AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i202_exonuclease_sbcc_mthe_reg_300.orf -o202_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH00536 107 M.thermo #2 RTH00449 194 M.thermo Motif number 1 TGCCCCACTAGAGCAGAGACCATGGCAGTGC 1 11 1 GAGCAGAGCC 0.907822 -97 GCAGAGACCATGGCAGTGCCCCGACTGAGGC 1 23 1 TGGCAGTGCC 0.863807 -85 GGCAGTGCCCCGACTGAGGCCCTTCACCAGA 1 34 1 CGACTGAGCC 0.934564 -74 TGAGAAAAAGGGTATGAGGCCTGGAACGGTG 2 94 1 GGTATGAGCC 0.925234 -101 GGAACGGTGAGATCTGAGCCCGAGAAAGCTG 2 116 1 GATCTGAGCC 0.66502 -79 AAGGAGTATGGAGCTGACTCCAACTTCTGCG 2 170 1 GAGCTGACCC 0.984596 -25 ******** ** Masking position 6 Map Score: 8.35272 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 272 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 TGCCCCACTAGAGCAGAGACCATGGCAG 1 3 1 CCCTAGGGAG 0.971768 -105 GTGTTATTATGGTTACGAGTGAAGAGATGAAGAGGA 2 51 1 GGTGAGGGAG 0.995759 -144 AAGGGTATGAGGCCTGGAACGGTGAGATCTGAGCCC 2 101 1 GGCGAAGGAG 0.998948 -94 TGAGATCTGAGCCCGAGAAAGCTGAGAAGTTCTGTC 2 123 1 GCCGAAGGAG 0.998482 -72 TCCAAACTGTGGCAAGGAGTATGGAGCTGACTCCAA 2 157 1 GGCGAGAGAG 0.996573 -38 TCGTCGCAGAAGTTGGAGTCAGCTCCAT 2 177 0 GTCGAATGAG 0.978918 -18 *** *** * *** Masking position 8 Map Score: 6.72554 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 142 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 GAGGCCCTTCACCAGAAAAACCACAAACTA 1 49 1 ACCAGAAAAA 0.945948 -59 GAAAATAAATGTTATAAATAGTTTGTGGTT 1 67 0 GTTATAAATA 0.858132 -41 ATTGCAGCTTGTTATAATAAGGTTACC 2 8 0 GTTATAATAA 0.91857 -187 ATAACAAGCTGCAATAAAAATAATTATGGT 2 23 1 GCAATAAAAA 0.94985 -172 CCATAATAACACCATAATTATTTTTATTGC 2 33 0 ACCATAATTA 0.96248 -162 TTCACTCGTAACCATAATAACACCATAATT 2 44 0 ACCATAATAA 0.979534 -151 ********** Masking position 6 Map Score: 3.11929 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 229 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 AATTATTTTTATTGCAGCTTGTTATAATAA 2 18 0 ATTGCAGCTT 0.953299 -177 CATACCCTTTTTCTCAGCGAGTCTCCTCTT 2 80 0 TTCTCAGCGA 0.988324 -115 TCGGGCTCAGATCTCACCGTTCCAGGCCTC 2 109 0 ATCTCACCGT 0.98762 -86 TGGACAGAACTTCTCAGCTTTCTCGGGCTC 2 131 0 TTCTCAGCTT 0.992819 -64 ********** Masking position 6 Map Score: 1.67514 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 57 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ********** No masking Map Score: 7.69818e-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: 7.69818e-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: 7.69818e-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