AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_excinuclease_abc_ctra_reg_300.orf -o201_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 RCT00554 300 Chlamydia_trachomatis #2 RCT00557 198 Chlamydia_trachomatis #3 RCT00558 24 Chlamydia_trachomatis Motif number 1 GTTAACTATACGATTTTTCTTCCCATGGTAGTT 1 44 1 CGATTTCTCC 0.987203 -257 CCCTAAAAATAGACTTTTCTACCGGAGGGATAC 1 113 1 AGACTTCTCC 0.976122 -188 ATTATTGGGTACAGTATCCCTCCGGTAGAAAAG 1 126 0 ACAGTCCCCC 0.986346 -175 AGGTATCTGGAGAGCTTTCTTACTTTATTCATC 1 168 1 AGAGTTCTAC 0.952174 -133 TAAAAAGGAGCGAGGCTTCCTCCCCTACAAGGG 1 260 1 CGAGTTCCCC 0.995773 -41 TCTATAATCCTTCCTAACAATCAT 2 2 1 CTATTCCTCC 0.921245 -197 AAGCAAGGAGCGAGGTTTTTTCCCAAACAGGGT 2 157 1 CGAGTTTTCC 0.969283 -42 TTTTTCCCAAACAGGGTCCCGCCTCGTGAGTCA 2 173 1 ACAGTCCCCC 0.986343 -26 **** **** ** Masking position 3 Map Score: 8.35698 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 128 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 TACAAAAGACTTATCCCTAAAAATAGACTTTTC 1 99 1 TATCCTAAAA 0.79413 -202 TCCTTTAACCTCATTCGTCCATGCTTATGGACA 1 201 1 TATTCTCATG 0.942019 -100 TCCTTTATATTGATTTGTCCATAAGCATGGACG 1 216 0 TATTTTCATA 0.965203 -85 TTAGTTGCTTTAATTCCTTTATATTGATTTGTC 1 230 0 TATTCTTATA 0.743377 -71 GAAGCCTCGCTCCTTTTTAGTTGCTTTAATTCC 1 246 0 TCTTTTATTG 0.64415 -55 TCTATAATCCTTCCTAACAATCATCTT 2 5 1 TATCCTCTAA 0.889639 -194 TTCCTAACAATCATCTTTCTAAAGATGATGTTA 2 21 1 TATCTTCAAA 0.935978 -178 CCCTAAAGCCTGCTTTTTAAAAATAGTCTGATT 2 65 0 TCTTTTAAAA 0.804879 -134 CTTTAGGGGCTTATTTTTCGTAAAAATCCAGAG 2 90 1 TATTTTCTAA 0.932257 -109 CTTTAATTCTTAATTTATCGATGCAAGACATCT 2 121 0 TATTTTCATG 0.945572 -78 CCTCGCTCCTTGCTTTTTCTTTAATTCTTAATT 2 139 0 TCTTTTCTTA 0.911057 -60 * **** ** *** Masking position 8 Map Score: 6.08582 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 360 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 ACAGGCAGGTCCAGGGCTCTAAAATCTC 1 9 1 GTCCAGGGCT 0.988476 -292 CTTCCTCCCCTACAAGGGCTTCACCTCGTG 1 275 1 TACAAGGGCT 0.989987 -26 AATAGTCTGATTCAGGGGCTATGTAACATC 2 47 0 TTCAGGGGCT 0.997418 -152 AAAAGCAGGCTTTAGGGGCTTATTTTTCGT 2 81 1 TTTAGGGGCT 0.989824 -118 ********** Masking position 10 Map Score: 4.05627 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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 ACTGTAGCAACTACCATGGGAAGAAAAATC 1 55 0 CTACCATGGG 0.945992 -246 ATAGACTTTTCTACCGGAGGGATACTGTAC 1 121 1 CTACCGGAGG 0.962076 -180 GCTTCCTCCCCTACAAGGGCTTCACCTCGT 1 274 1 CTACAAGGGC 0.991958 -27 AAATAGTCTGATTCAGGGGCTATGTAACAT 2 48 0 ATTCAGGGGC 0.973799 -151 AAAAAGCAGGCTTTAGGGGCTTATTTTTCG 2 80 1 CTTTAGGGGC 0.9738 -119 ********** Masking position 2 Map Score: 0.881625 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 112 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 TGATTTGTCCATAAGCATGGACGAATGAGG 1 209 0 ATAAGCATGG 0.969535 -92 AAAGCAACTAAAAAGGAGCGAGGCTTCCTC 1 252 1 AAAAGGAGCG 0.968286 -49 ACTATTTTTAAAAAGCAGGCTTTAGGGGCT 2 71 1 AAAAGCAGGC 0.987929 -128 GAATTAAAGAAAAAGCAAGGAGCGAGGTTT 2 145 1 AAAAGCAAGG 0.98772 -54 ********** Masking position 4 Map Score: 0.427518 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 67 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 GTTTATCACGAGGTGAAGCCCTTGT 1 286 0 TCACGAGGTG 0.993499 -15 CAATCATCTTTCTAAAGATGATGTTACATA 2 28 1 TCTAAAGATG 0.901162 -171 TTCGTAAAAATCCAGAGATGTCTTGCATCG 2 106 1 TCCAGAGATG 0.981715 -93 AGCTGACTCACGAGGCGGGACCCTGTT 2 182 0 TCACGAGGCG 0.988968 -17 ********** Masking position 6 Map Score: 0.591793 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 7 ********** No masking Map Score: 1.23167e-12 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: 1.23167e-12 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: 1.23167e-12 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