AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00480_tpal_reg_300.orf -o00480_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #2 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #3 TP0479 111 T. pallidum predicted coding region TP0479 Motif number 1 CTCCTCTCTCCCGCTACGTTCTAGTGTCGT 1 30 0 CCGCTACGTT 0.972848 -31 GGGCGAACATCCTCCTCTCTCCCGCTACGT 1 41 0 CCTCCTCTCT 0.94381 -20 GGCAGACTCTCCGCTCCCTAAGGCA 2 6 0 CCGCTCCCTA 0.986008 -67 CCGGTGTAGGTCGCACCGTTGAAAGAAGGG 2 46 1 TCGCACCGTT 0.989075 -27 AAACCGCCCCTTCTTTCAACGGT 2 60 0 CCGCCCCTTC 0.987026 -13 GAGCTCCTCCTTTTTCTAAAGG 3 3 1 GCTCCTCCTT 0.965612 -109 AATAATTGCCTCGCAGCCTTTAGAAAAAGG 3 19 0 TCGCAGCCTT 0.933559 -93 GGCGTTTAGCGCGCGCCGTCAAGTTTTTCT 3 50 1 GCGCGCCGTC 0.965543 -62 GTCAAGTTTTTCTCACCGTTTGGCATACTC 3 67 1 TCTCACCGTT 0.979424 -45 TTGGCATACTCCTCTTCGCAAGGAAGGGGG 3 86 1 CCTCTTCGCA 0.904039 -26 GCCCTCCCCCCTTCCTTGCGAA 3 100 0 CCTCCCCCCT 0.99345 -12 ********** Masking position 4 Map Score: 16.9424 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1186 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 GTTCTAGTGTCGTTCAAGGCTCGGCATTAC 1 13 0 CGTTCAAGGC 0.981368 -48 GACTCTCCGCTCCCTAAGGCA 2 2 0 TCCCTAAGGC 0.950921 -71 ACACCGGATGTGCCGCAGGCAGACTCTCCG 2 23 0 TGCCGCAGGC 0.969979 -50 ACCGCCCCTTCTTTCAACGGTGCGACCTAC 2 51 0 CTTTCAACGG 0.851325 -22 CTCCTCCTTTTTCTAAAGGCTGCGAGGCAA 3 14 1 TTCTAAAGGC 0.980385 -98 TGACGGCGCGCGCTAAACGCCTAATAATTG 3 41 0 CGCTAAACGC 0.992698 -71 AAGAGGAGTATGCCAAACGGTGAGAAAAAC 3 72 0 TGCCAAACGG 0.98292 -40 ********** Masking position 7 Map Score: 4.10871 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 810 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 GCTACGTTCTAGTGTCGTTCAAGGCTCGGC 1 18 0 AGTGTCGTTC 0.837477 -43 GCGGGAGAGAGGAGGATGTTCGCCC 1 46 1 GGAGGATGTT 0.962508 -15 TAGGGAGCGGAGAGTCTGCCTGCGGCACAT 2 16 1 AGAGTCTGCC 0.960908 -57 CGGCACATCCGGTGTAGGTCGCACCGTTGA 2 38 1 GGTGTAGGTC 0.994498 -35 TTTAGAAAAAGGAGGAGCTC 3 1 0 GGAGGAGCTC 0.989036 -111 CTTGCGAAGAGGAGTATGCCAAACGGTGAG 3 78 0 GGAGTATGCC 0.989009 -34 CGCAAGGAAGGGGGGAGGGC 3 102 1 GGGGGAGGGC 0.987997 -10 ********** Masking position 4 Map Score: 7.60862 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 407 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 ********** No masking Map Score: 1.16119e-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 5 ********** No masking Map Score: 1.16119e-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 6 ********** No masking Map Score: 1.16119e-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