AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_hpyl_reg_100.orf -o00730_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0845 44 thiamin phosphate pyrophosphorylase/hyroxyethylthiazole kinase (thiM) #2 HP0846 290 type I restriction enzyme R protein (hsdR) Motif number 1 TAAGGCTCAAAAAAAGCGCCGTTTA 1 30 1 AAAAAGCGCC 0.993844 -15 CTAAAAGCTTAATAAACGCCCTTT 2 5 0 AATAAACGCC 0.961703 -286 CTATGAATTTAAAAAAATCCACAAAGAAGA 2 45 1 AAAAAAATCC 0.984328 -246 AAAGACAATTTAAAAGAGCAGTTAGAAAAG 2 82 1 TAAAAGAGCA 0.919781 -209 AAAGAGCAGTTAGAAAAGCTTAATGATCAT 2 94 1 TAGAAAAGCT 0.87632 -197 GGCTAAAACGAAAAAGATCCAAGAAGATCC 2 192 1 AAAAAGATCC 0.990062 -99 AAAAAGATCCAAGAAGATCCGATTTTTAAT 2 202 1 AAGAAGATCC 0.989863 -89 CATTGATAAGAAAAATATCCATAGAAACGC 2 270 1 AAAAATATCC 0.950226 -21 AAAATATCCATAGAAACGCC 2 281 1 TAGAAACGCC 0.981251 -10 ********** Masking position 5 Map Score: 15.5914 Number of sites scoring better than the average of aligned sites = 974 Number in coding regions = 915 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 TTTGAGCCTTAATGCAAAAGCGTTCATGAA 1 11 0 AATGCAAAAG 0.956925 -34 CTTTTGCATTAAGGCTCAAAAAAAGCGCCG 1 21 1 AAGGCTCAAA 0.945424 -24 GTTTTTCTAAAAGCTTAATAAACGCCCTTT 2 11 0 AAGCTTAATA 0.886049 -280 CAAGGCTATGAATTTAAAAAAATCCACAAA 2 40 1 AATTTAAAAA 0.795204 -251 AATTTAAAAAAATCCACAAAGAAGAAGAAT 2 50 1 AATCCACAAA 0.934833 -241 ATTAAAAGACAATTTAAAAGAGCAGTTAGA 2 78 1 AATTTAAAAG 0.80794 -213 GCAGTTAGAAAAGCTTAATGATCATTCTTT 2 99 1 AAGCTTAATG 0.893891 -192 TCATTCTTTCACGCCTAAAGAATGGGACAC 2 120 1 ACGCCTAAAG 0.936748 -171 CGATGACTATAAGGCTAAAACGAAAAAGAT 2 180 1 AAGGCTAAAA 0.97578 -111 GAGAACGGGAAAACCAAAAACATTAAAATC 2 241 1 AAACCAAAAA 0.910235 -50 ********** Masking position 8 Map Score: 7.33327 Number of sites scoring better than the average of aligned sites = 2754 Number in coding regions = 2451 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 3 GTGGATTTTTTTAAATTCATAGCCTTGTTTTT 2 35 0 TTAAATCATG 0.995565 -256 ACTCTTTATTCTCAATTCATCGCTAATAAAAA 2 148 1 CTCAATCATG 0.98733 -143 CGTTTTAGCCTTATAGTCATCGTTTTTATTAG 2 170 0 TTATATCATG 0.988931 -121 ACCAAAAACATTAAAATCATTGATAAGAAAAA 2 253 1 TTAAATCATG 0.995565 -38 ***** **** * Masking position 7 Map Score: 3.65276 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TAAATTGTCTTTTAATTCTTCTTCTTTGTG 2 64 0 TTTAATTCTT 0.915708 -227 AACTGCTCTTTTAAATTGTCTTTTAATTCT 2 75 0 TTAAATTGTC 0.850211 -216 ATGGGACACTCTTTATTCTCAATTCATCGC 2 141 1 CTTTATTCTC 0.965716 -150 TAGTCATCGTTTTTATTAGCGATGAATTGA 2 159 0 TTTTATTAGC 0.925933 -132 AAGATCCGATTTTTAATCTCACGCTAGAGA 2 215 1 TTTTAATCTC 0.975505 -76 TTATCAATGATTTTAATGTTTTTGGTTTTC 2 249 0 TTTTAATGTT 0.881773 -42 CTATGGATATTTTTCTTATCAATGATTTTA 2 264 0 TTTTCTTATC 0.925936 -27 ********** Masking position 7 Map Score: 2.45342 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 627 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 TTAATGCAAAAGCGTTCATGAA 1 3 0 AGCGTTCATG 0.980769 -42 GCTTTTTTTGAGCCTTAATGCAAAAGCGTT 1 17 0 AGCCTTAATG 0.988812 -28 TTAAATTCATAGCCTTGTTTTTCTAAAAGC 2 27 0 AGCCTTGTTT 0.976917 -264 CGTTTTTATTAGCGATGAATTGAGAATAAA 2 152 0 AGCGATGAAT 0.898226 -139 TTTTCGTTTTAGCCTTATAGTCATCGTTTT 2 176 0 AGCCTTATAG 0.977297 -115 ********** Masking position 6 Map Score: 2.11934 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 458 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 ********** No masking Map Score: 2.43208e-15 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: 2.43208e-15 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: 2.43208e-15 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