AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i341_synecho_ctra_300.orf -o341_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 RCT00329 300 Chlamydia_trachomatis #2 RCT00330 61 Chlamydia_trachomatis #3 RCT00331 53 Chlamydia_trachomatis #4 RCT00675 166 Chlamydia_trachomatis #5 RCT00676 300 Chlamydia_trachomatis Motif number 1 GTTTCTAGTTAAAAAGTTTTATAAATAAGA 1 23 0 AAAAAGTTTT 0.85997 -278 TATGAGTGAAAAGAAGCTCGTCGGTGATAA 1 62 0 AAGAAGCTCG 0.980802 -239 TAAACACAAGAAAAAGCTCGTTATGAGTGA 1 83 0 AAAAAGCTCG 0.964886 -218 CTTGCAAGGTAAGAGGTTTTGGAATGTAGG 1 210 0 AAGAGGTTTT 0.934847 -91 AAGCAAGAGGAAGTCGCTTGTTAGGGCATA 1 237 1 AAGTCGCTTG 0.834434 -64 CTTATGAGCTAAGAAGCTTTCGGGTTGTTT 2 26 0 AAGAAGCTTT 0.986478 -36 CTTAGAGTACAAGAAGTTTGCCGGTGTAG 3 10 0 AAGAAGTTTG 0.970229 -44 CTTGTACTCTAAGAAGGTCTTTGTTATCCT 3 27 1 AAGAAGGTCT 0.843075 -27 TGATCGCAGGAAAACGCTTGACCCAAGAGA 4 14 1 AAAACGCTTG 0.955704 -153 ATTGGACTGCAAACAGCTTTAAAAAGGGGA 5 55 0 AAACAGCTTT 0.87028 -246 AAACTTTGGAAAAAGGTTTTTTGAGAAGGT 5 108 0 AAAAGGTTTT 0.82432 -193 AGGTTTTACAAAAAAACTTTGGAAAAAGGT 5 121 0 AAAAAACTTT 0.721694 -180 GAAGCGGGTGATGAGGCTTGAACTCACGAC 5 249 0 ATGAGGCTTG 0.870886 -52 ********** Masking position 1 Map Score: 15.6152 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 475 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 GATAACAGGTAGGAGTTTCTAGTTAAAAAGTTTT 1 33 0 AGAGTTTGTT 0.904835 -268 ATGAGTGAAAAGAAGCTCGTCGGTGATAACAGGT 1 57 0 AGAGCTCGGT 0.996197 -244 TTATGAGCTAAGAAGCTTTCGGGTTGTTTCCAAC 2 21 0 AGAGCTTGGT 0.988487 -41 TTAGAGTACAAGAAGTTTGCCGGTGTAG 3 5 0 AGAGTTTGGT 0.966677 -49 TTGTACTCTAAGAAGGTCTTTGTTATCCTTTTGT 3 28 1 AGAGGTCGTT 0.984932 -26 TCTATGTTTAAGTGTCTCTTGGGTCAAGCGTTTT 4 24 0 AGGTCTCGGT 0.926217 -143 GAGGAAGAAGAGAGGGTCAAAATTTTCATTGATT 5 15 0 AGGGGTCATT 0.862856 -286 TTCTCGCGGGTGTAGCTCAGTGGTAGAGCGCCAC 5 200 1 TGAGCTCGGT 0.988064 -101 GTTGCCAACGTGAAGGTCGTGAGTTCAAGCCTCA 5 234 1 TGAGGTCAGT 0.925432 -67 ** ***** *** Masking position 7 Map Score: 8.64302 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 194 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 TATAAATAAGAGAGGATAAGAAG 1 2 0 AGAGGATAAA 0.98208 -299 CCACAGTTTCAGAGAAAAATTATAACTTCCAC 1 119 0 AGAGAAAAAA 0.898537 -182 GATATAAATAAGACGAGAATGAAAACAATTTC 1 161 0 AGACGAGAAA 0.911123 -140 TCTTCCTTAAAGAGGATATTGA 1 289 1 AGAGGATATA 0.863901 -12 GGACAAAAGGATAACAAAGACCTTCTT 3 37 0 AAAGGATAAA 0.916041 -17 TCTTGACCCTAGAAAAGAAAGACCCCATCTAA 4 91 0 AGAAAAGAAA 0.819189 -76 AAATGATTTGAGAGGAAGCACACAT 4 152 1 AGAGGAAGCA 0.886121 -15 GGGGAAAAATAGAGGAAGAAGAGAGGGTCAAA 5 28 0 AGAGGAAGAA 0.978414 -273 ACAGCTTTAAAAAGGGGAAAAATAGAGGAAGA 5 41 0 AAAGGGGAAA 0.876407 -260 AGAGGTGGTAAAAAAAGAAAAATTGGACTGCA 5 74 0 AAAAAAGAAA 0.474236 -227 AGGTTTTTTGAGAAGGTGAAGAGGTGGTAAAA 5 93 0 AGAAGGTGAA 0.90092 -208 TACACCCGCGAGAAGAAGAGCATTCTAGATAA 5 182 0 AGAAGAAGAA 0.935979 -119 GGGAAAGAGAAGCGGGTGATGAGGCTTGAACT 5 255 0 AGCGGGTGAA 0.816393 -46 ********* * Masking position 1 Map Score: 8.43587 Number of sites scoring better than the average of aligned sites = 1293 Number in coding regions = 1105 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 AAAGTTTTATAAATAAGAGAGGATAAGAAG 1 11 0 AAATAAGAGA 0.602304 -290 GCTCGTTATGAGTGAAAAGAAGCTCGTCGG 1 68 0 AGTGAAAAGA 0.722022 -233 CTTGCTTGCAAGGTAAGAGGTTTTGGAATG 1 214 0 AGGTAAGAGG 0.906017 -87 CTTACCTTGCAAGCAAGAGGAAGTCGCTTG 1 227 1 AAGCAAGAGG 0.918943 -74 TATCCTCTTTAAGGAAGAGATCTCTCAAGG 1 277 0 AAGGAAGAGA 0.913063 -24 GGACAAAAGGATAACAAAGA 3 44 0 GGACAAAAGG 0.851345 -10 GTGTCTCTTGGGTCAAGCGTTTTCCTGCGA 4 17 0 GGTCAAGCGT 0.705826 -150 TCTTTTCTAGGGTCAAGAGTAGCCATAACG 4 105 1 GGTCAAGAGT 0.938316 -62 AAAAATAGAGGAAGAAGAGAGGGTCAAAAT 5 26 0 GAAGAAGAGA 0.943384 -275 TTTTTGAGAAGGTGAAGAGGTGGTAAAAAA 5 91 0 GGTGAAGAGG 0.988007 -210 ACACCCGCGAGAAGAAGAGCATTCTAGATA 5 183 0 GAAGAAGAGC 0.85901 -118 AAGAGAAGCGGGTGATGAGGCTTGAACTCA 5 253 0 GGTGATGAGG 0.897616 -48 TAAGTTATCCGGGAAAGAGAAGCGGGTGAT 5 267 0 GGGAAAGAGA 0.896126 -34 ********** Masking position 5 Map Score: 9.22055 Number of sites scoring better than the average of aligned sites = 1416 Number in coding regions = 1237 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 5 TTCCACTAAGCCTAAACACAAGAAAAAGCTCG 1 93 0 CCTAAACAAG 0.938821 -208 CAATTCCATCCCTACATTCCAAAACCTCTTAC 1 200 1 CCTACACCAA 0.974088 -101 AACCTCTTACCTTGCAAGCAAGAGGAAGTCGC 1 222 1 CTTGCACAAG 0.653049 -79 CAAGCGTTTTCCTGCGATCAAAA 4 2 0 CCTGCGCAAA 0.990226 -165 TCAAAATACACCTACGCATCAAAATGATGAAT 4 58 0 CCTACGTCAA 0.804558 -109 CGTAAGCACACCTGTAACCAAATGATTTGAGA 4 133 1 CCTGTACAAA 0.942166 -34 TTTTGTAAAACCTACAAGCAAAGGATTGCGAA 5 138 1 CCTACACAAA 0.985093 -163 ACGTGAAGGTCGTGAGTTCAAGCCTCATCACC 5 241 1 CGTGAGCAAG 0.753128 -60 ****** **** Masking position 11 Map Score: 2.97528 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 379 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 TCCCAAACCTGCTGTACTTATG 2 50 0 CCAAACCTGC 0.959059 -12 CTACACCGGCAAACTTCTTG 3 1 1 CTACACCGGC 0.989913 -53 CTAATTCAAAATACACCTACGCATCAAAAT 4 65 0 ATACACCTAC 0.839064 -102 CATAACGTAAGCACACCTGTAACCAAATGA 4 128 1 GCACACCTGT 0.843025 -39 TTTACCACCTCTTCACCTTCTCAAAAAACC 5 94 1 CTTCACCTTC 0.936148 -207 TACCACTGAGCTACACCCGCGAGAAGAAGA 5 195 0 CTACACCCGC 0.994494 -106 GTTCAAGCCTCATCACCCGCTTCTCTTTCC 5 256 1 CATCACCCGC 0.959808 -45 ********** Masking position 5 Map Score: 3.64348 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 515 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ********** No masking Map Score: 3.79592e-14 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: 3.79592e-14 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: 3.79592e-14 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