AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ifruR_hinf_opreg_100.orf -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 HI0050 74 conserved hypothetical transmembrane protein #2 HI0051 38 conserved hypothetical transmembrane protein #3 HI0052 26 conserved hypothetical protein #4 HI0053 109 zinc-type alcohol dehydrogenase #5 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #6 HI0449 86 H. influenzae predicted coding region HI0449 #7 HI0451 71 conserved hypothetical protein #8 HI0452 50 conserved hypothetical protein #9 HI0453 26 conserved hypothetical protein #10 HI0454 54 conserved hypothetical protein #11 HI0457 69 conserved hypothetical protein #12 HI0458 70 stationary phase survival protein SurA, putative #13 HI0459 131 pyrimidine operon regulatory protein (pyrR) #14 HI0524 110 fructose-bisphosphate aldolase (fba) #15 HI0525 101 phosphoglycerate kinase (pgk) #16 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #17 HI0982 95 6-phosphofructokinase (pfkA) #18 HI0985 300 DNA processing chain A (dprA) #19 HI1711 59 PTS system, glucose-specific IIA component (crr) #20 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #21 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 GTACACCAAGAAATAACAATAAGAATAAACTACACAA 1 34 0 AAAAAAAATA 0.919939 -41 AAAACATAATCAATAAGGAGAAAGTT 3 8 1 AAAAAAAAAG 0.942865 -19 TACTCAAAAATATAAAAGAAAACGACCGCACTT 8 28 0 AATAAAAAAC 0.900518 -23 CAAAGTATCAAAAATAAAGGGGCTTAATT 11 3 1 AAATAAAAAG 0.786479 -67 AGAAAGAGAAAATAAAAAACAACAAAAGGGGCAATTA 11 35 0 AAAAAAAAAA 0.976628 -35 TGGATAGTATAACGAACAAGAAAAATGGTGCAAATGC 13 38 1 AAAAAAAATG 0.819429 -94 TTCAATGCACAAAGTATAAAGAAAATACGCCTAAAAA 13 81 0 AATAAAAATA 0.892225 -51 TTATCCCGCTAAACATAAAAAGGAAACACAAGT 14 88 1 AAATAAAAAC 0.737138 -23 TAGCACGAAGTAGGTATAATACGAAAAGTTTTCAATT 15 40 1 TATAAAAAAA 0.757113 -62 GTTAAAATTAAAATTAAAATTGAAAACTTTTCGTATT 15 57 0 AATAAAAAAC 0.900518 -45 AGTCACCTCTAATATATAAGATTAAAATTTAACTGTG 16 145 0 AATAAAAAAA 0.967851 -28 GTTTATTTTTAATATAAAATGCCAAAAAATAGTTTGA 18 28 0 AATAAAAAAA 0.967851 -273 ATATACATTTAACTAATAAACTTAATAAAATTAGCAT 18 83 1 AAAAAAAATA 0.919939 -218 GAAAATGTAAAAAATCCAATAAGAAAAATTTGTTGAT 18 140 0 AATCAAAAAA 0.751678 -161 CTTTTTAATGAATAAAAAATTGCAAAATTTTTCTTAT 18 180 0 AAAAAAAAAA 0.976628 -121 GAGGGAGAGAAACGATTAATTTAAAAGCATTTTGCGA 18 234 0 AAATAAAAAG 0.786479 -67 TTTATTTGAAAATCTAGTATGGAAAAAACGAGGGAGA 18 263 0 AATATAAAAA 0.628514 -38 CTAGATTTTCAAATAAAAAGGAAAAAAT 18 283 1 AAAAAAAAAA 0.976628 -18 TTGCTATTTTAACGTAAAATCAAATAATTTTGT 19 7 0 AATAAAATAA 0.757113 -53 AGTAATAAATAAACAATAGCCATAAAATTTCACAATT 20 28 0 AAAAAGAAAA 0.776809 -52 CTTCCGAAACAATTAACAAAGTAATAAATAAACAATA 20 47 0 AAAAAAATAA 0.81226 -33 AATTAAATCATAAAAATAAGCTAAATAGTTTATTTAT 21 29 0 TAAAAAAATA 0.543324 -130 CAAAATAATCAAGAATAAACACTAAAAAGCCTGAATT 21 62 0 AAATAAAAAA 0.903162 -97 AATAATTAAAAATATAAAACCAGAAAATTGCCCTAGT 21 113 0 AATAAAAAAA 0.967851 -46 ** ** ** **** Masking position 14 Map Score: 32.7669 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 473 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 2 GGTACACCAAGAAATAACAATAAGAATAAACTA 1 39 0 GAAAACAAAA 0.67607 -36 AAAACATAATCAATAAGGAGAAA 3 1 1 AAAATAATAA 0.757071 -26 ACCAGCAGCTTATTGAAAAACAA 5 1 0 TATAAAAAAA 0.64075 -71 GCTCCTTAATAATTTAAAAAGAAAGCTGCGGAT 5 45 0 AATAAAAAAA 0.893671 -27 TTTGTAGAGAAATGGATAAAAATTTACCGCACT 7 12 0 AATATAAAAT 0.653678 -60 TTATGTTATAAAACCATAAAAAATTTGAGGTTA 7 46 1 AAAATAAAAA 0.969181 -26 TACTCAAAAATATAAAAGAAAACGACCGC 8 32 0 AAAATAAAGA 0.706951 -19 GCCTTAGGCATAAGGAAAAATAATT 10 40 1 TAAAAAAAAA 0.85165 -15 CAAAGTATCAAAAATAAAGGGGCT 11 2 1 AAAATCAAAA 0.932389 -68 AAGAAAGAGAAAATAAAAAACAACAAAAGGGGC 11 40 0 AAAAAAAAAA 0.964352 -30 CTCATCCAAAAAAGAGTCAATAACGTTGGTTAG 12 48 0 AAAGTCAAAA 0.669637 -23 TTGGATAGTATAACGAACAAGAAAAATGGTGCA 13 37 1 TAAAACAAAA 0.715705 -95 TTCAATGCACAAAGTATAAAGAAAATACGCCTA 13 85 0 AAAATAAAAA 0.969181 -47 TGTTAAGTTAAAATTAAAATTAAAATTGAAAAC 15 67 0 AAAAAAATAA 0.728324 -35 AATGGATGTCAATATAAAAAAATGTTAAGTAGA 16 103 0 AATAAAAAAT 0.618857 -70 TTGGCATTTTATATTAAAAATAAACCTACTTAC 18 40 1 ATAAAAAAAA 0.583331 -261 TCTTATTTTGAAAATGTAAAAAATCCAATAAGA 18 153 0 AAAGTAAAAA 0.822135 -148 TTACATTTTCAAAATAAGAAAAATTTTGCAATT 18 167 1 AAAAAGAAAA 0.731187 -134 AATTCTTTTTAATGAATAAAAAATTGCAAAATT 18 188 0 AATATAAAAA 0.907152 -113 CTAGATTTTCAAATAAAAAGGAAAAAAT 18 283 1 AAAAAAAGAA 0.692619 -18 TTAACAAAGTAATAAATAAACAATAGCCATAAA 20 39 0 AATATAAAAA 0.907152 -41 ATACCTTCCGAAACAATTAACAAAGTAATAAAT 20 55 0 AAAATTAAAA 0.68086 -25 TTGAGATTGTGAATAATAAATAAACTATTTAGC 21 14 1 GAAATAAAAA 0.846922 -145 AGCCTGAATTAAATCATAAAAATAAGCTAAATA 21 39 0 AAAATAAAAT 0.858662 -120 TTTCAAAGCAAAATAATCAAGAATAAACACTAA 21 74 0 AAAATCAAAA 0.932389 -85 GACTAATCAATAATTAAAAATATAAAACCAGAA 21 125 0 TAAAAAAAAT 0.525843 -34 *** ***** ** Masking position 9 Map Score: 24.2629 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 751 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 3 ACAGTATAATGGCGGCGTTTTATTAACTTTA 6 59 1 GCGGCGTTTT 0.984909 -28 CCTAAAAAGCGACGGCATTTGCACCATTTTT 13 58 0 GCGGCATTTG 0.984909 -74 TTGTATTGATGATGGCATTTTTGATGCCACC 14 39 0 GTGGCATTTT 0.983011 -72 CCGACATTGTGTCGGGATTGTTT 16 3 0 GCGGGATTGT 0.980271 -170 CCGACACAATGTCGGGATTTTTGCTCTATAT 16 19 1 GCGGGATTTT 0.993845 -154 AGCAAAATTTGACGGGATTTTGATCTACA 17 9 0 GCGGGATTTT 0.993845 -87 CAAACTATTTTTTGGCATTTTATATTAAAAA 18 29 1 TTGGCATTTT 0.882424 -272 * ********* Masking position 8 Map Score: 8.37827 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 14 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 AAAACATAATCAATAAGGAGAAAG 3 5 1 CATAATCAAT 0.690391 -22 TTGTTTTTCAATAAGCTGCTGG 5 3 1 GTTTTTCAAT 0.719068 -69 ATCTATTGTGAACCTTCAATAGAATTGTTA 12 16 1 AACCTTCAAT 0.567 -55 TTTTCCCAGCTTTATCAATAGTATTTCAA 13 113 0 CTTTATCAAT 0.872801 -19 TTTTTGATGCCACCATCAATATGTTATAGA 14 23 0 CACCATCAAT 0.844509 -88 TCAAAAATGCCATCATCAATACAAATTCTT 14 46 1 CATCATCAAT 0.945025 -65 ATCAATACAAATTCTTCAAATTGTGGGCTT 14 60 1 ATTCTTCAAA 0.628568 -51 ATCTTATGCCCATTTTCAATTATGGTTAAA 17 64 1 CATTTTCAAT 0.943849 -32 CCTACTTACACTTCATCAAATATACATTTA 18 64 1 CTTCATCAAA 0.87528 -237 GGATTTTTTACATTTTCAAAATAAGAAAAA 18 160 1 CATTTTCAAA 0.914828 -141 TTCCATACTAGATTTTCAAATAAAAAGGAA 18 276 1 GATTTTCAAA 0.719068 -25 AAATAGCAACCATCTTGAATGGATAGGAGA 19 35 1 CATCTTGAAT 0.724242 -25 CCCTAGTATCCTTTTTCAAAGCAAAATAAT 21 90 0 CTTTTTCAAA 0.872827 -69 ********** Masking position 8 Map Score: 7.02362 Number of sites scoring better than the average of aligned sites = 943 Number in coding regions = 855 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 AATACCAAATATCTATTTTT 4 1 0 ATCTATTTTT 0.913669 -109 GAAACATAAAAACTCTTTTTGGAATACCAA 4 23 0 AACTCTTTTT 0.961239 -87 AATTATTTTTCCTTATGCCT 10 45 0 AATTATTTTT 0.827297 -10 CAACGTTATTGACTCTTTTTTGGATGAG 12 53 1 GACTCTTTTT 0.958665 -18 TGCAAATGCCGTCGCTTTTTAGGCGTATTT 13 66 1 GTCGCTTTTT 0.779983 -66 TAAGAACTTTACCTCTTTTTAGTGATATTG 16 52 0 ACCTCTTTTT 0.943464 -121 TGTTAAGTAGATCTCATTTTTAAACATTTT 16 84 0 ATCTCATTTT 0.718915 -89 CTGGCTGTCAAACTATTTTTTGGCATTTTA 18 21 1 AACTATTTTT 0.928762 -280 GTGTAAGTAGGTTTATTTTTAATATAAAAT 18 45 0 GTTTATTTTT 0.784314 -256 AGATCGCAAAAATTCTTTTTAATGAATAAA 18 201 0 AATTCTTTTT 0.901101 -100 AAACTATTTAGCTTATTTTTATGATTTAAT 21 35 1 GCTTATTTTT 0.750915 -124 ********** Masking position 7 Map Score: 8.18182 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 108 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 GAGCTTATAATGTTACTATTATTT 1 4 1 CTTTAATGTT 0.919105 -71 TCCAAAAAGAGTTTTTATGTTTCATAATCAT 4 30 1 GTTTTATGTT 0.92619 -80 AATAAAATTACTTGTTATGTTTAACTATGAT 4 61 0 CTTTTATGTT 0.982055 -49 CCGCAGCTTTCTTTTTAAATTATTAAGGAGC 5 47 1 CTTTTAAATT 0.844998 -25 CTTGTGTTTCCTTTTTATGTTTAGCGGGATA 14 89 0 CTTTTATGTT 0.982055 -22 AATCTATCCTCTTGTTAAGTTAAAATTAAAA 15 81 0 CTTTTAAGTT 0.97676 -21 ATATGCTAATTTTATTAAGTTTATTAGTTAA 18 91 0 TTTTTAAGTT 0.866703 -210 *** ******* Masking position 7 Map Score: 5.49043 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TAAACATAACAAGTAATTTTATTCTGTCAAT 4 69 1 AAGTAATTTA 0.451905 -41 AATGGCATATAAGGAGTCTAAAA 4 97 1 AAGGAGCTAA 0.873919 -13 ATACTGTCTAAAGGGGATTAAGCAAGGAAGC 6 35 0 AAGGGGTTAA 0.959456 -52 TTTTGTAGAGAAATGGATAAAAATTTACCGC 7 15 0 AAATGGTAAA 0.636654 -57 ATCAAAAATAAAGGGGCTTAATTGCCCCTTT 11 17 1 AAGGGGTTAA 0.959456 -53 ACCTAGCACGAAGTAGGTATAATACGAAAAG 15 37 1 AAGTAGTATA 0.8657 -65 ATATCACTAAAAAGAGGTAAAGTTCTTAAAA 16 54 1 AAAGAGTAAA 0.796933 -119 TTATGGTTAAAAGTAGGTAAATT 17 83 1 AAGTAGTAAA 0.934365 -13 GATGAAGTGTAAGTAGGTTTATTTTTAATAT 18 50 0 AAGTAGTTTA 0.904189 -251 CTTGAATGGATAGGAGATTAAA 19 48 1 TAGGAGTTAA 0.82384 -12 ****** **** Masking position 2 Map Score: 2.38656 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 208 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 ACTTGTTATGTTTAACTATGATATGATTATG 4 52 0 TTTAACATGA 0.668133 -58 GCGGCGTTTTATTAACTTTAATCGGGT 6 70 1 ATTAACTTAA 0.690695 -17 ATTTAACCTCAAATTTTTTATG 7 60 0 TTTAACTCAA 0.802073 -12 CAATTTTAATTTTAATTTTAACTTAACAAGA 15 72 1 TTTAATTTAA 0.76077 -30 TTTACCTACTTTTAACCATAATTGAAAATGG 17 73 0 TTTAACATAA 0.883444 -23 TAGGTTTATTTTTAATATAAAATGCCAAAAA 18 37 0 TTTAATTAAA 0.821161 -264 CAAATATACATTTAACTAATAAACTTAATAA 18 80 1 TTTAACAATA 0.833806 -221 AATTAGCATATTTAACCAATACAACCCTAAT 18 111 1 TTTAACAATA 0.834018 -190 AAAAATTCTTTTTAATGAATAAAAAATTGCA 18 193 0 TTTAATAATA 0.648647 -108 GAGAGAAACGATTAATTTAAAAGCATTTTGC 18 236 0 ATTAATTAAA 0.540822 -65 TGGTTGCTATTTTAACGTAAAATCAAATAAT 19 16 0 TTTAACTAAA 0.920809 -44 ****** **** Masking position 5 Map Score: 2.80593 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 206 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 ATCAATATGTTATAGAGGAAAAGTGCGG 14 8 0 TTAGAGGAAA 0.941776 -103 GTTGTAACGATTTAGATCAAAGAAATTC 15 8 0 TTAGATCAAA 0.961926 -94 GATATTGTGATATAGAGCAAAAATCCCGACA 16 28 0 TTAGAGCAAA 0.982743 -145 TGTAGATCAAAATCCCGTCAA 17 1 1 TTAGATCAAA 0.961943 -95 GTCAAATTTTGCTAGAGCAGATTCTTTGAAT 17 27 1 GTAGAGCAGA 0.920368 -69 * ********* Masking position 6 Map Score: 0.184745 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 31 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ********** No masking Map Score: 1.71484e-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 11 ********** No masking Map Score: 1.71484e-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 12 ********** No masking Map Score: 1.71484e-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