAGGAAGTCTTGCTGTT 6 51 0 AGGAAGGAAG 0.876126 -41 CCTTATAGTGAGATAGAAAGCTAGAGGAGC 8 10 1 GGATAGAAAG 0.894497 -27 * ********* Masking position 6 Map Score: 11.4048 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 522 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 CGACTTCCTCTTGCTTGCAAGGTAAGAGGT 1 223 0 TTGCTTGCAA 0.942036 -78 AGCTTTCGGGTTGTTTCCAACAGTATATGC 2 12 0 TTGTTTCCAA 0.757476 -50 TAACAAAGACCTTCTTAGAGTACAAGAAGT 3 23 0 CTTCTTAGAG 0.711075 -31 CAATTATTTCCTGCTTACAATGAGCGAT 4 9 0 CTGCTTACAA 0.964314 -27 GAATGCTCTTCTTCTCGCGGGTGTAGCTCA 5 47 0 CTTCTCGCGG 0.842474 -254 TCGCAATCCTTTGCTTGTAGGTTTTACAAA 5 97 1 TTGCTTGTAG 0.828528 -204 TTTCCAAAGTTTTTTTGTAAAACCTACAAG 5 110 0 TTTTTTGTAA 0.381275 -191 CTCAAAAAACCTTTTTCCAAAGTTTTTTTG 5 123 0 CTTTTTCCAA 0.814383 -178 CTTTTTAAAGCTGTTTGCAGTCCAATTTTT 5 177 0 CTGTTTGCAG 0.935285 -124 CTGCTTACGAGTTGTATAAT 6 1 1 CTGCTTACGA 0.926055 -91 TCTTGCTGTTCTGCCTACAGATATTCCTTC 6 31 0 CTGCCTACAG 0.910361 -61 TATTCGCGTCCTTCCCGCAAGGGAAGGAAG 6 61 0 CTTCCCGCAA 0.82152 -31 ********** Masking position 2 Map Score: 4.66036 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 721 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 0.941852 -288 ACAGTTTCAGAGAAAAATTATAACTTCCACTA 1 117 0 AGAAAATATA 0.881281 -184 GAAACTGTGGAGAGACATAAGAAATTGTTTTC 1 141 1 AGAACATAGA 0.946399 -160 TGTTGCAAAGATATAAATAAGACGAGAATGAA 1 170 0 ATAAAATAGA 0.962942 -131 TGGTAAAAAAAGAAAAATTGGACTGCAAACAG 5 165 1 AGAAAATGGA 0.974122 -136 GCAAACAGCTTTAAAAAGGGGAAAAATAGAGG 5 189 1 TTAAAAGGGA 0.838551 -112 GGGGAAAAATAGAGGAAGAAGAGAGGGTCAAA 5 206 1 AGAGAAGAGA 0.909076 -95 ATACTCAACCTGAAAAATCAGATAGCGAGAGA 9 11 1 TGAAAATAGA 0.976436 -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 GTCGGTGATAACAGGTAGGAGTTTCTAGTTA 1 42 0 ACAGTAGGAG 0.863115 -259 TCTTGCTTGCAAGGTAAGAGGTTTTGGAATG 1 214 0 AAGGAAGAGG 0.912497 -87 TCTTACCTTGCAAGCAAGAGGAAGTCGCTTG 1 226 1 CAAGAAGAGG 0.912496 -75 TTTTTTTGTAAAACCTACAAGCAAAGGATTG 5 100 0 AAACTACAAG 0.862234 -201 TAAAAAGGGGAAAAATAGAGGAAGAAGAGAG 5 200 1 AAAATAGAGG 0.943156 -101 GCGGAAGTAAAAAGGTACAAGTAACAGGTCT 5 253 1 AAAGTACAAG 0.936838 -48 TTCTCCTCTAAAACATAGGGGGTTGACAGAC 5 280 0 AAACTAGGGG 0.962444 -21 AGTGAGATAGAAAGCTAGAGGAGCGGCACG 8 17 1 AAAGTAGAGG 0.990762 -20 **** ****** Masking position 7 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 CACGACCTTCACGTTGGCAACGT 5 4 1 GACCTTCACG 0.970341 -297 CTCAGTGGTAGAGCGCCACGTTGCCAACGT 5 21 0 GAGCGCCACG 0.994604 -280 CTCTACCACTGAGCTACACCCGCGAGAAGA 5 38 1 GAGCTACACC 0.970341 -263 AAAGCTAGAGGAGCGGCACG 8 27 1 GAGCGGCACG 0.99706 -10 GATAGCGAGAGAGATGCAAGG 9 31 1 GAGATGCAAG 0.92024 -11 ********** Masking position 8 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 ACAAGAAAAAGCTCGTTATGAGTGAAAAGAAG 1 76 0 GCTCGTATAG 0.939161 -225 TTGTGTTTAGGCTTAGTGGAAGTTATAATTTT 1 104 1 GCTTATGGAG 0.977706 -197 GAGCTAAGAAGCTTTCGGGTTGTTTCCAACAG 2 19 0 GCTTTGGGTG 0.815762 -43 ATCGCTCATTGTAAGCAGGAAATAA 4 4 1 GCTCATGTAG 0.96758 -32 CGCGGGTGTAGCTCAGTGGTAGAGCGCCACGT 5 30 0 GCTCATGGAG 0.985903 -271 CTGCTTACGAGTTGTATAATGAAG 6 3 1 GCTTAGAGTG 0.93043 -89 GACTTCCTTCCCTTGCGGGAAGGACGCGAATA 6 59 1 CCTTGGGGAG 0.831969 -33 TTCATACTCTTAGTAGGTGGCCT 7 8 1 TCTTATAGTG 0.86026 -16 TAGCTTTCTATCTCACTATAAGG 8 2 0 TCTCATATAG 0.85982 -35 CTTGCATCTCTCTCGCTATCTGATTTTTCAGG 9 19 0 TCTCGTATTG 0.775569 -23 ***** *** ** Masking position 3 Map Score: 5.24598 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 201 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