AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i046_synecho_ctra_300.orf -o046_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCT00325 34 Chlamydia_trachomatis #2 RCT00326 28 Chlamydia_trachomatis #3 RCT00843 196 Chlamydia_trachomatis #4 RCT00327 300 Chlamydia_trachomatis Motif number 1 AAAAAATCTTTGTTAGTGGTGTTTCG 2 3 1 AAAACTTTAG 0.96681 -26 CTTTTGGGACAACAACTTTTCAAGAGTTTTGTTT 3 20 1 AACACTTAAG 0.955667 -177 AAGAAGGTTATACAACTTAAGTATCTCTTGAAGC 3 80 1 TACACTATAT 0.7385 -117 CGGGGATTGTAACACCACTTTTATTTAGGCTTCA 3 108 0 AACACCTTAT 0.979599 -89 CAACTAGTTCAAAATCCTTGGAAGAGCAAGGGTT 4 15 1 AAAACTTAAG 0.952146 -286 GATATACTACAAAATCGCAACAATTAGTGCATCT 4 82 1 AAAACCAAAT 0.932014 -219 TGCAATTGATAAAAACCCTGCTATACTTTCTCGT 4 119 0 AAAACCTTAT 0.977937 -182 TTCGATAAATAACAGTTTTTCTATTCAACTTCTC 4 158 0 AACATTTTAT 0.794767 -143 ACTTTACTAAAAAAGCTCATTTATAATTCGATAA 4 184 0 AAAACCATAT 0.952534 -117 TATAACCGTTAAAACCGTTTTAATTCAAAAATTA 4 243 0 AAAACTTAAT 0.96545 -58 **** * ** *** Masking position 4 Map Score: 10.3346 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 215 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 AACCTTCTTTGAATTATAAAAATTACCAAA 3 59 0 GAATTATAAA 0.975376 -138 AAGAGACCGGGGATTGTAACACCACTTTTA 3 119 0 GGATTGTAAC 0.977173 -78 AAGAGAAGTTGAATAGAAAAACTGTTATTT 4 156 1 GAATAGAAAA 0.812812 -145 GTTATTTATCGAATTATAAATGAGCTTTTT 4 179 1 GAATTATAAA 0.975376 -122 ATTAATTTTTGAATTAAAACGGTTTTAACG 4 241 1 GAATTAAAAC 0.97064 -60 TTTAGACAAAGGATTATAACCGTTAAAACC 4 261 0 GGATTATAAC 0.980989 -40 ********** Masking position 4 Map Score: 7.00425 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 97 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 AAAGAAGGATCTTTTTAGCTGAGAGGG 1 7 1 GGATCTTTTA 0.904143 -28 ACTTTTCAAGAGTTTTGTTTACTTGTTTGGT 3 34 1 AGTTTTTTTA 0.978912 -163 TTGTAACACCACTTTTATTTAGGCTTCAAGA 3 105 0 ACTTTTTTTA 0.978912 -92 ATACGTAATTGGTTTTATTTAATAACGCGCG 3 165 0 GGTTTTTTTA 0.963351 -32 GTTTAATATTACTTCTTCTTACCGATATACT 4 59 1 ACTTCTCTTA 0.923576 -242 TTTCTATTCAACTTCTCTTTGCTGCAATTGA 4 144 0 ACTTCTTTTG 0.923576 -157 GAATAGAAAAACTGTTATTTATCGAATTATA 4 166 1 ACTGTTTTTA 0.924978 -135 CTAAACTCCTAGATTGATTTAGACAAAGGAT 4 277 0 AGATTGTTTA 0.81863 -24 ****** **** Masking position 9 Map Score: 4.1224 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 87 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 ACAACAACTTTTCAAGAGTTTTGTTTACTT 3 28 1 TTCAAGAGTT 0.959362 -169 AAGAGTTTTGTTTACTTGTTTGGTAATTTT 3 41 1 TTTACTTGTT 0.777221 -156 TTATTTAGGCTTCAAGAGATACTTAAGTTG 3 92 0 TTCAAGAGAT 0.880539 -105 CCAAGGATTTTGAACTAGTTGCCCA 4 6 0 TGAACTAGTT 0.846992 -295 AAGGGTTGTGTGCACATGTTTAATATTACT 4 42 1 TGCACATGTT 0.95568 -259 TCGTGTTAGATGCACTAATTGTTGCGATTT 4 93 0 TGCACTAATT 0.907073 -208 CTGCTATACTTTCTCGTGTTAGATGCACTA 4 106 0 TTCTCGTGTT 0.855291 -195 TTCTCTTTGCTGCAATTGATAAAAACCCTG 4 133 0 TGCAATTGAT 0.865513 -168 ACCGTTTTAATTCAAAAATTAATTCGCTGT 4 234 0 TTCAAAAATT 0.674087 -67 ********** Masking position 1 Map Score: 2.86986 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 647 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 AGCTAAAAAGATCCTTCTTT 1 1 0 ATCCTTCTTT 0.957706 -34 TAAGTTGTATAACCTTCTTTGAATTATAAA 3 69 0 AACCTTCTTT 0.986738 -128 TTCGATAAATAACAGTTTTTCTATTCAACT 4 162 0 AACAGTTTTT 0.934417 -139 GCCAAATCAAAACCGACTTTACTAAAAAAG 4 203 0 AACCGACTTT 0.980747 -98 TAACCGTTAAAACCGTTTTAATTCAAAAAT 4 245 0 AACCGTTTTA 0.957706 -56 ********** Masking position 8 Map Score: 3.09575 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 157 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 ********** No masking Map Score: -1.11312e-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 7 ********** No masking Map Score: -1.11312e-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: -1.11312e-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