AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_ctra_reg_300.orf -o216_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 RCT00022 75 Chlamydia_trachomatis #2 RCT00023 187 Chlamydia_trachomatis #3 RCT00025 59 Chlamydia_trachomatis #4 RCT00028 25 Chlamydia_trachomatis #5 RCT00029 63 Chlamydia_trachomatis #6 RCT00628 300 Chlamydia_trachomatis #7 RCT00629 98 Chlamydia_trachomatis Motif number 1 GTTATCTAGAGAAAAGCGGGGCGAACACCCCGC 2 28 1 GAAAAGGGGG 0.996229 -160 ATTAAAACAAAAAAAGCGGGGTGTTCGCCCCGC 2 43 0 AAAAAGGGGG 0.992242 -145 AGTCAGATTCAAAAAGAGAGACTTATTAAAACA 2 67 0 AAAAAGGAGT 0.981079 -121 ACTTTACTCTGAAAAGTCAGATTCAAAAAGAGA 2 81 0 GAAAAGCAGT 0.97835 -107 AGATACTAGAGTAAAGGCAGAAGAAGTCGTTC 2 166 1 GTAAAGCAGG 0.971744 -22 TCTTTGCGGTAAAAAGTGAGGAGAAAATATTAG 3 35 0 AAAAAGGAGG 0.994767 -25 TAAAGAAAAGAGAGCGGCATTAAGCCC 5 5 1 GAAAAGGAGG 0.997459 -59 ****** *** * Masking position 5 Map Score: 11.3681 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 GGAGAGCATACCCGAACATTTT 1 3 0 CCCGAACATT 0.980289 -73 TTGACAACCCCAAAATCACTATCTTAG 1 59 0 CCCCAAAATC 0.855903 -17 TAGACTTTACTCTGAAAAGTCAGATTCAAA 2 87 0 TCTGAAAAGT 0.514906 -101 TCTAGTGTTCCCCAAAAATTGATTGCCAAT 2 113 1 CCCAAAAATT 0.960113 -75 AGTTCTTTATCGCAAAAATTATCTAATATT 3 13 1 CGCAAAAATT 0.701478 -47 TGTATTTCACCTAAAAATTCTTTTT 4 7 0 CCTAAAAATT 0.827356 -19 TATTTATTTAGCCAAACCTTTAAGCAGATT 6 35 1 GCCAAACCTT 0.893291 -266 ACATGCAACTCCCAAACCTCCAGAGCCATA 6 68 0 CCCAAACCTC 0.966761 -233 CTGTAAGAATCCCGAACTGCTGTTTCAATA 6 115 0 CCCGAACTGC 0.906284 -186 ACAGATCATGCCCCAATTTTGCTAGCCTGT 6 141 1 CCCCAATTTT 0.603594 -160 AACAAAACTATCTAAACTTTCGAGAAGAAC 6 186 0 TCTAAACTTT 0.641743 -115 TATTCAACCTTCCAAACCGTTAAGAAATGT 6 217 0 TCCAAACCGT 0.931719 -84 ATAAATCTTTTCCGAACCGTATCATGGAAG 6 244 1 TCCGAACCGT 0.927332 -57 ********** Masking position 5 Map Score: 8.63555 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 407 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 ATGCTCTCCCTTCTGTTATGTGAGATTTTCA 1 24 1 TTCTGTTATT 0.949435 -52 TAACAGAAAGTTCTGTTCAAA 2 1 0 TTCTGTTCAA 0.933975 -187 GAACAGAACTTTCTGTTATCTAGAGAAAAGC 2 14 1 TTCTGTTATT 0.949435 -174 ACCCCGCTTTTTTTGTTTTAATAAGTCTCTC 2 54 1 TTTTGTTTTA 0.938558 -134 AAGCCCTTTCTGCTGTTCTCAACGTCAAGAG 5 32 1 TGCTGTTCTA 0.956296 -32 AATCCCGAACTGCTGTTTCAATAAACTTATC 6 107 0 TGCTGTTTCA 0.890365 -194 GTTTAGATAGTTTTGTTAACATTTCTTAACG 6 199 1 TTTTGTTAAA 0.811086 -102 AAAGACGAAGTCCTGTTTTAAGGAGGCTTG 6 281 1 TCCTGTTTTA 0.934817 -20 TTTTGTTTTTTAAGTAAGAAG 7 1 1 TTTTGTTTTT 0.88905 -98 ********* * Masking position 6 Map Score: 6.07318 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 183 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 TTTTTTGTTTTAATAAGTCTCTCTTTTTGA 2 62 1 TAATAAGTCT 0.944605 -126 AGTAAAGGCAGAAGAAGTCGTTC 2 175 1 GAAGAAGTCG 0.9418 -13 AGTTTGTTTGTAACAAATCGGAATC 6 6 0 TAACAAATCG 0.938417 -295 TCCAGAGCCATAGGAAATCTGCTTAAAGGT 6 50 0 TAGGAAATCT 0.931856 -251 TAAGAAATGTTAACAAAACTATCTAAACTT 6 197 0 TAACAAAACT 0.828252 -104 TCCAAACCGTTAAGAAATGTTAACAAAACT 6 207 0 TAAGAAATGT 0.908239 -94 TTGGAAGGTTGAATAAATCTTTTCCGAACC 6 232 1 GAATAAATCT 0.907846 -69 GTTTTTTAAGTAAGAAGTATAAAATAGATT 7 15 1 TAAGAAGTAT 0.867476 -84 ********** Masking position 5 Map Score: 2.30743 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 249 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 AGAAAATATTAGATAATTTTTGCGATAAAGA 3 16 0 AATAATTTTT 0.75516 -44 TTTCACCTAAAAATTCTTTTT 4 1 0 AATTCTTTTT 0.906036 -25 TTTGTTACAAACAAACTATTTATTTAGCCAA 6 19 1 AAAACTATTT 0.92189 -282 AATAGTATCTATAATCTATTTTATACTTCTT 7 26 0 AAATCTATTT 0.941017 -73 AATAGATTATAGATACTATTTTTATTTTTCT 7 37 1 AATACTATTT 0.92189 -62 CAAATCCTACACAAGCTTTTTTCTGAAGGTG 7 72 0 AAAGCTTTTT 0.930944 -27 * ********* Masking position 7 Map Score: 1.92845 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 208 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: -4.73059e-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 7 ********** No masking Map Score: -4.73059e-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: -4.73059e-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