AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_ctra_reg_300.orf -o182_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 RCT00385 300 Chlamydia_trachomatis #2 RCT00699 41 Chlamydia_trachomatis #3 RCT00700 109 Chlamydia_trachomatis Motif number 1 CTGCAGGACGCTCAAGATACCACGGTTTTTATTTTAATG 1 67 1 CTCTACTTTT 0.998175 -234 TGAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGC 1 128 1 CTCTAATTTT 0.993342 -173 TACGGGCGGTCTCGGAGTATAATTATTTTTTGATTATAA 1 160 1 CTCTAATTTT 0.993342 -141 GAGAGGGCTTTTTCGTGTATCTAGTTTTTCAAGATTGCT 1 228 1 TTTTACTTTT 0.950864 -73 CCTTGCATCTCTCTCGCTATCTGATTTTTCAGGTTGAGT 2 11 1 CTCTACTTTT 0.998175 -31 CAAAGAACGTTTCCCACTGGCTAAGTTTTCCTCAAAAAC 3 67 1 TTCTGCTTTT 0.978681 -43 TCTCAATCTACCCCGTTTTTGAGGAAAACT 3 90 0 CTCTACTTTT 0.998175 -20 *** ** * **** Masking position 8 Map Score: 11.8769 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 TAACACAATTCTTGATTGTGA 1 2 1 AACACAATTC 0.979157 -299 AAAAAAAATCACCACAAATCACAATCAAGA 1 20 0 ACCACAAATC 0.983328 -281 GCGACTTTTGAAAAAAAATCACCACAAATC 1 30 0 AAAAAAAATC 0.889861 -271 TATCCATTAAAATAAAAACCGTGGTATCTT 1 80 0 AATAAAAACC 0.831823 -221 GGTTCTTTTCAACACAAGACACAGGATTTT 1 109 0 AACACAAGAC 0.964981 -192 CTAGGTCGTGACAACAATACTTTTTAGCAA 1 262 0 ACAACAATAC 0.88172 -39 CGCAGAGTATAACACAAACCTCTACTTTCT 3 17 0 AACACAAACC 0.989542 -93 ********** Masking position 6 Map Score: 6.26436 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 108 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 GTGGTGATTTTTTTTCAAAAGTCGCCTAAT 1 35 1 TTTTTCAAAA 0.900068 -266 AGAAGAGGTTCTTTTCAACACAAGACACAG 1 115 0 CTTTTCAACA 0.975458 -186 TAGAGAAAACCTTTCTAAGAAGAGGTTCTT 1 132 0 CTTTCTAAGA 0.887637 -169 GTGTATCTAGTTTTTCAAGATTGCTAAAAA 1 242 1 TTTTTCAAGA 0.983281 -59 GACAACAATACTTTTTAGCAATCTTGAAAA 1 253 0 CTTTTTAGCA 0.942045 -48 CGCTATCTGATTTTTCAGGTTGAGTAT 2 25 1 TTTTTCAGGT 0.940555 -17 ATCTACCCCGTTTTTGAGGAAAACTTAGCC 3 85 0 TTTTTGAGGA 0.955553 -25 ********** Masking position 7 Map Score: 5.08619 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 314 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 AACCTTTCTAAGAAGAGGTTCTTTTCAACA 1 125 0 AGAAGAGGTT 0.98907 -176 GATCAAGGCAAACAGCGGTTACTTATAATC 1 191 0 AACAGCGGTT 0.879965 -110 GTCACGACCTAGCAAAGGTATTTAATTGTC 1 280 1 AGCAAAGGTA 0.960991 -21 GGTCGCAGAAAGTAGAGGTTTGTGTTATAC 3 11 1 AGTAGAGGTT 0.98907 -99 ********** Masking position 4 Map Score: 1.52079 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 74 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 CAAGATACCACGGTTTTTATTTTAATGGATA 1 79 1 CGGTTTTTTT 0.937506 -222 CACAAGACACAGGATTTTATCCATTAAAATA 1 96 0 AGGATTTTTC 0.972102 -205 TTCTAAGAAGAGGTTCTTTTCAACACAAGAC 1 119 0 AGGTTCTTTC 0.975095 -182 TCTTCTTAGAAAGGTTTTCTCTACGGGCGGT 1 139 1 AAGGTTTTTC 0.931375 -162 GTTTTCTCTACGGGCGGTCTCGGAGTATAAT 1 152 1 CGGGCGGTTC 0.873676 -149 AAGCCCTCTCCGGATCTGATCAAGGCAAACA 1 207 0 CGGATCTGTC 0.811727 -94 AGATCCGGAGAGGGCTTTTTCGTGTATCTAG 1 221 1 AGGGCTTTTC 0.982425 -80 CAGAAAGTAGAGGTTTGTGTTATACTCTGCG 3 16 1 AGGTTTGTTT 0.856194 -94 CAGTGGGAAACGTTCTTTGTCTATAATCCCC 3 55 0 CGTTCTTTTC 0.843705 -55 CCCACTGGCTAAGTTTTCCTCAAAAACGGGG 3 79 1 AAGTTTTCTC 0.763882 -31 ******** ** Masking position 10 Map Score: 5.11696 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 497 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 CGCCCGTAGAGAAAACCTTTCTAAGAAGAG 1 138 0 GAAAACCTTT 0.910317 -163 TAGCAATCTTGAAAAACTAGATACACGAAA 1 238 0 GAAAAACTAG 0.98505 -63 TACTCAACCTGAAAAATCAGATAGCGAGAG 2 21 0 GAAAAATCAG 0.961522 -21 CGTTTTTGAGGAAAACTTAGCCAGTGGGAA 3 77 0 GAAAACTTAG 0.985021 -33 ********** Masking position 5 Map Score: 0.676284 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 60 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: 2.29806e-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: 2.29806e-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 9 ********** No masking Map Score: 2.29806e-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