AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_ctra_reg_100.orf -o057_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 RCT00348 169 Chlamydia_trachomatis #2 RCT00363 300 Chlamydia_trachomatis Motif number 1 GAAAAGGATTTTATTTTGTTGTTATAATTA 1 39 0 TTATTTTGTT 0.72387 -131 GAAATAAGTTCTATTTTTTTGTTATGAAAA 1 64 0 CTATTTTTTT 0.939847 -106 ATGCAAAAAACTCTTCCGAAGACTACATTA 1 115 1 CTCTTCCGAA 0.829574 -55 ACTACATTAGCTATTCATTTTTAACCTTTT 1 136 1 CTATTCATTT 0.896704 -34 ATGTCTATTTTCTAAAAAGGTTAA 1 156 0 CTATTTTCTA 0.883944 -14 GCATATTCAGCTCTTCCTTTGAGTAGTTTC 2 60 0 CTCTTCCTTT 0.986396 -241 TTTAATGATGCTATTCTGATCCGTTAGGCA 2 155 0 CTATTCTGAT 0.92911 -146 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 2 179 1 CTCTTCTCTT 0.993478 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 2 190 0 CTCTTCTCTT 0.993478 -111 AAAAATCTTTCTATTTCTTTTCTCTTCCCT 2 226 1 CTATTTCTTT 0.935946 -75 TATTTCTTTTCTCTTCCCTGTGTGTATGAT 2 237 1 CTCTTCCCTG 0.967436 -64 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 2 273 0 TTCTTCTCTT 0.954883 -28 ********** Masking position 5 Map Score: 17.689 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 781 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 2 ATTAATCTTGTTGAAAGATTTTATGTTTTTTT 1 11 0 TTGAAGATTT 0.9883 -159 CTTATTTCCCTCGTATGATCTTAAATATCATG 1 86 1 TCGATGATTT 0.972552 -84 GAAGAGTTTTTTGCATGATATTTAAGATCATA 1 99 0 TTGATGATTT 0.981363 -71 AATGTAGTCTTCGGAAGAGTTTTTTGCATGAT 1 112 0 TCGAAGAGTT 0.937879 -58 AGCTATTCATTTTTAACCTTTTTAGAAAATAG 1 144 1 TTTAACCTTT 0.755776 -26 TGAGGCGCTATTTCAAGCTTTTCTTACGACGC 2 93 1 TTTAAGCTTT 0.949232 -208 GAAGAGAACGTTTAATGATGCTATTCTGATCC 2 163 0 TTTATGATCT 0.845364 -138 AGAAAAGAAATAGAAAGATTTTTCAATGAAAA 2 217 0 TAGAAGATTT 0.954211 -84 *** ***** ** Masking position 5 Map Score: 5.72164 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 147 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 GTCTTCGGAAGAGTTTTTTGCATGATATTTA 1 107 0 GAGTTTTTTC 0.991716 -63 CTCTTCCTTTGAGTAGTTTCCTACAATAACA 2 49 0 GAGTAGTTTC 0.975178 -252 GCTATTTCAAGCTTTTCTTACGACGCTGATA 2 99 1 GCTTTTCTTC 0.962752 -202 AGAGAAGAGGGCGTTTTTTTCATTGAAAAAT 2 201 1 GCGTTTTTTC 0.992321 -100 TAGATTTGTTTTCCTTGTTTCTT 2 288 0 GATTTGTTTC 0.982867 -13 ********* * Masking position 4 Map Score: 3.78917 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 32 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 AAATAGAACTTATTTCCCTCGTATGATCTTA 1 78 1 TATTTCCTCG 0.93429 -92 GAATAGCTAATGTAGTCTTCGGAAGAGTTTT 1 121 0 TGTAGCTTCG 0.886657 -49 AGGCGTTATGTGTTTAACTTGTAGTTTGCTT 2 18 1 TGTTTACTTG 0.973863 -283 TTTAACTTGTAGTTTGCTTTGTTATTGTAGG 2 30 1 AGTTTCTTTG 0.94746 -271 AAGAGGGCGTTTTTTTCATTGAAAAATCTTT 2 205 1 TTTTTCATTG 0.841728 -96 CTTCCCTGTGTGTATGATTTGCTGTTCATGA 2 249 1 TGTATATTTG 0.911567 -52 TAGATTTGTTTTCCTTGTTTCTTCTCT 2 284 0 TGTTTCCTTG 0.992732 -17 ***** ***** Masking position 3 Map Score: 2.9021 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 158 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 CATAAAATCTTTCAACAAGATTAATTATAA 1 18 1 TTCAACAAGA 0.891821 -152 CAAGATTAATTATAACAACAAAATAAAATC 1 33 1 TATAACAACA 0.958739 -137 ATAAAATCCTTTTCATAACAAAAAAATAGA 1 55 1 TTTCATAACA 0.935981 -115 TTGCATGATATTTAAGATCATACGAGGGAA 1 91 0 TTTAAGATCA 0.926634 -79 AGTAGTTTCCTACAATAACAAAGCAAACTA 2 39 0 TACAATAACA 0.946933 -262 TAGGCAACTGTTTAATATCAGAAATTACAT 2 131 0 TTTAATATCA 0.955599 -170 ********** Masking position 5 Map Score: 1.75191 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 TTGTTGAAAGATTTTATGTTTTTTT 1 6 0 ATTTTATGTT 0.94272 -164 TATGAAAAGGATTTTATTTTGTTGTTATAA 1 42 0 ATTTTATTTT 0.717952 -128 GAAGAGCTGAATATGCTGATGAGGCGCTAT 2 74 1 ATATGCTGAT 0.954818 -227 TGATAGATGTAATTTCTGATATTAAACAGT 2 125 1 AATTTCTGAT 0.923124 -176 TTTAATGATGCTATTCTGATCCGTTAGGCA 2 155 0 CTATTCTGAT 0.905192 -146 TGTGTGTATGATTTGCTGTTCATGAGTTAA 2 255 1 ATTTGCTGTT 0.975782 -46 ********** Masking position 4 Map Score: 1.80839 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 206 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: -1.32571e-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: -1.32571e-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: -1.32571e-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