AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i283_synecho_ctra_300.orf -o283_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 RCT00379 31 Chlamydia_trachomatis #2 RCT00380 245 Chlamydia_trachomatis #3 RCT00382 165 Chlamydia_trachomatis #4 RCT00385 300 Chlamydia_trachomatis Motif number 1 TCTTCGTTTTCTTTAAGGTTTAAGCGTCTT 2 38 1 CTTTAAGGTT 0.956624 -208 TGCTTAACCGCCTTCAGGTGAGTGTACAGA 2 107 1 CCTTCAGGTG 0.886886 -139 AGTGTACAGATTTTCATGTTATTAAACCCT 2 127 1 TTTTCATGTT 0.936142 -119 AAAAATGCCTTTTGAGGGTTTAATAACATG 2 141 0 TTTGAGGGTT 0.894339 -105 AATACTAAAGCCTTCGAGTTCAGAAATAAG 2 219 1 CCTTCGAGTT 0.920255 -27 GAAACTTGATTTTTAATGTTTTATATGCGA 3 21 1 TTTTAATGTT 0.843409 -145 TATATGCGATCCTTCGGGATACCCTCGTTT 3 42 1 CCTTCGGGAT 0.926027 -124 TGTCTCAGCCCTTTAGGGTTGTCATAGTTT 3 105 1 CTTTAGGGTT 0.967316 -61 TGTCATAGTTTTTGCAGGTTGTTCGTTTAG 3 124 1 TTTGCAGGTT 0.944956 -42 GGAGAGGGCTTTTTCGTGTATCTAGTTTTT 4 227 1 TTTTCGTGTA 0.734621 -74 TGTATCTAGTTTTTCAAGATTGCTAAAAAG 4 243 1 TTTTCAAGAT 0.717394 -58 ********** Masking position 3 Map Score: 8.46709 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 619 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 2 GCTATATTAAAAAAATGTCTT 1 2 0 AAAAATGTCT 0.921728 -30 ACGAAGAGAGAAAACCCTCTTCGTTAAAAG 2 15 0 AAAACCCTCT 0.956126 -231 AAACCACAGAAAAGACGCTTAAACCTTAAA 2 49 0 AAAGACGCTT 0.84398 -197 TGTGGTTTCAAAAAATGTTTAGTGTAACAT 2 71 1 AAAAATGTTT 0.828691 -175 TTAATAACATGAAAATCTGTACACTCACCT 2 122 0 GAAAATCTGT 0.667149 -124 TTTACAGATAAAAAATGCCTTTTGAGGGTT 2 151 0 AAAAATGCCT 0.86836 -95 TTTTTTTTCAAAAGTCGCCTAATATCTGCA 4 42 1 AAAGTCGCCT 0.780772 -259 TTTAATGGATAAAATCCTGTGTCTTGTGTT 4 99 1 AAAATCCTGT 0.832921 -202 TTGTGTTGAAAAGAACCTCTTCTTAGAAAG 4 122 1 AAGAACCTCT 0.896876 -179 CGCCCGTAGAGAAAACCTTTCTAAGAAGAG 4 138 0 GAAAACCTTT 0.882221 -163 GATACACGAAAAAGCCCTCTCCGGATCTGA 4 219 0 AAAGCCCTCT 0.931473 -82 AGACAATTAAATACCTTTGCTAGGTCGT 4 283 0 AAATACCTTT 0.769957 -18 ********** Masking position 2 Map Score: 6.49983 Number of sites scoring better than the average of aligned sites = 1156 Number in coding regions = 940 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 3 AGAGAGAAAACCCTCTTCGTTAAAAGATCT 2 11 0 CCCTCTTCGT 0.997191 -235 AGAGGGTTTTCTCTCTTCGTTTTCTTTAAG 2 25 1 CTCTCTTCGT 0.988934 -221 GGCTGAGACAGACTCTTCGTCCTCTTTACC 3 85 0 GACTCTTCGT 0.970876 -81 GTTGAAAAGAACCTCTTCTTAGAAAGGTTT 4 126 1 ACCTCTTCTT 0.944825 -175 CACGAAAAAGCCCTCTCCGGATCTGATCAA 4 215 0 CCCTCTCCGG 0.986309 -86 ********** Masking position 6 Map Score: 4.80832 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 86 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GAAGGCTTTAGTATTCTGTTAACTCAATAT 2 204 0 GTATTCTGTT 0.960323 -42 TCACAATCAAGAATTGTGTTA 4 2 0 GAATTGTGTT 0.983464 -299 TCTTGATTGTGATTTGTGGTGATTTTTTTT 4 20 1 GATTTGTGGT 0.962135 -281 AAAATCCTGTGTCTTGTGTTGAAAAGAACC 4 109 1 GTCTTGTGTT 0.980388 -192 TTGCTAAAAAGTATTGTTGTCACGACCTAG 4 262 1 GTATTGTTGT 0.946319 -39 ********** Masking position 5 Map Score: 1.85181 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 122 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TACTTTCACCGCTATATTAAAA 1 20 0 CTTTCACCGC 0.984377 -12 AGATCTTTTAACGAAGAGGGTTTT 2 5 1 CTTTTAACGA 0.919953 -241 TATCAACTGGCTTTTACAGATAAAAAATGC 2 163 0 CTTTTACAGA 0.959992 -83 GACGAAGAGTCTGTCTCAGCCCTTTAGGGT 3 94 1 CTGTCTCAGC 0.948322 -72 TAGAGAAAACCTTTCTAAGAAGAGGTTCTT 4 132 0 CTTTCTAAGA 0.943654 -169 ********** Masking position 4 Map Score: 0.0388989 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 182 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 ********** No masking Map Score: -7.15216e-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 7 ********** No masking Map Score: -7.15216e-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: -7.15216e-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