AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_6_1_1_17_ctra_reg_300.orf -o228_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 RCT00426 271 Chlamydia_trachomatis #2 RCT00427 300 Chlamydia_trachomatis Motif number 1 CTGTGCCCTTACAGAGAAGGCTCTATCT 1 9 0 ACAGAGAAGG 0.972857 -263 CTGTAAGGGCACAGCAGGGGAGAGCTTGGG 1 25 1 ACAGCAGGGG 0.937061 -247 CTCCGGAATTCCGGAGGAGGCCCAAGCTCT 1 45 0 CCGGAGGAGG 0.988574 -227 CTCCGGAATTCCGGAGGGGGGCTTTTTTTT 1 59 1 CCGGAGGGGG 0.984046 -213 TGCCTGATTCATAGGACAGGAACCCGGGAC 1 199 1 ATAGGACAGG 0.871914 -73 GGACAGGAACCCGGGACGGGGTGTTCATTT 1 212 1 CCGGGACGGG 0.982731 -60 CGCTACTAACCCAGGAAAGGAAACTTTTCT 1 251 0 CCAGGAAAGG 0.979518 -21 AAATCCTTAAAAAGAGAAGGTAACATTTTC 2 92 0 AAAGAGAAGG 0.778459 -209 GCCATTATTCACAAGACAGGCCAAGATGAG 2 239 1 ACAAGACAGG 0.923098 -62 TTTTAAGTGGACGAGGGAGGACTAAACAGT 2 278 1 ACGAGGGAGG 0.964589 -23 ********** Masking position 9 Map Score: 11.8547 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 262 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 2 CTTTTTCAACAAAAAAAAAGCCCCCCTCCGG 1 69 0 AAAAAAAAGC 0.914538 -203 TTTTTTTTGTTGAAAAAGAGCTCCGAAAAAC 1 82 1 TAAAAAGAGC 0.982346 -190 CTTTAACAAAACTAAAATAACGAGTTTTTCG 1 105 0 ATAAAATAAC 0.727005 -167 TGTTCATTTCATAAAGATAGAAAAGTTTCCT 1 233 1 AAAAGATAGA 0.859741 -39 AAACTTTGTTTCAAAAATAGCATTTATTTTT 2 28 1 TAAAAATAGC 0.989923 -273 AAGCGGTTTGTTAAAAATAAATGCTATTTTT 2 40 0 TAAAAATAAA 0.942485 -261 TGCAAAATCCTTAAAAAGAGAAGGTAACATT 2 95 0 TAAAAAGAGA 0.965894 -206 GAGCGCTTACTGAAAAATTGCAAAATCCTTA 2 113 0 TAAAAATTGC 0.939358 -188 CCTCGTCCACTTAAAAATAAATCCTCTCATC 2 263 0 TAAAAATAAA 0.942485 -38 * ********* Masking position 5 Map Score: 8.16428 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 275 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 CCTTCTCTGTAAGGGCACAGCAGGGGAGAG 1 19 1 AAGGGCACAG 0.873096 -253 CACAGCAGGGGAGAGCTTGGGCCTCCTCCG 1 34 1 GAGAGCTTGG 0.94176 -238 TTTGTTGAAAAAGAGCTCCGAAAAACTCGT 1 87 1 AAGAGCTCCG 0.957067 -185 TTTAGGAACATAGGGCTTTGAACGGTCCGA 1 164 1 TAGGGCTTTG 0.970644 -108 CTTATTAATCAAGCGGTTTGTTAAAAATAA 2 51 0 AAGCGGTTTG 0.873049 -250 ATTTTTCAGTAAGCGCTCGCTACACTAGGA 2 126 1 AAGCGCTCGC 0.934755 -175 ATAGAGTGGAAAGGGCTTGTCCGACTTAGA 2 163 1 AAGGGCTTGT 0.924104 -138 CCCAGTCTCTTAGAGCTATGCTTATTGAAT 2 194 0 TAGAGCTATG 0.822692 -107 TCTTGTGAATAATGGCTCTGTGACCTTCTA 2 225 0 AATGGCTCTG 0.931162 -76 ********** Masking position 2 Map Score: 3.79952 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 243 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 GGGGGCTTTTTTTTTGTTGAAAAAGAGCTC 1 75 1 TTTTTGTTGA 0.890086 -197 CGTTATTTTAGTTTTGTTAAAGTCGCCAAG 1 114 1 GTTTTGTTAA 0.989452 -158 TTGAAACAAAGTTTTGTAAAGTTTTTTACA 2 12 0 GTTTTGTAAA 0.973769 -289 TTAATCAAGCGGTTTGTTAAAAATAAATGC 2 47 0 GGTTTGTTAA 0.976884 -254 ATCTTGGCCTGTCTTGTGAATAATGGCTCT 2 236 0 GTCTTGTGAA 0.961222 -65 ********** Masking position 5 Map Score: 3.26108 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 45 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 CCCTCCGGAATTCCGGAGGAGGCCCAAGCT 1 47 0 TTCCGGAGGA 0.995208 -225 TCCTCCGGAATTCCGGAGGGGGGCTTTTTT 1 57 1 TTCCGGAGGG 0.996781 -215 ATAACGAGTTTTTCGGAGCTCTTTTTCAAC 1 90 0 TTTCGGAGCT 0.97656 -182 ********** Masking position 7 Map Score: 0.629618 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 13 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 CCAGGAAAGGAAACTTTTCTATCTTTATGA 1 241 0 AAACTTTTCT 0.962057 -31 AAAGTTTTGTAAAGTTTTTTACAA 2 5 0 AAAGTTTTTT 0.976084 -296 AAACTTTACAAAACTTTGTTTCAAAAATAG 2 18 1 AAACTTTGTT 0.962057 -283 GCTTGATTAATAAGTTTTTTGTTGGGAAAA 2 67 1 TAAGTTTTTT 0.944817 -234 ********** Masking position 5 Map Score: 0.408482 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 61 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: 1.24588e-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: 1.24588e-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: 1.24588e-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