AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_mixed22_ctra_reg_300.orf -o308_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 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 0.829762 -64 GAAACTACTCAAAGGAAGAGCTGAATATGC 3 60 1 AAAGGAAGAG 0.983123 -241 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 3 179 0 AAGAGAAGAG 0.983123 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 3 190 1 AAGAGAAGAG 0.983123 -111 AGGGAAGAGAAAAGAAATAGAAAGATTTTT 3 226 0 AAAGAAATAG 0.925658 -75 ATCATACACACAGGGAAGAGAAAAGAAATA 3 237 0 CAGGGAAGAG 0.870913 -64 TTCATGAGTTAAGAGAAGAAACAAGGAAAA 3 273 1 AAGAGAAGAA 0.943645 -28 GATAATTCCTAAAAAAATAAAAATAACAAA 4 14 1 AAAAAAATAA 0.829762 -281 AACTTACGCAAAAAGAATTAATTATGTTTT 4 125 0 AAAAGAATTA 0.850263 -170 CCTCCTGTTAAAAAAAATTGCAAGGCAACG 4 177 0 AAAAAAATTG 0.887006 -118 GAAGAATCTAAAAAGAATTGCTTTTTTAAA 5 33 1 AAAAGAATTG 0.951818 -121 TTTTAAATAGAAAAAAAGTGAGAAACCCTT 5 56 1 AAAAAAAGTG 0.935874 -98 TTGGAAGATAAAAGGTAGAGACTTCTTCCG 5 87 1 AAAGGTAGAG 0.861096 -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 0.954877 -57 CAGCTCTTCCTTTGAGTAGTTTCCTACAATAA 3 51 0 TTTGATATTT 0.86222 -250 ATTTTTATTTTTTTAGGAATTATCGCG 4 6 0 TTTTAGATTA 0.973939 -289 TTAAAAACGTTTTTATTAATTAACTTGTTAAA 4 78 0 TTTTATATTA 0.959285 -217 ATAAAAACGTTTTTAATATTTTGCTTTTAATA 4 94 1 TTTTATATTT 0.959285 -201 TCCGCTATGATTTTAAGACTTTACTATTCAGT 4 265 0 TTTTAGATTT 0.973939 -30 AAAGCAATTCTTTTTAGATTCTTCTAGATGCA 5 25 0 TTTTTGATCT 0.885677 -129 TTTCTCACTTTTTTTCTATTTAAAAAAGCAAT 5 49 0 TTTTTTATTA 0.896106 -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 0.861324 -26 CGTTATGTGTTTAACTTGTAGTTTGCTTTGT 3 21 1 TTACTTGTAG 0.880958 -280 AACTTGTAGTTTGCTTTGTTATTGTAGGAAA 3 33 1 TTGTTTGTTA 0.746594 -268 ACTAACAATATTAAATTCTAACGATCTGATT 4 49 1 TTAATTCTAA 0.764551 -246 TTTTTATTAATTAACTTGTTAAATCAGATCG 4 70 0 TTACTTGTTA 0.909162 -225 GCGTGTGTCGTTGCCTTGCAATTTTTTTTAA 4 169 1 TTGCTTGCAA 0.949516 -126 TCTCTACCTTTTATCTTCCAATAAGGGTTTC 5 77 0 TTACTTCCAA 0.925726 -77 GCCTTCTAATTCAGCTTGTAATCTAATGATG 5 127 0 TCACTTGTAA 0.962986 -27 AATCTCGCCTTCTAATTCAGCTTGT 5 139 0 TCGCTTCTAA 0.964392 -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 0.981876 -205 CCTCCTGCGCGAAAGGCTTGGACTTCACGC 4 215 1 GAAAGGCTTG 0.987705 -80 AATCATAGCGGAGATGCTTT 4 285 1 GAGATGCTTT 0.964775 -10 AATCTAAAAAGAATTGCTTTTTTAAATAGA 5 37 1 GAATTGCTTT 0.948661 -117 ATCTAATGATGAAATTCTTGACGGAAGAAG 5 108 0 GAAATTCTTG 0.96329 -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 AATAAGGCCCCTTAATCGTT 1 19 0 AATAAGGCCC 0.971003 -10 AAGTTAAACACATAACGCCTTGTATAA 3 8 0 CATAACGCCT 0.980081 -293 AAAAGCTTGAAATAGCGCCTCATCAGCATA 3 85 0 AATAGCGCCT 0.984626 -216 TTTCAATGAAAAAAACGCCCTCTTCTCTTG 3 199 0 AAAAACGCCC 0.972853 -102 AATCTCGCCTTCTAATTCAG 5 144 0 AATCTCGCCT 0.951148 -10 ********** Masking position 2 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 GAGACAGCACGAGAGAAAGCGTGAAGTCCA 4 233 0 GAGAGAAAGC 0.99391 -62 ACTATTCAGTGAGAGACAGCACGAGAGAAA 4 245 0 GAGAGACAGC 0.992762 -50 TAGAAAAAAAGTGAGAAACCCTTATTGGAA 5 63 1 GTGAGAAACC 0.980504 -91 ********** Masking position 6 Map Score: 0.562929 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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 0.955714 -36 TTTTTTTTAACAGGAGGTACCGTTACCTCC 4 190 1 CAGGAGGTAC 0.992644 -105 GCCTTTCGCGCAGGAGGTAACGGTACCTCC 4 202 0 CAGGAGGTAA 0.99381 -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