AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_hinf_reg_300.orf -o00680_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 HI0185 122 alcohol dehydrogenase, class III (adhC) #2 HI0885 191 thiol:disulfide interchange protein (dsbD) #3 HI0886 111 H. influenzae predicted coding region HI0886 #4 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #5 HI0888 95 phosphoribosylamine--glycine ligase (purD) #6 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #7 HI0928 265 catalase (hktE) #8 HI1444 300 5,10 methylenetetrahydrofolate reductase (metF) Motif number 1 TAACAATAAAAAAGTGCGGTGATTTTTTAC 2 78 1 AAAGTGCGGT 0.998284 -114 ATAATTTCTTAAAGTGCGGTAAAAATACGA 4 84 0 AAAGTGCGGT 0.998284 -104 CCTCTTTTGTAAAGAGGGGGATAGTTAGAT 5 14 0 AAAGAGGGGG 0.981711 -82 CCTCTTTACAAAAGAGGGGGAATTGCAGGT 5 27 1 AAAGAGGGGG 0.981711 -69 TAATTTAAAAAAAGTACGGCTATTTTTTAC 5 55 0 AAAGTACGGC 0.946116 -41 ATAAAGGCGAAAAATGCGGTTGAAAATCAG 7 68 1 AAAATGCGGT 0.991351 -198 AACGAAAAAGAAAGTGCGGTAATTTTTTGT 8 78 0 AAAGTGCGGT 0.998284 -223 TTTTCGTTGTAAAATGGGGTAAATCATTGC 8 100 1 AAAATGGGGT 0.983352 -201 ATTGCTAACAAAAGTGCGGTAGTTTTGAGT 8 125 1 AAAGTGCGGT 0.998284 -176 ********** Masking position 3 Map Score: 23.6356 Number of sites scoring better than the average of aligned sites = 1349 Number in coding regions = 870 Number in noncoding regions = 479 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 2 TTATTCCCTTTAAACAAAAATGATAAAAAA 1 14 1 TAAACAAAAA 0.851 -109 ACAAAAATGATAAAAAAACACTTGCTTTAG 1 27 1 TAAAAAAACA 0.947035 -96 GAAAATCAGGTAAAAAATCACCGCACTTTT 2 87 0 TAAAAAATCA 0.946953 -105 GAATTGAGTATAAAAATATAGATGCTCGAA 2 171 0 TAAAAATATA 0.847362 -21 TTACCAAAAGTAAAAAATAA 3 1 0 TAAAAAATAA 0.91741 -111 AACGGGTAGTTAAACAATAATTAAAATTGA 3 41 0 TAAACAATAA 0.850994 -71 AATTCATCTTTAAACAAAAGGAAAGCAA 3 94 1 TAAACAAAAG 0.834269 -18 AAAATAAGGATAAAATTATGAAACTACAAC 4 15 0 TAAAATTATG 0.573039 -173 TAAAGTGCGGTAAAAATACGATAAATTTCA 4 75 0 TAAAAATACG 0.940332 -113 ATTAAATAGTTAAAAATAAGCGATGAGAAT 4 154 0 TAAAAATAAG 0.907412 -34 GAATTGCAGGTAAAAAATAGCCGTACTTTT 5 46 1 TAAAAAATAG 0.907412 -50 ATTTCATTCCTAAATTTTCATCACTTAAAT 6 38 0 TAAATTTTCA 0.502228 -86 AAAATTTAATTAAAATTTCATTCCTAAATT 6 52 0 TAAAATTTCA 0.807072 -72 TGTTTATGGATAAAAATTTAATTAAAATTT 6 64 0 TAAAAATTTA 0.675121 -60 AAAATCTACCTAAATATTCAAAATTACTTA 7 119 0 TAAATATTCA 0.799361 -147 AAAACTATACTAAAATAAAACTTAAAATCT 7 142 0 TAAAATAAAA 0.746091 -124 TAGAAAGGTTTAAACAATCGAAATCTATTA 7 184 0 TAAACAATCG 0.890044 -82 AAATGCGTGTTAAATAAATACAATAGATTT 8 30 0 TAAATAAATA 0.588999 -271 TATCTTTCTATAAAAATACACAAAAAATTA 8 59 1 TAAAAATACA 0.946953 -242 TGTGTTGATCTAAAAATTAGTTATTATTGA 8 156 1 TAAAAATTAG 0.907333 -145 ********** Masking position 1 Map Score: 19.4539 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 588 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 3 TTTTTATTCCCTTTAAACAAAAATGATAAAA 1 4 1 TTTCTTAAAA 0.856643 -119 TGATTTTCCTTTTTGTGATCTAAATCATAGTTTTAGGT 2 109 1 TTGATTAAAT 0.799221 -83 GTAAAAAGTATTTTTCAATTTTAATTATTGTTTAACTA 3 27 1 TTTATTTAAT 0.89671 -85 TGTGGGCTTTTTTATGCCTGAAATTTATCGTATTTTTA 4 57 1 TTTCTAAAAT 0.88267 -131 TTACCGCACTTTAAGAAATTATATTTAATCTTTTCTAT 4 92 1 TTGATATAAA 0.875762 -96 TATTTAATCTTTTCTATATTTAAGCAAACGTTTGCGTT 4 113 1 TTTATTAAAA 0.896021 -75 AAGCAAACGTTTGCGTTATAATTCTCATCGCTTATTTT 4 134 1 TTGATATTAT 0.591587 -54 TTAAATGAAATTAATTCATCATAATGATATGGA 6 6 0 TTTATATAAT 0.924539 -118 TTCCTAAATTTTCATCACTTAAATGAAATTAATTCATC 6 24 0 TTTCTAAAAA 0.893936 -100 ATTTTTCGCCTTTATCCCTTTTACGGATTCAAGTATAA 7 45 0 TTTCTTTAAT 0.856647 -221 AATTACTTACTTGATATATCTTTATAAAGCCTGATTTT 7 90 0 TTTATTTTAA 0.669519 -176 ATAGTTTTTTTTGATTAATTTAATAGATTTCGATTGTT 7 164 1 TTTATTAAAT 0.885703 -102 TGTTTAAACCTTTCTATATGATACGCAAGAAATTCATT 7 198 1 TTTATATAAA 0.931663 -68 ATTTTTTGCGCTAAAAAACAAATCTATTGTA 8 4 1 TTGCTAAAAA 0.812339 -297 TGGATAATTATTGTTCAATAATAACTAATTTTTAGATC 8 162 0 TTTATATAAA 0.927201 -139 AATTATCCATTTATTGAATTATTAATAATAATCATACT 8 191 1 TTTATATTAA 0.760413 -110 TCAATTTCAATTTATTCATTAAAAGTATGATTATTATT 8 214 0 TTTATAAAAT 0.91622 -87 ** * ** *** ** Masking position 9 Map Score: 14.7466 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 396 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 CTCTAAAGCAAGTGTTTTTTTATCATTTTT 1 29 0 AGTGTTTTTT 0.835532 -94 CCATCCTTATACTTATTTTGGCGTATGCTA 2 14 1 ACTTATTTTG 0.726423 -178 AAAAAAGTGCGGTGATTTTTTACCTGATTT 2 85 1 GGTGATTTTT 0.922415 -107 TGATTTTTTACCTGATTTTCCTTTTTGTGA 2 97 1 CCTGATTTTC 0.869222 -95 TTTGGTAAAAAGTATTTTTCAATTTTAATT 3 23 1 AGTATTTTTC 0.723865 -89 ATAATTTTATCCTTATTTTTGCCCACATTT 4 26 1 CCTTATTTTT 0.882291 -162 AATTCTCATCGCTTATTTTTAACTATTTAA 4 153 1 GCTTATTTTT 0.882291 -35 AAAAAGTACGGCTATTTTTTACCTGCAATT 5 47 0 GCTATTTTTT 0.835532 -49 AAAAAATAGCCGTACTTTTTTTAAATTAGG 5 57 1 CGTACTTTTT 0.695914 -39 CTTTATAAAGCCTGATTTTCAACCGCATTT 7 79 0 CCTGATTTTC 0.869222 -187 ATATCAAGTAAGTAATTTTGAATATTTAGG 7 111 1 AGTAATTTTG 0.795391 -155 ATTTTAGTATAGTTTTTTTTGATTAATTTA 7 156 1 AGTTTTTTTT 0.762066 -110 AAGAAAGTGCGGTAATTTTTTGTGTATTTT 8 71 0 GGTAATTTTT 0.916482 -230 TTCAATAATAACTAATTTTTAGATCAACAC 8 157 0 ACTAATTTTT 0.910141 -144 ********** Masking position 6 Map Score: 9.33479 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 522 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 GGCAACTTTGTCAATGAATTAAGAGGAAAAACA 1 100 1 TAATAATTAA 0.966376 -23 TTTTAACTATTTAATGAAAGGAAAATACA 4 169 1 TAATAAAGAA 0.892277 -19 TTTCATCACTTAAATGAAATTAATTCATCATAAT 6 19 0 TAATAAATAT 0.870963 -105 CTATCTGCCATAAATTACATAACAGGAGAACACA 6 100 1 TAATACATAA 0.913893 -24 ACCAACATTTTTAATCACATTAGATCAACGATT 7 10 0 TAATACATAA 0.913893 -256 ATATTCAAAATTACTTACTTGATATATCTTTATA 7 102 0 TACTACTTAA 0.772207 -164 CGAAATCTATTAAATTAATCAAAAAAAACTATAC 7 162 0 TAATAATCAA 0.884175 -104 CCTTGTAAAGTTAATAAATTTAGTTAGGTTGAAA 7 234 0 TAATAATTAT 0.919665 -32 AAATGCGTGTTAAATAAATACAATAGATTTGTTT 8 26 0 TAATAATAAT 0.672296 -275 TATTAATAATTCAATAAATGGATAATTATTGTTC 8 184 0 TAATAATGAA 0.933549 -117 ATACTTTTAATGAATAAATTGAAATTGACTCATA 8 224 1 TAATAATTAA 0.966376 -77 * *** **** * * Masking position 7 Map Score: 5.57857 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 179 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 ATTCCCTTTAAACAAAAATGATAAAAAAACA 1 16 1 AACAAAAATA 0.946796 -107 ACATTATTGTAACAATAAAAAAGTGCGGTGA 2 69 1 AACAATAAAA 0.956379 -123 CGGGTAGTTAAACAATAATTAAAATTGAAAA 3 38 0 AACAATAATA 0.966157 -74 TATTAAATTAATCAAAAAAAACTATACTAAA 7 158 0 ATCAAAAAAA 0.710076 -108 CCCATTTTACAACGAAAAAGAAAGTGCGGTA 8 87 0 AACGAAAAAA 0.784017 -214 ATTATTGTTCAATAATAACTAATTTTTAGAT 8 163 0 AATAATAACA 0.746292 -138 GTTATTATTGAACAATAATTATCCATTTATT 8 175 1 AACAATAATA 0.966157 -126 TTGAATTATTAATAATAATCATACTTTTAAT 8 204 1 AATAATAATA 0.867193 -97 ********* * Masking position 5 Map Score: 3.69908 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 144 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 TTATACTTATTTTGGCGTATGCTATCAAAG 2 20 1 TTTGGCGTAT 0.953544 -172 ATGCCTGAAATTTATCGTATTTTTACCGCA 4 70 1 TTTATCGTAT 0.869483 -118 GTTGTAGTCCTTGCGTATGCCTAATTTA 5 78 0 CCTTGCGTAT 0.944229 -18 GAAATGAATTTCTTGCGTATCATATAGAAA 7 208 0 TCTTGCGTAT 0.98215 -58 AAAAAACAAATCTATTGTATTTATTTAACA 8 23 1 TCTATTGTAT 0.731063 -278 TGCGGTAATTTTTTGTGTATTTTTATAGAA 8 64 0 TTTTGTGTAT 0.93901 -237 AGTGCGGTAGTTTTGAGTATGTGTTGATCT 8 137 1 TTTTGAGTAT 0.897237 -164 ********** Masking position 9 Map Score: 2.56489 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 100 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 CGTATGCTATCAAAGCTATCATTCTATCTG 2 35 1 CAAAGCTATC 0.832609 -157 TAGATGCTCGAAATTCTATCACAAAGAAAT 2 153 0 AAATTCTATC 0.810693 -39 TACTTTTGGTAAAAAGTATTTTTCAATTTT 3 19 1 AAAAAGTATT 0.565254 -93 TTTTATGCCTGAAATTTATCGTATTTTTAC 4 66 1 GAAATTTATC 0.58998 -122 AATAAAACTTAAAATCTACCTAAATATTCA 7 129 0 AAAATCTACC 0.914422 -137 ATTAATCAAAAAAAACTATACTAAAATAAA 7 153 0 AAAAACTATA 0.712567 -113 TTAAACAATCGAAATCTATTAAATTAATCA 7 175 0 GAAATCTATT 0.83078 -91 CGCTAAAAAACAAATCTATTGTATTTATTT 8 19 1 CAAATCTATT 0.877375 -282 AAAATACACAAAAAATTACCGCACTTTCTT 8 71 1 AAAAATTACC 0.622089 -230 AACACATACTCAAAACTACCGCACTTTTGT 8 132 0 CAAAACTACC 0.883829 -169 GACTCATATTAAAACCTATTTTATTGTACA 8 250 1 AAAACCTATT 0.785835 -51 TTTATTGTACAAATACTATTTTAGAATCCT 8 269 1 AAATACTATT 0.692451 -32 ********** Masking position 3 Map Score: 1.18077 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 330 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 ********** No masking Map Score: 3.47699e-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: 3.47699e-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: 3.47699e-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