AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i198_enolase_ctra_reg_300.orf -o198_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 RCT00554 300 Chlamydia_trachomatis #2 RCT00557 198 Chlamydia_trachomatis #3 RCT00558 24 Chlamydia_trachomatis #4 RCT00560 161 Chlamydia_trachomatis Motif number 1 TATACGATTTTTCTTCCCATGGTAGTTGCTACAGTAATCC 1 50 1 TTCTTCCTCT 0.850037 -251 GGGTACAGTATCCCTCCGGTAGAAAAGTCTATTTTTAGGG 1 113 0 TCCCTCCACT 0.996412 -188 GGAGGAAGCCTCGCTCCTTTTTAGTTGCTTTAATTCCTTT 1 243 0 TCGCTCCATT 0.994254 -58 GGAGCGAGGCTTCCTCCCCTACAAGGGCTTCACCTCGTGA 1 266 1 TTCCTCCATT 0.985385 -35 TCTATAATCCTTCCTAACAATCATCTTTCTAAAGATG 2 8 1 TCCTTCCATT 0.985385 -191 GGAAAAAACCTCGCTCCTTGCTTTTTCTTTAATTCTTAAT 2 140 0 TCGCTCCTTT 0.99161 -59 CCAAACAGGGTCCCGCCTCGTGAGTCAGCT 2 179 1 TCCCGCCACT 0.983025 -20 CAGAATTGAATCCCTCGCTATGATCCTTTTCTACTAAGGG 4 22 1 TCCCTCGATT 0.990503 -140 TAAGGGAATCTCCCTCCGAGCCTTCTCTTTGTATTGCGGT 4 56 1 TCCCTCCTTT 0.99626 -106 TGAAAGCAGTTCGCTCGTTTTATCTAATTTCCTCCGATGA 4 105 0 TCGCTCGTTT 0.96933 -57 ******* * ** Masking position 1 Map Score: 17.026 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 83 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 CCTCCGGTAGAAAAGTCTATTTTTAGGGATAAGTCTTT 1 103 0 AAAGTTAGGG 0.99111 -198 AATAATATAGAAAAGAGGTATCTGGAGAGCTTTCTTAC 1 153 1 AAAGGTGAGA 0.972519 -148 ATCATCTTTAGAAAGATGATTGTTAGGAAGGATTATAG 2 12 0 GAAGGTAGGA 0.950804 -187 GCTTTTTAAAAATAGTCTGATTCAGGGGCTATGTAACA 2 49 0 AAAGTTGGGG 0.995676 -150 ACTATTTTTAAAAAGCAGGCTTTAGGGGCTTATTTTTC 2 71 1 AAAGGTGGGG 0.997902 -128 CCCTTAGTAGAAAAGGATCATAGCGAGGGATTCAATTC 4 24 0 AAAGTTGAGG 0.984329 -138 CCGCAATACAAAGAGAAGGCTCGGAGGGAGATTCCCTT 4 57 0 AAAGGTAGGG 0.995676 -105 ** ** * * **** Masking position 4 Map Score: 8.03075 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 50 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 GAGATTTTAGAGCCCTGGACCTGCCTGT 1 9 0 AGCCCTGGAC 0.983941 -292 CACGAGGTGAAGCCCTTGTAGGGGAGGAAG 1 275 0 AGCCCTTGTA 0.986024 -26 GATGTTACATAGCCCCTGAATCAGACTATT 2 47 1 AGCCCCTGAA 0.996386 -152 ACGAAAAATAAGCCCCTAAAGCCTGCTTTT 2 81 0 AGCCCCTAAA 0.985797 -118 ********** Masking position 1 Map Score: 2.96873 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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 AAAAGACTTATCCCTAAAAATAGACTTTTCT 1 102 1 TCCCTAAAAT 0.983072 -199 AGGGATACTGTACCCAATAATATAGAAAAGA 1 138 1 TACCCAAAAT 0.916019 -163 TATTGATTTGTCCATAAGCATGGACGAATGA 1 211 0 TCCATAACAT 0.835221 -90 CGAGGCTTCCTCCCCTACAAGGGCTTCACCT 1 270 1 TCCCCTAAAG 0.953326 -31 TCTATAATCCTTCCTAACAATCATCTTTCTA 2 11 1 TTCCTAAAAT 0.965651 -188 GGGCTTATTTTTCGTAAAAATCCAGAGATGT 2 96 1 TTCGTAAAAT 0.843883 -103 GCGAGGTTTTTTCCCAAACAGGGTCCCGCCT 2 166 1 TTCCCAACAG 0.947857 -33 GGAGGGAGATTCCCTTAGTAGAAAAGGATCA 4 42 0 TCCCTTATAG 0.837153 -120 ******* *** Masking position 7 Map Score: 2.9714 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 241 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 AAAGCAACTAAAAAGGAGCGAGGCTTCCTC 1 252 1 AAAAGGAGCG 0.994584 -49 TAAAGAAAAAGCAAGGAGCGAGGTTTTTTC 2 149 1 GCAAGGAGCG 0.986393 -50 CCCTTAGTAGAAAAGGATCATAGCGAGGGA 4 32 0 AAAAGGATCA 0.957229 -130 CAATACAAAGAGAAGGCTCGGAGGGAGATT 4 62 0 AGAAGGCTCG 0.961598 -100 GAAATTAGATAAAACGAGCGAACTGCTTTC 4 114 1 AAAACGAGCG 0.976802 -48 ACCGTTCTAGACAAGGATCTTGTT 4 148 1 ACAAGGATCT 0.960246 -14 ********** Masking position 4 Map Score: 5.08009 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 71 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 ATGGTAGTTGCTACAGTAATCCTGTTCCGTT 1 68 1 CTCAGTAATC 0.900601 -233 GAGAGCTTTCTTACTTTATTCATCTCCTTTA 1 177 1 TTCTTTATTC 0.93224 -124 CTTTATTCATCTCCTTTAACCTCATTCGTCC 1 190 1 CTCTTTAACC 0.974574 -111 TCCTTTTTAGTTGCTTTAATTCCTTTATATT 1 238 0 TTCTTTAATT 0.949607 -63 CTCCTTGCTTTTTCTTTAATTCTTAATTTAT 2 136 0 TTCTTTAATT 0.949607 -63 AGCGAACTGCTTTCATTAACCGTTCTAGACA 4 130 1 TTCATTAACC 0.961209 -32 ** ******** Masking position 7 Map Score: 1.50861 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 52 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: -1.76682e-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: -1.76682e-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 9 ********** No masking Map Score: -1.76682e-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