AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis_+_PPS_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 HI0556 85 oxidoreductase, putative (devB) #2 HI0557 82 H. influenzae predicted coding region HI0557 #3 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #4 HI0559 194 sulfite synthesis pathway protein (cysQ) #5 HI1302 147 asparaginyl-tRNA synthetase (asnS) #6 HI1573 300 pyruvate kinase, type II (pykA) #7 HI1574 33 replicative DNA helicase (dnaB) #8 HI1576 54 glucose-6-phosphate isomerase (pgi) Motif number 1 ACGATCATCACCCCACCAAAAATGCAGA 1 68 0 CACCCCACCA 0.97941 -18 AGCGTGGCTAAAGCCCACCCTACATTAGAT 2 14 0 AAGCCCACCC 0.990025 -69 GGGTGGGCTTTAGCCCACAATTTATTATGT 2 51 0 TAGCCCACAA 0.879332 -32 TTGTGGGCTAAAGCCCACCCTACGGAAAAT 2 61 1 AAGCCCACCC 0.990025 -22 GAAAAAAACCAATCGAACCAA 3 2 0 AATCGAACCA 0.916018 -74 ATTGTTCATAACCCGCACCAACACTATATT 5 82 1 ACCCGCACCA 0.990379 -66 GACTAGCTGGACTCGAACCAGTGACCCCCA 6 12 1 ACTCGAACCA 0.899968 -289 CGAACCAGTGACCCCCACCATGTCAAGGTG 6 25 1 ACCCCCACCA 0.992219 -276 CTCAGTTGGTTAGAGCACCACCTTGACATG 6 43 0 TAGAGCACCA 0.854674 -258 ********** Masking position 7 Map Score: 9.77948 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 301 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 TCACCCCACCAAAAATGCAGATTTTTCCAG 1 59 0 AAAAATGCAG 0.963121 -27 TAATGTCGAAAATAATGCCGTATTCTAGAG 3 31 0 AATAATGCCG 0.903854 -45 AAAATCGCGTATATTCAATA 5 1 1 AAAATCGCGT 0.912044 -147 TATGAACAATAAAATCGCCTTAAAAATGAG 5 62 0 AAAATCGCCT 0.978366 -86 ATTTTTATGGAAAATTTCCTTCATTAAGGT 5 109 1 AAAATTTCCT 0.80362 -39 ATAAAATTGCCGATAGTTTACC 5 136 0 AAAATTGCCG 0.98988 -12 TTTGGAAATCAAAAACGGCTCAGTTATTTA 6 182 0 AAAAACGGCT 0.892008 -119 AGCCAGATAAAAAATCGGTGCACATTATAC 6 222 0 AAAATCGGTG 0.814256 -79 CCTCTGTTCAAAAAATGCAGTGA 8 4 0 AAAAATGCAG 0.963121 -51 CTCCCTAATAAAAATTCCAGAAA 8 42 1 AAAATTCCAG 0.847453 -13 ********** Masking position 4 Map Score: 7.64652 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 711 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 GTTATTATTTAAAACCCTAGCCAAATCACCTTAT 1 11 1 AAAACCTGAA 0.965047 -75 TTCTAGAGAAAAAAACCAATCGAACCAA 3 5 0 AAAAACATAA 0.691131 -71 TGTTTTTGATAAAACTGTTGCAAATGCTTACCTG 4 137 0 AAAACTTGAA 0.959735 -58 CAGTTTTATCAAAAACAGGTTCATGTTGAATTGA 4 154 1 AAAAACGTAT 0.782046 -41 GAGTCCTAAATAAAATAGGGTAAAGCCTTATTAA 5 31 0 TAAAATGGAA 0.876538 -117 TTCATTAAGGTAAACTATCGGCAATTTTAT 5 128 1 TAAACTTGAA 0.894451 -20 TGTTCAAGTTAAAAATATCTATAATCACGACTAC 6 93 0 AAAAATTTAA 0.902953 -208 TATTTTTCTTAAAACCCGATATAACTGGCAAAAA 6 131 1 AAAACCGTAA 0.958566 -170 AAAAGTAAACAAAACCAGCTTAAATAACTGAGCC 6 162 1 AAAACCGTAA 0.958592 -139 TTATACGCTTAAAACTTTTGGAAATCAAAAACGG 6 194 0 AAAACTTGAA 0.959735 -107 TAGCCAGATAAAAAATCGGTGCACATTATACGCT 6 219 0 AAAAATGTAC 0.722529 -82 ATAACACCTTTAAAATTTTGTAATTATTGACGGA 6 270 1 TAAAATTGAT 0.567791 -31 ****** * * ** Masking position 4 Map Score: 6.33869 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 497 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 ATGTAGGGTGGGCTTTAGCCACGCTCTTAC 2 19 1 GGCTTTAGCC 0.547733 -64 CCGTAGGGTGGGCTTTAGCCCACAATTTAT 2 56 0 GGCTTTAGCC 0.547733 -27 ATATTAATAAGGCTTTACCCTATTTTATTT 5 28 1 GGCTTTACCC 0.818616 -120 ********** Masking position 7 Map Score: 5.05173 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 4 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TTAATTTGTTCCGCATAAGGTGATTTGGCTA 1 28 0 CCGATAAGGT 0.987661 -58 TATTCGGCTTCCGAGTAATGTCGAAAATAAT 3 45 0 CCGGTAATGT 0.987661 -31 TACTCGGAAGCCGAATAAGGAATAATT 3 59 1 CCGATAAGGA 0.982413 -17 TAGTGTTGGTGCGGGTTATGAACAATAAAAT 5 77 0 GCGGTTATGA 0.920988 -71 AAAGTTTTAAGCGTATAATGTGCACCGATTT 6 210 1 GCGATAATGT 0.980732 -91 *** ******* Masking position 6 Map Score: 1.53019 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 30 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GTTATTATTTAAAACCCTAGCC 1 3 1 TATTATTTAA 0.902369 -83 GCCCACAATTTATTATGTTAGTAAGAGCGT 2 39 0 TATTATGTTA 0.863092 -44 ACATGCGGAATGGTATTTTATGCTCTATTT 4 13 1 TGGTATTTTA 0.934283 -182 AAAACGGCTCAGTTATTTAAGCTGGTTTTG 6 171 0 AGTTATTTAA 0.837182 -130 ATTTTAAAGGTGTTATTTTACTTCGCTACA 6 256 0 TGTTATTTTA 0.974919 -45 CGCTCTTTTATTTTAACATATTTAG 7 19 0 TTTTATTTTA 0.907232 -15 ********** Masking position 5 Map Score: 1.08295 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 149 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 AAAAATGCAGATTTTTCCAGTTAATTTGTT 1 49 0 ATTTTTCCAG 0.822629 -37 AAAAATCTGCATTTTTGGTGGGGTGATGAT 1 63 1 ATTTTTGGTG 0.689917 -23 CGGAATGGTATTTTATGCTCTATTTGTAAT 4 18 1 TTTTATGCTC 0.713696 -177 TATTCTCTTGTTTTTGGCAGCAACCACGGC 4 48 0 TTTTTGGCAG 0.964555 -147 AAGAGAATAATTTTATGCTGACGCTAACGA 4 69 1 TTTTATGCTG 0.944923 -126 TTTGTTTACTTTTTTGCCAGTTATATCGGG 6 145 0 TTTTTGCCAG 0.933439 -156 CGGCTCAGTTATTTAAGCTGGTTTTGTTTA 6 167 0 ATTTAAGCTG 0.732289 -134 CTTCGCTACATATTAGCCAGATAAAAAATC 6 236 0 TATTAGCCAG 0.845197 -65 CTGGAATTTTTATTAGGGAGAATGACTCCC 8 32 0 TATTAGGGAG 0.763424 -23 ********** Masking position 4 Map Score: 1.09051 Number of sites scoring better than the average of aligned sites = 776 Number in coding regions = 681 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 8 ********** No masking Map Score: 2.8375e-12 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: 2.8375e-12 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 10 ********** No masking Map Score: 2.8375e-12 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