AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_weak_ctra_reg_300.orf -o337_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 RCT00675 166 Chlamydia_trachomatis #2 RCT00676 300 Chlamydia_trachomatis Motif number 1 CGCAGGAAAACGCTTGACCCAAGAGACACT 1 18 1 CGCTTGACCC 0.994432 -149 GTTATGGCTACTCTTGACCCTAGAAAAGAA 1 104 0 CTCTTGACCC 0.997271 -63 ATCAATGAAAATTTTGACCCTCTCTTCTTC 2 16 1 ATTTTGACCC 0.875839 -285 TTTTGACCCTCTCTTCTTCCTCTATTTTTC 2 27 1 CTCTTCTTCC 0.965712 -274 TTTTTACCACCTCTTCACCTTCTCAAAAAA 2 92 1 CTCTTCACCT 0.993304 -209 ATCTAGAATGCTCTTCTTCTCGCGGGTGTA 2 184 1 CTCTTCTTCT 0.902256 -117 TCTACCACTGAGCTACACCCGCGAGAAGAA 2 197 0 AGCTACACCC 0.886457 -104 GAGGCTTGAACTCACGACCTTCACGTTGGC 2 237 0 CTCACGACCT 0.909517 -64 GAGTTCAAGCCTCATCACCCGCTTCTCTTT 2 254 1 CTCATCACCC 0.993057 -47 ********** Masking position 9 Map Score: 14.8071 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 168 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 AGAGACACTTAAACATAGAATTCATCATTT 1 39 1 AAACATAGAA 0.849068 -128 CTCTTGACCCTAGAAAAGAAAGACCCCATC 1 94 0 TAGAAAAGAA 0.878168 -73 TTCTAGGGTCAAGAGTAGCCATAACGTAAG 1 109 1 AAGAGTAGCC 0.860173 -58 AAAATAGAGGAAGAAGAGAGGGTCAAAATT 2 25 0 AAGAAGAGAG 0.973792 -276 TAAAAAGGGGAAAAATAGAGGAAGAAGAGA 2 36 0 AAAAATAGAG 0.91857 -265 AAGAGGTGGTAAAAAAAGAAAAATTGGACT 2 77 0 AAAAAAAGAA 0.937444 -224 TAAAACCTACAAGCAAAGGATTGCGAAAAA 2 143 1 AAGCAAAGGA 0.890975 -158 CACCCGCGAGAAGAAGAGCATTCTAGATAA 2 182 0 AAGAAGAGCA 0.973792 -119 TTATCCGGGAAAGAGAAGCGGGTGATGAGG 2 263 0 AAGAGAAGCG 0.955502 -38 ********** Masking position 7 Map Score: 5.91915 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 612 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 3 AGAGACACTTAAACATAGAATTCATCATTT 1 39 1 AAACATAGAA 0.769973 -128 CCTACGCATCAAAATGATGAATTCTATGTT 1 50 0 AAAATGATGA 0.900053 -117 TAAATCAATGAAAATTTTGACCCTCTCTTC 2 13 1 AAAATTTTGA 0.850242 -288 AAAAGGGGAAAAATAGAGGAAGAAGAGAGG 2 34 0 AAATAGAGGA 0.92288 -267 AAACAGCTTTAAAAAGGGGAAAAATAGAGG 2 45 0 AAAAAGGGGA 0.977013 -256 GTAAAAAAAGAAAAATTGGACTGCAAACAG 2 69 0 AAAAATTGGA 0.961273 -232 TTTTACAAAAAAACTTTGGAAAAAGGTTTT 2 118 0 AAACTTTGGA 0.967716 -183 CATTCTAGATAATCTGGGGAGTTTTTCGCA 2 164 0 AATCTGGGGA 0.90194 -137 ********** Masking position 2 Map Score: 4.58009 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 266 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 ATCTAATTCAAAATACACCTACGCATCAAA 1 67 0 AAATACACCT 0.977218 -100 CCTAGAAAAGAAAGACCCCATCTAATTCAA 1 86 0 AAAGACCCCA 0.968142 -81 GCCATAACGTAAGCACACCTGTAACCAAAT 1 126 1 AAGCACACCT 0.987662 -41 ATTTGAGAGGAAGCACACAT 1 157 1 AAGCACACAT 0.964373 -10 GGATTGCGAAAAACTCCCCAGATTATCTAG 2 160 1 AAACTCCCCA 0.952602 -141 AGAATACCCATTGGTAAGTTA 2 290 0 GAATACCCAT 0.892875 -11 ********** Masking position 2 Map Score: 2.62653 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 114 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 ATGAATTCTATGTTTAAGTGTCTCTTGGGTCAA 1 31 0 TGTTAGTGTT 0.905776 -136 ATCATTTTGATGCGTAGGTGTATTTTGAATTAG 1 62 1 TGCTAGTGTT 0.980456 -105 TCAAATCATTTGGTTACAGGTGTGCTTACGTTA 1 130 0 TGGTAAGGTT 0.987592 -37 AAAATTGGACTGCAAACAGCTTTAAAAAGGGGA 2 55 0 TGCAAAGCTT 0.957416 -246 AAAAAAACTTTGGAAAAAGGTTTTTTGAGAAGG 2 109 0 TGGAAAGGTT 0.983904 -192 CGCAATCCTTTGCTTGTAGGTTTTACAAAAAAA 2 135 0 TGCTGAGGTT 0.979104 -166 CCGGATAACTTACCAATGGGTATTCT 2 285 1 TACAAGGGTT 0.948237 -16 *** ** **** * Masking position 11 Map Score: 3.33732 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 TTTTGATCGCAGGAAAACGCTTG 1 3 1 TTGTCGCAGG 0.99586 -164 CTCAAATCATTTGGTTACAGGTGTGCTTACG 1 133 0 TTGTTACAGG 0.97711 -34 CTTTTTAAAGCTGTTTGCAGTCCAATTTTTC 2 59 1 CTGTTGCAGT 0.978765 -242 TCGCAATCCTTTGCTTGTAGGTTTTACAAAA 2 138 0 TTGTTGTAGG 0.977115 -163 GAATGCTCTTCTTCTCGCGGGTGTAGCTCAG 2 189 1 CTTTCGCGGG 0.95729 -112 *** ******* Masking position 5 Map Score: 2.04193 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 42 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: -6.51267e-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 8 ********** No masking Map Score: -6.51267e-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: -6.51267e-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