AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_mixed22_ctra_reg_100.orf -o308_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 RCT00361 28 Chlamydia_trachomatis #2 RCT00362 68 Chlamydia_trachomatis #3 RCT00363 300 Chlamydia_trachomatis #4 RCT00547 294 Chlamydia_trachomatis #5 RCT00734 153 Chlamydia_trachomatis Motif number 1 ATGATTCTTAAAAAAAATAAGAAT 2 5 0 AAAAAAATAA 0.830663 -64 GAAACTACTCAAAGGAAGAGCTGAATATGC 3 60 1 AAAGGAAGAG 0.983229 -241 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 3 179 0 AAGAGAAGAG 0.983229 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 3 190 1 AAGAGAAGAG 0.983229 -111 AGGGAAGAGAAAAGAAATAGAAAGATTTTT 3 226 0 AAAGAAATAG 0.926097 -75 ATCATACACACAGGGAAGAGAAAAGAAATA 3 237 0 CAGGGAAGAG 0.871629 -64 TTCATGAGTTAAGAGAAGAAACAAGGAAAA 3 273 1 AAGAGAAGAA 0.943984 -28 GATAATTCCTAAAAAAATAAAAATAACAAA 4 14 1 AAAAAAATAA 0.830663 -281 AACTTACGCAAAAAGAATTAATTATGTTTT 4 125 0 AAAAGAATTA 0.851074 -170 CCTCCTGTTAAAAAAAATTGCAAGGCAACG 4 177 0 AAAAAAATTG 0.887645 -118 GAAGAATCTAAAAAGAATTGCTTTTTTAAA 5 33 1 AAAAGAATTG 0.95211 -121 TTTTAAATAGAAAAAAAGTGAGAAACCCTT 5 56 1 AAAAAAAGTG 0.936256 -98 TTGGAAGATAAAAGGTAGAGACTTCTTCCG 5 87 1 AAAGGTAGAG 0.861858 -67 ********** Masking position 7 Map Score: 18.7803 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 705 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 TTCTTATTTTTTTTAAGAATCATGTTGGGTAT 2 12 1 TTTTAGATCA 0.951134 -57 CAGCTCTTCCTTTGAGTAGTTTCCTACAATAA 3 51 0 TTTGATATTT 0.85198 -250 ATTTTTATTTTTTTAGGAATTATCGCG 4 6 0 TTTTAGATTA 0.97173 -289 TTAAAAACGTTTTTATTAATTAACTTGTTAAA 4 78 0 TTTTATATTA 0.95589 -217 ATAAAAACGTTTTTAATATTTTGCTTTTAATA 4 94 1 TTTTATATTT 0.95589 -201 TCCGCTATGATTTTAAGACTTTACTATTCAGT 4 265 0 TTTTAGATTT 0.97173 -30 AAAGCAATTCTTTTTAGATTCTTCTAGATGCA 5 25 0 TTTTTGATCT 0.876932 -129 TTTCTCACTTTTTTTCTATTTAAAAAAGCAAT 5 49 0 TTTTTTATTA 0.888058 -105 ***** ** *** Masking position 8 Map Score: 6.21432 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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 GGCCCCTTAATCGTTTTCTAAAA 1 3 0 TCGTTTCTAA 0.86208 -26 CGTTATGTGTTTAACTTGTAGTTTGCTTTGT 3 21 1 TTACTTGTAG 0.881621 -280 AACTTGTAGTTTGCTTTGTTATTGTAGGAAA 3 33 1 TTGTTTGTTA 0.747791 -268 ACTAACAATATTAAATTCTAACGATCTGATT 4 49 1 TTAATTCTAA 0.765648 -246 TTTTTATTAATTAACTTGTTAAATCAGATCG 4 70 0 TTACTTGTTA 0.909684 -225 GCGTGTGTCGTTGCCTTGCAATTTTTTTTAA 4 169 1 TTGCTTGCAA 0.949785 -126 TCTCTACCTTTTATCTTCCAATAAGGGTTTC 5 77 0 TTACTTCCAA 0.926158 -77 GCCTTCTAATTCAGCTTGTAATCTAATGATG 5 127 0 TCACTTGTAA 0.96321 -27 AATCTCGCCTTCTAATTCAGCTTGT 5 139 0 TCGCTTCTAA 0.964608 -15 *** ******* Masking position 6 Map Score: 4.32518 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 114 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 AGCGTCGTAAGAAAAGCTTGAAATAGCGCC 3 96 0 GAAAAGCTTG 0.982619 -205 CCTCCTGCGCGAAAGGCTTGGACTTCACGC 4 215 1 GAAAGGCTTG 0.988212 -80 AATCATAGCGGAGATGCTTT 4 285 1 GAGATGCTTT 0.966197 -10 AATCTAAAAAGAATTGCTTTTTTAAATAGA 5 37 1 GAATTGCTTT 0.950701 -117 ATCTAATGATGAAATTCTTGACGGAAGAAG 5 108 0 GAAATTCTTG 0.964769 -46 ********** Masking position 8 Map Score: 3.0495 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 64 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 AACGATTAAGGGGCCTTATT 1 19 1 GGGCCTTATT 0.975061 -10 TTATACAAGGCGTTATGTGTTTAACTT 3 8 1 AGGCGTTATG 0.98289 -293 TATGCTGATGAGGCGCTATTTCAAGCTTTT 3 85 1 AGGCGCTATT 0.986801 -216 CAAGAGAAGAGGGCGTTTTTTTCATTGAAA 3 199 1 GGGCGTTTTT 0.976658 -102 CTGAATTAGAAGGCGAGATT 5 144 1 AGGCGAGATT 0.957861 -10 ********** Masking position 9 Map Score: 1.72479 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 39 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 TGGACTTCACGCTTTCTCTCGTGCTGTCTC 4 233 1 GCTTTCTCTC 0.993621 -62 TTTCTCTCGTGCTGTCTCTCACTGAATAGT 4 245 1 GCTGTCTCTC 0.99242 -50 TTCCAATAAGGGTTTCTCACTTTTTTTCTA 5 63 0 GGTTTCTCAC 0.979592 -91 ********** Masking position 5 Map Score: 0.562929 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 14 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 ATTTGCTGTTCATGAGTTAAGAGAAGAAAC 3 265 1 CATGAGTTAA 0.95598 -36 TTTTTTTTAACAGGAGGTACCGTTACCTCC 4 190 1 CAGGAGGTAC 0.99269 -105 GCCTTTCGCGCAGGAGGTAACGGTACCTCC 4 202 0 CAGGAGGTAA 0.993849 -93 ********** Masking position 5 Map Score: 0.126727 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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: 1.44541e-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: 1.44541e-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: 1.44541e-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