AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_ctra_reg_300.orf -o217_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 RCT00240 300 Chlamydia_trachomatis #2 RCT00753 300 Chlamydia_trachomatis Motif number 1 GTATCTTTTCCATGCACTTGGAAAATAACC 1 79 0 CATGCACTTG 0.894586 -222 GAGCAGAGTTGAATCTCTTGTAAGCAAAAG 1 157 1 GAATCTCTTG 0.916272 -144 ACGCATTCCTAAGGCACTAGCCCACGCTCC 2 23 1 AAGGCACTAG 0.969053 -278 TTTATCCGGGAAGGCTCTTGTTTGCAATTC 2 60 0 AAGGCTCTTG 0.995724 -241 AATTCTGAGCAAGTCTCTTATTGTCAAAAA 2 134 0 AAGTCTCTTA 0.955764 -167 AACTCGTCCCTAGTCTCTTGGGGGCAGAGT 2 248 1 TAGTCTCTTG 0.979479 -53 AATACTCTTGAAGTCTCTAGGGACTCTGCC 2 270 0 AAGTCTCTAG 0.986078 -31 ATACTCTCCTAATACTCTTGAAGTCTCTAG 2 280 0 AATACTCTTG 0.941323 -21 ********** Masking position 2 Map Score: 9.23597 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 173 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 TGTAGAGTCGCTTTCAGATGTGGACGCTAGCAAT 1 16 0 CTTTCGGGGA 0.961637 -285 CTACATTAAACTTTTTGATGTAGAGAGGGGGGAT 1 45 1 CTTTTGGAGA 0.980537 -256 TAGTATGAAGCTCCGTTCGGAAGAGCAGAGTTGA 1 135 1 CTCCGTGAGA 0.91032 -166 AGAGTTGAATCTCTTGTAAGCAAAAGACGATTCT 1 161 1 CTCTTTGAAA 0.973305 -140 AACCTCTCCACTTCTTGTCGAGAATCGTCTTTTG 1 181 0 CTTCTGGGAA 0.965707 -120 TGGGTTCTCCCTATGGGGAGGGAAGCCTCGTTCC 1 265 0 CTATGGGGAA 0.818095 -36 TCCGGGAAGGCTCTTGTTTGCAATTCTGTGTATG 2 52 0 CTCTTTGAAT 0.890952 -249 TGTTAATCCTCCTTTATCCGGGAAGGCTCTTGTT 2 68 0 CCTTTTGGAA 0.843731 -233 CTGAGCAAGTCTCTTATTGTCAAAAAGTGAGGAA 2 126 0 CTCTTTTAAA 0.723488 -175 AAAGAAAGTACTTCCATTAGTAGATAGAATTCTG 2 157 0 CTTCCTGAGA 0.883265 -144 CTGTATTGATCTTTTAGGTGAGATCCTTTAAACT 2 218 1 CTTTTGGGAT 0.918615 -83 CGTCCCTAGTCTCTTGGGGGCAGAGTCCCTAGAG 2 252 1 CTCTTGGAGA 0.985425 -49 ***** * * *** Masking position 1 Map Score: 7.60656 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 532 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 AAATAACCATCCCCCCTCTCTACATCAAAA 1 57 0 CCCCCCTCTC 0.981749 -244 GGTATCTTTTCCATGCACTTGGAAAATAAC 1 80 0 CCATGCACTT 0.843962 -221 AGAGATTCAACTCTGCTCTTCCGAACGGAG 1 145 0 CTCTGCTCTT 0.979134 -156 AAGACAAAACCTCTCCACTTCTTGTCGAGA 1 192 0 CTCTCCACTT 0.884284 -109 GGGAGGGAAGCCTCGTTCCTATCAAGGTTG 1 254 0 CCTCGTTCCT 0.836387 -47 AGGAACGAGGCTTCCCTCCCCATAGGGAGA 1 264 1 CTTCCCTCCC 0.92483 -37 TCTCTGCTCTCTACGCATTCC 2 2 1 CTCTGCTCTC 0.983717 -299 AGGCACTAGCCCACGCTCCATACACAGAAT 2 34 1 CCACGCTCCA 0.879451 -267 ACAAAATTTACCCTTTTCCTCACTTTTTGA 2 111 1 CCCTTTTCCT 0.727952 -190 TCTCTAGGGACTCTGCCCCCAAGAGACTAG 2 257 0 CTCTGCCCCC 0.96239 -44 ********** Masking position 8 Map Score: 7.00508 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 523 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 GAGTTGAATCTCTTGTAAGCAAAAGACGATTC 1 162 1 TCTTGTACAA 0.978363 -139 CCTCTCCACTTCTTGTCGAGAATCGTCTTTTG 1 181 0 TCTTGTGGAA 0.985298 -120 CCGGGAAGGCTCTTGTTTGCAATTCTGTGTAT 2 53 0 TCTTGTTCAA 0.978363 -248 ATTTTGTTCCTCTAGTTGTTAATCCTCCTTTA 2 86 0 TCTAGTGTAA 0.917732 -215 TGAGCAAGTCTCTTATTGTCAAAAAGTGAGGA 2 127 0 TCTTATGCAA 0.973337 -174 GTCCCTAGTCTCTTGGGGGCAGAGTCCCTAGA 2 253 1 TCTTGGGCAG 0.969277 -48 ****** * *** Masking position 3 Map Score: 2.28621 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 90 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 TGATGTAGAGAGGGGGGATGGTTATTTTCC 1 60 1 AGGGGGGATG 0.992551 -241 GTCATTTTATAGAGGGTATCTTTTCCATGC 1 94 0 AGAGGGTATC 0.957677 -207 TCTCATCCGAGGTGGGTTCTCCCTATGGG 1 282 0 AGGTGGGTTC 0.989176 -19 TTGATCTTTTAGGTGAGATCCTTTAAACTC 2 223 1 AGGTGAGATC 0.983086 -78 ********** Masking position 9 Map Score: 0.954487 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 ********** No masking Map Score: 1.30983e-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: 1.30983e-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: 1.30983e-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