AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_ctra_reg_300.orf -o060_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 RCT00346 236 Chlamydia_trachomatis #2 RCT00347 169 Chlamydia_trachomatis Motif number 1 CATCTAAAGTTCTTTCTCTAAATAAATTAGG 1 29 1 TCTTTCCTAA 0.918967 -208 CAAACTTGCTCTTTTTCCTAATTTATTTAGA 1 45 0 CTTTTTCTAA 0.99114 -192 CCTGTTGGAGCTATTTACTCACTTATACTAT 1 94 1 CTATTTCTCA 0.963516 -143 TTTCTTTTAGCCATTTTCTAAGAGGATCCTA 1 138 1 CCATTTCTAA 0.990453 -99 GGCCTATGCTTTTTTTCATAATACTATCAGC 1 196 0 TTTTTTATAA 0.892269 -41 ATGTCTATTTTCTAAAAAGGTTAAA 2 5 1 CTATTTCTAA 0.988472 -165 AAAATAAAATCCTTTTCATAACAAAAAAATA 2 108 0 CCTTTTATAA 0.973584 -62 ****** **** Masking position 11 Map Score: 8.52627 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 111 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 GCAAACTTGCTCTTTTTCCTAATTTATTTA 1 47 0 TCTTTTTCCT 0.981926 -190 GAATTTGCTTTGCTTTTCCTGTTGGAGCTA 1 77 1 TGCTTTTCCT 0.968241 -160 TCCTGTTGGAGCTATTTACTCACTTATACT 1 93 1 GCTATTTACT 0.885624 -144 GTTTCTTTTAGCCATTTTCTAAGAGGATCC 1 137 1 GCCATTTTCT 0.97585 -100 ACAAGGCCTATGCTTTTTTTCATAATACTA 1 201 0 TGCTTTTTTT 0.87321 -36 ATGTCTATTTTCTAAAAAGGTTA 2 4 1 TCTATTTTCT 0.978255 -166 GGAAATAAGTTCTATTTTTTTGTTATGAAA 2 96 1 TCTATTTTTT 0.924657 -74 CAAAATAAAATCCTTTTCATAACAAAAAAA 2 110 0 TCCTTTTCAT 0.930221 -60 ********** Masking position 5 Map Score: 8.372 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 392 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 TATTTAGAGAAAGAACTTTAGATGTGCACCTG 1 21 0 AAAACTTAGA 0.940545 -216 ATTCATTTTTAACCTTTTTAGAAAATAGACAT 2 11 0 AACTTTTAGA 0.891588 -159 ATCATGCAAAAAACTCTTCCGAAGACTACATT 2 47 0 AACTCTTCGA 0.993684 -123 TATGATCTTAAATATCATGCAAAAAACTCTTC 2 60 0 AAATCATCAA 0.971726 -110 CATGATATTTAAGATCATACGAGGGAAATAAG 2 73 1 AAATCATCGA 0.990264 -97 AAAAAAACATAAAATCTTTCAACAAGATTAAT 2 148 0 AAATCTTCAA 0.984645 -22 ** ***** *** Masking position 8 Map Score: 3.48609 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 116 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 AGTGAGTAAATAGCTCCAACAGGAAAAGCA 1 87 0 TAGCTCCAAC 0.973463 -150 GTGGAACCTATAGGATCCTCTTAGAAAATG 1 149 0 TAGGATCCTC 0.911274 -88 GAGGATCCTATAGGTTCCACAATGGTGGAT 1 159 1 TAGGTTCCAC 0.972976 -78 TATCAGCAACTCTCATCCACCATTGTGGAA 1 173 0 TCTCATCCAC 0.931084 -64 TTCATAATACTATCAGCAACTCTCATCCAC 1 183 0 TATCAGCAAC 0.896937 -54 CCTCCCAGTATCTCCGACAAGGCCTATG 1 219 0 TATCTCCGAC 0.962311 -18 AAATAGAACTTATTTCCCTCGTATGATCTT 2 83 0 TATTTCCCTC 0.882273 -87 ********** Masking position 1 Map Score: 2.27969 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 172 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 GATGTGCACCTGAATATTTTTG 1 2 0 TGAATTTTTT 0.950658 -235 ATTCGCAAACTTGCTCTTTTTCCTAATTTAT 1 50 0 TTGCTTTTTT 0.904857 -187 CTATTCATTTTTAACCTTTTTAGAAAATAGA 2 14 0 TTAACTTTTT 0.941906 -156 GGAAATAAGTTCTATTTTTTTGTTATGAAAA 2 96 1 TCTATTTTTT 0.950658 -74 TGAAAAGGATTTTATTTTGTTGTTATAATTA 2 121 1 TTTATTTGTT 0.972571 -49 GTTGTTATAATTAATCTTGTTGAAAGATTTT 2 139 1 TTAATTTGTT 0.972571 -31 GTTGAAAGATTTTATGTTTTTTT 2 157 1 TTTATTTTTT 0.981376 -13 ***** ***** Masking position 7 Map Score: 5.83009 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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: -5.09159e-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: -5.09159e-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: -5.09159e-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