AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00473_hinf_reg_300.orf -o00473_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #2 HI1129 201 conserved hypothetical protein #3 HI1130 30 conserved hypothetical protein #4 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #5 HI1137 21 cell division protein (ftsW) #6 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #7 HI1140 71 D-alanine--D-alanine ligase (ddlB) #8 HI1573 300 pyruvate kinase, type II (pykA) #9 HI1574 33 replicative DNA helicase (dnaB) Motif number 1 AAATAAGTAATTGAATAGGTATAAAAGCAAAT 1 2 0 TAAAAAAAAA 0.864828 -180 GTATTCTATTTCAAATTACGTCAAATCAAAATTGAATTTAA 1 110 0 TATAAATAAA 0.987016 -72 TTAAAGCAACTGATTTTTATCAAAATAAAAAAGCCGTTTGA 2 51 0 TTTAAATAAA 0.964029 -151 TTTAAAATTATATCATTGATGGAAATATAAATTTCCTTTAC 4 66 0 TATAAATAAA 0.986611 -57 TTAAAATTTATAGCAATTAAGAAGAAAGAAA 4 102 1 TATAGAAAAA 0.954544 -21 GCCTCAGTCATAAGTATTTTTTATATCCAAAAGTGCTAATA 6 33 1 TTTATATAAA 0.790581 -105 TATCCAAAAGTGCTAATATTAGAAATAAAAACGTTGCGAAT 6 56 1 TATAAATAAA 0.984651 -82 AGTTGAGTTTTGTCATTGGGAGAAAAGGAAAAATAA 6 112 1 TATAAAAAAA 0.98218 -26 TAAAACCCGATATAACTGGCAAAAAAGTAAACAAAACCAGC 8 140 1 TATAAAAAAA 0.982216 -161 ATTATACGCTTAAAACTTTTGGAAATCAAAAACGGCTCAGT 8 188 0 TATAAATAAA 0.986953 -113 TTTACTTCGCTACATATTAGCCAGATAAAAAATCGGTGCAC 8 229 0 TTTAGATAAA 0.911704 -72 TCAACAATCTAAATATGTTAAAATAAAAGAGCG 9 8 1 TATAAAAAAA 0.81078 -26 * * * **** *** Masking position 13 Map Score: 18.3846 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 103 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 TGTAAAATCTAAAACATCCATTAAAATGCTAATAAAT 1 39 0 AAACACTTAT 0.923406 -143 CACAAATCTTATAAAAATCTTTAAATTCAATTTTGAT 1 90 1 AAAAATTTTT 0.89148 -92 TATATGCCCTAAACAAGCGGCTGTATTCTATTTCAAA 1 136 0 AACAACCTTT 0.668765 -46 TTTAGGGCATATAAATACTTTTACTTTATTTT 1 160 1 AAAATCTTTT 0.76429 -22 AAATTTTATGAAAAAAGCCGTTTGAATTGTTTATTCA 2 17 1 AAAAACTTAT 0.934616 -185 TTATCAAAATAAAAAAGCCGTTTGAATAAACAATTCA 2 39 0 AAAAACTTAT 0.934616 -163 TTTATTTTGATAAAAATCAGTTGCTTTAATGTGGAAT 2 63 1 TAAAACTTTT 0.929854 -139 ACTTATTTTTAGAAAATCTCTAAAAATCTCCACAAAA 2 156 0 AAAAACTAAT 0.933909 -46 TGATATAATTTTAAAATTTATAGCAATTAAGAAGAAA 4 92 1 TAAAATTAAT 0.517403 -31 AATATTAGAAATAAAAACGTTGCGAATTTTAACCGCA 6 70 1 AAAAACTGAT 0.938476 -68 TGTGTTCAAGTTAAAAATATCTATAATCACGACTACT 8 92 0 TAAAATCTAT 0.670445 -209 TCGGGTTTTAAGAAAAATACTTGTGTTCAAGTTAAAA 8 113 0 AAAAATTTTT 0.89138 -188 AAAAAAGTAAACAAAACCAGCTTAAATAACTGAGCCG 8 160 1 AAAAACCTAT 0.964032 -141 CTTTTGGAAATCAAAAACGGCTCAGTTATTTAAGCTG 8 177 0 TAAAACCTTT 0.880544 -124 TTAGCCAGATAAAAAATCGGTGCACATTATACGCTTA 8 217 0 AAAAACTGAT 0.938477 -84 GCGAAGTAAAATAACACCTTTAAAATTTTGTAATTAT 8 260 1 AAACACTATT 0.734775 -41 * **** * ** ** Masking position 3 Map Score: 14.903 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 450 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 AAATTTAAGATAAAAGTACTACATTATTTT 3 11 0 TAAAAGTACT 0.87426 -20 CTTTCAAAAGTGAAAGAGCGAACCTAGCTA 4 17 0 TGAAAGAGCG 0.991013 -106 CTTTCACTTTTGAAAGAGCGACCTTTTTTA 4 31 1 TGAAAGAGCG 0.991013 -92 TTTTTATATCCAAAAGTGCTAATATTAGAA 6 50 1 CAAAAGTGCT 0.942639 -88 AAAACTCAACTAAAAGTGCGGTTAAAATTC 6 93 0 TAAAAGTGCG 0.992538 -45 TATGTTAAAATAAAAGAGCG 9 24 1 TAAAAGAGCG 0.992538 -10 ********** Masking position 5 Map Score: 8.16917 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 298 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 ATACAAGTCACAAATCTTATAAAAATCTTT 1 82 1 CAAATCTTAT 0.627123 -100 AATCTTATAAAAATCTTTAAATTCAATTTT 1 94 1 AAATCTTTAA 0.651115 -88 CTTTTTTCATAAAATTTTATTGA 2 4 0 AAAATTTTAT 0.897305 -198 GTTGAGCGAACAAATTATAAACTTGCCAGA 2 109 1 CAAATTATAA 0.804242 -93 TGTTTTGTGGAGATTTTTAGAGATTTTCTA 2 154 1 AGATTTTTAG 0.742123 -48 AAAATAAGTTCAATTTTTAAGGCGTAAT 2 184 1 CAATTTTTAA 0.894551 -18 TTAGTAAAGGAAATTTATATTTCCATCAAT 4 63 1 AAATTTATAT 0.759229 -60 TATAAATTTTAAAATTATATCATTGATGGA 4 84 0 AAAATTATAT 0.785082 -39 TATAATTTTAAAATTTATAGCAATTAAGAA 4 95 1 AAATTTATAG 0.792012 -28 AAAAACGTTGCGAATTTTAACCGCACTTTT 6 82 1 CGAATTTTAA 0.756385 -56 GGATTGATTGAAAATCTTAGTATTAGAAAA 7 19 1 AAAATCTTAG 0.753877 -53 GTGATTATAGATATTTTTAACTTGAACACA 8 99 1 ATATTTTTAA 0.597072 -202 TTGATTTCCAAAAGTTTTAAGCGTATAATG 8 200 1 AAAGTTTTAA 0.797433 -101 CAATAATTACAAAATTTTAAAGGTGTTATT 8 269 0 AAAATTTTAA 0.936794 -32 ********** Masking position 3 Map Score: 7.31083 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 524 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 5 TGCCCTAAACAAGCGGCTGTATTCTATTTC 1 139 0 AAGCGGCTGT 0.982371 -43 TAAACAATTCAAACGGCTTTTTTCATAAAA 2 20 0 AAACGGCTTT 0.970403 -182 TTGTTTATTCAAACGGCTTTTTTATTTTGA 2 43 1 AAACGGCTTT 0.970403 -159 TTCCACATTAAAGCAACTGATTTTTATCAA 2 69 0 AAGCAACTGA 0.905517 -133 GTGGTGCTCTAACCAACTGAGCTATAGTCG 8 52 1 AACCAACTGA 0.905517 -249 AAGTAAACAAAACCAGCTTAAATAACTGAG 8 164 1 AACCAGCTTA 0.95716 -137 TGGAAATCAAAAACGGCTCAGTTATTTAAG 8 180 0 AAACGGCTCA 0.961649 -121 ********** Masking position 2 Map Score: 4.58661 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 140 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ATGCTAATAAATAAGTAATTGAATAGGTAT 1 21 0 ATAAGTAATT 0.953701 -161 AAAATAAAGTAAAAGTATTTATATGCCCTA 1 162 0 AAAAGTATTT 0.94351 -20 CGCTCAACTTGCAAGTAATTCCACATTAAA 2 87 0 GCAAGTAATT 0.934868 -115 AGCCTCAGTCATAAGTATTTTTTATATCCA 6 32 1 ATAAGTATTT 0.967223 -106 TAACTTGAACACAAGTATTTTTCTTAAAAC 8 116 1 ACAAGTATTT 0.978559 -185 ********** Masking position 6 Map Score: 3.0701 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 31 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 GTGGAGAAAAGTGGTGTTTTGTGGAGATTT 2 140 1 GTGGTGTTTT 0.988983 -62 GTGGTGTTTTGTGGAGATTTTTAGAGATTT 2 150 1 GTGGAGATTT 0.972623 -52 GGGTTGTGGCGTTTTATAAATAGCC 6 6 1 GTGGCGTTTT 0.98692 -132 CGCACTTTTAGTTGAGTTTTGTCATTGGGA 6 103 1 GTTGAGTTTT 0.94506 -35 CCATGTCAAGGTGGTGCTCTAACCAACTGA 8 42 1 GTGGTGCTCT 0.959548 -259 ********** Masking position 8 Map Score: 3.37281 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 54 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -1.83077e-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: -1.83077e-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: -1.83077e-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