AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i139_NADH_Oxidoreductase_ctra_reg_100.orf -o139_ctra_100.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 RCT00265 300 Chlamydia_trachomatis #2 RCT00604 21 Chlamydia_trachomatis #3 RCT00605 113 Chlamydia_trachomatis #4 RCT00710 142 Chlamydia_trachomatis Motif number 1 AACAAGATAGACAAATCTCTCTTCCTGGAG 1 75 1 ACAAATCTCT 0.917271 -226 TTGTTATTCGACAAATATTTCCGGTCCTTT 1 120 0 ACAAATATTT 0.9549 -181 TTGTCGAATAACAAATATTAGAATCCTATA 1 136 1 ACAAATATTA 0.894425 -165 ATTTTTACGAATAAAAAACTCGGTTGTTTA 1 164 0 ATAAAAAACT 0.870475 -137 TTTTTTATTCGTAAAAATTTTAATAATTTG 1 176 1 GTAAAAATTT 0.793367 -125 TCAAAACGTAACAAATTATTAAAATTTTTA 1 187 0 ACAAATTATT 0.821635 -114 TGCTTTTACGACAAATTTTCCAAAGGGAAT 1 270 0 ACAAATTTTC 0.871164 -31 TGTCGTAAAAGCAAATTTCAACAC 1 287 1 GCAAATTTCA 0.607774 -14 ATATTACATCACAAAAAACAAGAAAAATTT 3 63 1 ACAAAAAACA 0.850048 -51 TTATTTAATAATAAAATTTTTCTTGTTTTT 3 76 0 ATAAAATTTT 0.872603 -38 AACAAAAATCTCGATCTTTTA 3 103 0 ACAAAAATCT 0.97146 -11 CTTCCTTGTAATAAAACTTTAAAAAACTCC 4 52 1 ATAAAACTTT 0.850468 -91 AGGTTACTCTATAAAAAATCAACGGAGTTT 4 75 0 ATAAAAAATC 0.775956 -68 AATTATAAAAATCCCTGGAATTTC 4 129 0 ATAAAAATCC 0.909656 -14 ********** Masking position 5 Map Score: 12.5186 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 525 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 ATCTCTCTTCCTGGAGCTTTACAAATGCAGCA 1 89 1 CGGGCTTTAC 0.99565 -212 ACAAATATTTCCGGTCCTTTGCTGCATTTGTA 1 108 0 CGGCCTTTGC 0.997067 -193 AGCCCAAGGACCTGGGCTTTGCTGAAAGGAGC 4 17 0 CTGGCTTTGC 0.998303 -126 AGCCCAGGTCCTTGGGCTTTGCTTCCTTGTAA 4 31 1 CTGGCTTTGC 0.998305 -112 * ** ******* Masking position 8 Map Score: 5.52234 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 ATCGCCGCCAACAAGATAGACAAATCTCTC 1 66 1 ACAAGATAGA 0.933376 -235 TTTGTAAAGCTCCAGGAAGAGAGATTTGTC 1 84 0 TCCAGGAAGA 0.959766 -217 GCAGCAAAGGACCGGAAATATTTGTCGAAT 1 115 1 ACCGGAAATA 0.948796 -186 CCCTTTTTAGTCCGGAAATATACGCCGAAT 3 19 1 TCCGGAAATA 0.889635 -95 ACGCCGAATAACAAAAAAGAGCAATATTAC 3 40 1 ACAAAAAAGA 0.89747 -74 ATCACAAAAAACAAGAAAAATTTTATTATT 3 70 1 ACAAGAAAAA 0.92822 -44 AAGTTTTATTACAAGGAAGCAAAGCCCAAG 4 41 0 ACAAGGAAGC 0.933212 -102 ********** Masking position 8 Map Score: 2.34671 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 319 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 ACTAGGTGTTTAGAAACGTTGAATAT 1 7 0 TAGAAACGTT 0.972231 -294 ACGTATTTACGATAATCGTTGTACTAGGTG 1 29 0 GATAATCGTT 0.835325 -272 ACGATTATCGTAAATACGTTTACTACATCG 1 40 1 TAAATACGTT 0.837459 -261 TTTTAATAATTTGTTACGTTTTGAACGTGT 1 193 1 TTGTTACGTT 0.89983 -108 CGTTTTGAACGTGTAACGTTCTCAACCTTT 1 209 1 GTGTAACGTT 0.960252 -92 TTGTGTCTGAGAGAAAGGTTGAGAACGTTA 1 222 0 GAGAAAGGTT 0.968266 -79 GTAGCGTCAAGTTATAGGTTACTCTATAAA 4 90 0 GTTATAGGTT 0.858774 -53 ********** Masking position 9 Map Score: 2.30554 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 159 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 TCTAATATTTGTTATTCGACAAATATTTCC 1 128 0 GTTATTCGAC 0.98276 -173 GAATCGACAAGTTTTTCGAGCATTGTGTCT 1 244 0 GTTTTTCGAG 0.982343 -57 TTGAAATTTGCTTTTACGACAAATTTTCCA 1 278 0 CTTTTACGAC 0.931873 -23 GATGGCTCCCCTTTTTAGTCCGGAAATATA 3 11 1 CTTTTTAGTC 0.881591 -103 GCTCTTTTTTGTTATTCGGCGTATATTTCC 3 32 0 GTTATTCGGC 0.971005 -82 AATTTTTCTTGTTTTTTGTGATGTAATATT 3 62 0 GTTTTTTGTG 0.881595 -52 ********** Masking position 5 Map Score: 2.33335 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 58 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: 8.40873e-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: 8.40873e-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: 8.40873e-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