AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i039_Mannose_Metabolism_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 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 = 0 Input sequences: #1 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #2 HI1336 111 dihydropteroate synthase (folP-1) #3 HI1337 37 mrsA protein (mrsA) Motif number 1 GATAAGATAAGATAAGATAAGATAAGATA 1 10 0 GATAAGATAA 0.960478 -291 AAAAAGATAAGATAAGATAAGATAAGATAA 1 25 0 GATAAGATAA 0.960478 -276 TAGAACAATGAAAAAGATAAGATAAGATAA 1 35 0 AAAAAGATAA 0.944509 -266 GGATAAGAGAGATAAAATCAAAATATCCCT 1 117 0 GATAAAATCA 0.972798 -184 ATACCCACCCGAAAAAATCATAATATACTA 1 154 0 GAAAAAATCA 0.985544 -147 CAGAATATTGGACAAAATAATAATAAACCC 1 231 0 GACAAAATAA 0.985581 -70 TATTCTGGAGGGAAAATTAATACCTTAAAC 1 254 1 GGAAAATTAA 0.84729 -47 AAATCATTAGGAAAAAATAAAGCCTTTCCG 2 29 0 GAAAAAATAA 0.988077 -83 TACATCCAAGAACAAAATCATTAGGAAAAA 2 43 0 AACAAAATCA 0.953832 -69 ATAATCGCCCACCAAAATCACTCTAAAAAT 2 80 1 ACCAAAATCA 0.795529 -32 AAAATCACTCTAAAAATTAACCGCATTTT 2 93 1 TAAAAATTAA 0.766903 -19 TTATAACGATAAAAAATTAAAGGAATTTTA 3 16 1 AAAAAATTAA 0.915431 -22 ********** Masking position 5 Map Score: 19.1518 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 474 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 CTTCCTTGCTTATTACTTTCTTTTTTGATTT 1 79 1 TATACTTTCT 0.73199 -222 ATTTTCATACAAATACTCTATACCCACCCGA 1 172 0 AAAACTCTAT 0.959525 -129 TTTGTATGAAAATTACTCTAATGTTAGCTAT 1 190 1 AATACTCTAA 0.959563 -111 AGGGAAAATTAATACCTTAAACTATATAAAG 1 262 1 AATCCTTAAA 0.877955 -39 ATATATAGAGAAAACCTTTATATAGTTTAAG 1 277 0 AAACCTTTAT 0.978529 -24 CTCATCAAAGCCTTTCTTCGGAAAGGC 2 7 1 AAACCTTTCT 0.95707 -105 CTTTCTTCGGAAAGGCTTTATTTTTTCCTAA 2 22 1 AAAGCTTTAT 0.928347 -90 CGCCCACCAAAATCACTCTAAAAATTAACCG 2 85 1 AATACTCTAA 0.959563 -27 AATAAAATTCCTTTAATTTTTTATCG 3 22 0 AATCCTTTAA 0.978556 -16 *** ******* Masking position 7 Map Score: 9.19675 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 248 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 AGATAAGATAAGATAAGATA 1 1 0 AGATAAGATA 0.995213 -300 AGATAAGATAAGATAAGATAAGATAAGATA 1 11 0 AGATAAGATA 0.995213 -290 AGATAAGATAAGATAAGATAAGATAAGATA 1 21 0 AGATAAGATA 0.995213 -280 ACAATGAAAAAGATAAGATAAGATAAGATA 1 31 0 AGATAAGATA 0.995213 -270 TTTGATTTTAAGATAAGGGATATTTTGATT 1 102 1 AGATAAGGGA 0.969012 -199 CTAAAATAGCGGATAAGAGAGATAAAATCA 1 127 0 GGATAAGAGA 0.991409 -174 CCAGAATATTGGACAAAATAATAATAAACC 1 232 0 GGACAAAATA 0.93482 -69 AAAATCATTAGGAAAAAATAAAGCCTTTCC 2 30 0 GGAAAAAATA 0.906338 -82 ********** Masking position 5 Map Score: 19.9464 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 5 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 CTTATCTTAAAATCAAAAAAGAAAGTAATA 1 89 0 AATCAAAAAA 0.970326 -212 AGAGAGATAAAATCAAAATATCCCTTATCT 1 112 0 AATCAAAATA 0.987915 -189 CACCCGAAAAAATCATAATATACTAAAATA 1 149 0 AATCATAATA 0.986242 -152 TATTGGACAAAATAATAATAAACCCTACCA 1 226 0 AATAATAATA 0.952391 -75 ********** Masking position 5 Map Score: 3.92987 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 52 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 ATACTCTATACCCACCCGAAAAAATCATAA 1 161 0 CCCACCCGAA 0.997673 -140 TAATAATAAACCCTACCAAATATATAGCTA 1 214 0 CCCTACCAAA 0.985635 -87 TATTAATTTTCCCTCCAGAATATTGGACAA 1 246 0 CCCTCCAGAA 0.996342 -55 AAAAATAAAGCCTTTCCGAAGAAAGGCTTT 2 17 0 CCTTTCCGAA 0.967346 -95 GCTATAATCGCCCACCAAAATCACTCTAAA 2 77 1 CCCACCAAAA 0.988295 -35 ********** Masking position 9 Map Score: 7.84502 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AAGGAAGCAGATATAAAGCACTAGAACAAT 1 56 0 ATATAAAGCA 0.903091 -245 TAATATACTAAAATAGCGGATAAGAGAGAT 1 134 0 AAATAGCGGA 0.938228 -167 CCTACCAAATATATAGCTAACATTAGAGTA 1 203 0 ATATAGCTAA 0.919577 -98 ACCTTAAACTATATAAAGGTTTTCTCTATA 1 275 1 ATATAAAGGT 0.881804 -26 TACATATATAGAGAAAACCTTTATA 1 286 0 ATATAGAGAA 0.977047 -15 TGGTGGGCGATTATAGCGAAATACATCCAA 2 64 0 TTATAGCGAA 0.974605 -48 TGGTTTTATAACGATAAAAAATTAA 3 6 1 TTATAACGAT 0.889925 -32 ********** Masking position 5 Map Score: 3.89025 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 249 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 ********** No masking Map Score: 5.92755e-14 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: 5.92755e-14 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: 5.92755e-14 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