AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_hinf_reg_300.orf -o00450_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 HI0086 300 cystathionine gamma-synthase (metB) #2 HI0122 274 cystathionine beta-lyase (metC) #3 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #4 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #5 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #6 HI0200 126 selenide, water dikinase (selD) #7 HI0701 108 conserved hypothetical protein #8 HI0706 23 lipoprotein #9 HI0707 132 DNA mismatch repair protein (mutS) #10 HI0708 205 L-seryl-tRNA selenium transferase (selA) #11 HI1102 152 cysteine synthetase, putative (cysZ) #12 HI1103 98 cysteine synthetase (cysK) #13 HI1171 41 anthranilate synthase component II (trpG) #14 HI1172 84 S-adenosylmethionine synthetase (metX) #15 HI1276 102 methionyl-tRNA synthetase (metG) Motif number 1 AGAAAAATTGACCGCACTTTAGCTAAAGAT 2 11 1 ACCGCACTTT 0.998807 -264 ATTAATTTTAACCGCACTTTTGCGCGCTTT 5 16 0 ACCGCACTTT 0.998807 -31 CACTAAAATAACCGCACTTTTGTTCTTGTT 7 24 0 ACCGCACTTT 0.998807 -85 GAGATTTTTTACCGCACTTTTTACAGGAAG 9 12 0 ACCGCACTTT 0.998807 -121 ACAAATTTTTACCGCACTTTTATCTGGCTT 9 43 1 ACCGCACTTT 0.998807 -90 CGCTAAAGTGACCGCAATTTCAACCACGGA 10 143 0 ACCGCAATTT 0.98507 -63 CCTTTAAAATTCCACACTTTGAAGTATTTT 11 86 0 TCCACACTTT 0.893431 -67 CTTAAAACAGACCGCACTTTTCCTTTAAAA 11 107 0 ACCGCACTTT 0.998807 -46 TATTTATAGTACCGCACTTTTGATTAAAAA 12 42 0 ACCGCACTTT 0.998807 -57 TATAACGAATACCGAACTGTT 13 31 1 ACCGAACTGT 0.92548 -11 AACTTAACATACCGCACTTTCC 15 3 0 ACCGCACTTT 0.998807 -100 ********** Masking position 6 Map Score: 48.1366 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 TAGCTAAAGTGCGGTCAATTTTTCT 2 4 0 GCGGTATTTT 0.99096 -271 GCGCAAAAGTGCGGTTAAAATTAATTACATTT 5 21 1 GCGGTAAATT 0.973506 -26 GCAGGTTGAGGCTGTAAAATTTCGCCTAAG 6 107 1 GCTGTAATTT 0.87906 -20 GAACAAAAGTGCGGTTATTTTAGTGGATAAAT 7 29 1 GCGGTATTTA 0.989276 -80 TGTAAAAAGTGCGGTAAAAAATCTCAACAAAT 9 17 1 GCGGTAAAAT 0.936044 -116 AGATAAAAGTGCGGTAAAAATTTGTTGAGATT 9 36 0 GCGGTAAATT 0.973506 -97 AGGTTTTGTGGCGGCTATTTTAGGTGCCGAAA 9 80 0 GCGGCATTTA 0.94557 -53 GGTTGAAATTGCGGTCACTTTAGCGTAAATTA 10 148 1 GCGGTATTTA 0.989276 -58 AAGGAAAAGTGCGGTCTGTTTTAAGCATATTT 11 112 1 GCGGTTTTTT 0.968226 -41 AATCAAAAGTGCGGTACTATAAATAAACCAAC 12 47 1 GCGGTCATAA 0.878411 -52 GGAAAGTGCGGTATGTTAAGTTAAAGTTT 15 8 1 GCGGTTTTAA 0.910826 -95 ***** * **** Masking position 2 Map Score: 13.3332 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 626 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 3 AAAATTTCATTTTTCCATCATTTTCTGTGATTT 1 204 0 TTTTCCTTTT 0.971076 -97 AAAAATGAAATTTTATGTAATTTTCTAATTTCT 1 223 1 TTTTATTTTT 0.854886 -78 TTATTTGTTGTTTTCTCTTTATTTTTTCCATTG 2 160 1 TTTTCTTATT 0.855094 -115 TCTCTTTATTTTTTCCATTGCCTAATACCGCAG 2 173 1 TTTTCCTCCT 0.939083 -102 CCGCACCTGATTTTACTTCATCTGCGGTATTAG 2 194 0 TTTTACTTCT 0.872294 -81 ATATTTCCTTATTTAAATTAACTT 2 261 0 TATTTCTTTT 0.74436 -14 TATTTTTCCCTAATCTAAATGGTAAA 3 11 0 TTTTCCTTCT 0.965004 -16 TCAGCCGAATTTTTTCTTCCATTTCTTATTTAC 6 57 0 TTTTTCTATT 0.728768 -70 TTTACCGCACTTTTATCTGGCTTTTTCCCCTTT 9 50 1 TTTTATTCTT 0.767086 -83 CACTTTGAAGTATTTTTTCACCTACTGAAATAT 11 69 0 TATTTTTCCT 0.48641 -84 TTTTCTTTCCTTTCAATAAAAAT 11 140 0 TTTTCTTTTT 0.95965 -13 AATATTTTCCTTTCGTTGGACTTCGTT 12 82 0 TTTTCCTGTT 0.875027 -17 ATTTTCTCTCTTCTTCTTTTAAAT 14 71 0 TTTTCTTTCT 0.951299 -14 AAATAGGGGATTTTTTCTAGTTTGAAAAACTTT 15 33 0 TTTTTTTTTT 0.884672 -70 TTATTATTCTCTTTTTTAGCATACAAA 15 86 0 TATTCTTTTT 0.864772 -17 ****** * *** Masking position 8 Map Score: 11.188 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 537 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 4 CAATTACAGATTTAAAAAAATTGTCTAACC 1 146 1 TTTAAAAAAA 0.897885 -155 TGTCTAACCGTTTAAAAAAAGTTCATTTTG 1 167 1 TTTAAAAAAA 0.897885 -134 TTGACCGCACTTTAGCTAAAGATGGTTTAT 2 18 1 TTTAGCTAAA 0.441816 -257 TCAGAGATAATTTAGAATAAACCATCTTTA 2 34 0 TTTAGAATAA 0.868049 -241 TTATCAATTATTTATAAAAAGCGACCTTAG 2 80 0 TTTATAAAAA 0.692696 -195 TATTTCCTTATTTAAATTAACTTATAGGGC 2 254 0 TTTAAATTAA 0.846069 -21 AGGGCTCTTTTTTATCGAAAATAATTGTGC 7 84 0 TTTATCGAAA 0.649293 -25 TACCGCACTTTTTACAGGAAGA 9 3 0 TTTACAGGAA 0.731513 -130 TTGCGGTCACTTTAGCGTAAATTAATTGGC 10 156 1 TTTAGCGTAA 0.853703 -50 TTTGAATCCGTTTAAAATAACGTTGAATTG 10 185 0 TTTAAAATAA 0.913295 -21 AGTGTGGAATTTTAAAGGAAAAGTGCGGTC 11 98 1 TTTAAAGGAA 0.921007 -55 TACATCCAAATTTAAAAGAAGAAGAGAGAA 14 62 1 TTTAAAAGAA 0.896786 -23 TTTGAAAAACTTTAACTTAACATACCGCAC 15 16 0 TTTAACTTAA 0.784133 -87 AAATCCCCTATTTAAAGTAAGATAAGCACA 15 53 1 TTTAAAGTAA 0.933926 -50 ********** Masking position 4 Map Score: 11.0613 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 249 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 5 CTCGTTTCCCGCTCCAATTCGTGGCGTGTT 1 8 0 GCTCATCGTG 0.963915 -293 TCCCGCATTCGCTGTTATTGGTGCGCATTTTAC 1 95 1 GCTTATGGTG 0.98072 -206 TTTATAAAAAGCGACCTTAGGTGGCTTTTTTTA 2 67 0 GCGCTTGGTG 0.983205 -208 TACTTCATCTGCGGTATTAGGCAATGGAAAAAA 2 181 0 GCGTTTGGCA 0.910073 -94 AATTTTAACCGCACTTTTGCGCGCTTTCCGAA 5 10 0 GCATTTCGCG 0.903899 -37 CTGCACCATGGCTGTATTGCGTCAGCCGAATTT 6 78 0 GCTTTTCGTC 0.91312 -49 GAAATTCTATGCGACTTTTCGTGATTTATCCAC 7 51 0 GCGCTTCGTG 0.980034 -58 TTTTGTGGCGGCTATTTTAGGTGCCGAAAGGGG 9 76 0 GCTTTTGGTG 0.988542 -57 GAGGACGCCAGCGTTCTTGGGTGGGTTCAACTC 10 67 0 GCGTTTGGTG 0.989415 -139 CGGCGAGAGTGCTATAAATGGTGCTAATGCTAC 11 35 1 GCTTAAGGTG 0.86601 -118 CGTATAGACGGCTATAATACGCATTTTTGCTTA 14 25 0 GCTTATCGCA 0.821993 -60 *** * ** **** Masking position 2 Map Score: 11.4141 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 172 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TTCGCTGTTATTGGTGCGCATTTTACGGAAATTC 1 102 1 TTGCCATTTT 0.867538 -199 AAAAATGAAATTTTATGTAATTTTCTAATTTCTA 1 223 1 TTTGAATTTT 0.600818 -78 TAATTTCTACTTTTATCACTTTTTCCTTTGTGCC 1 248 1 TTTCCTTTTT 0.891717 -53 TTAGCTAAAGTGCGGTCAATTTTTCT 2 3 0 TGGCATTTTT 0.833365 -272 AAAAGCGACCTTAGGTGGCTTTTTTTATCATCAG 2 60 0 TTGGCTTTTT 0.952332 -215 CGAGCTTTAATTTTATCAATTATTTATAAAAAGC 2 88 0 TTTCATTATT 0.581842 -187 CTGTATTGCGTCAGCCGAATTTTTTCTTCCATTT 6 66 0 TCGGATTTTT 0.77919 -61 CTTAGGCGAAATTTTACAGCCTCAA 6 112 0 TTGGAATTTT 0.838058 -15 CGCATAGAATTTCGCACAATTATTTTCGATAAAA 7 71 1 TTGCATTATT 0.827115 -38 AGTTAAGGGCTCTTTTTTATCGAAAAT 7 92 0 TAGCCTTTTT 0.883902 -17 TTGAGATTTTTTACCGCACTTTTTACAGGAAGA 9 10 0 TTCCCTTTTT 0.750692 -123 TACCGCACTTTTATCTGGCTTTTTCCCCTTTCGG 9 52 1 TTTGCTTTTT 0.85317 -81 TATGGTAGCATTAGCACCATTTATAGCACTCTCG 11 38 0 TTGCATTTAT 0.827115 -115 AATTCCACACTTTGAAGTATTTTTTCACCTACTG 11 75 0 TTGGATTTTT 0.957216 -78 AAAATAGTTATTTGATCTATTTATAACTGTAGG 12 10 0 TTGCATTTAT 0.827115 -89 TAGACGGCTATAATACGCATTTTTGCTTAATAAG 14 20 0 TATGATTTTT 0.636319 -65 TAAAGTAAGATAAGCACAATTTTTGTATGCTAAA 15 65 1 TAGCATTTTT 0.895024 -38 ** * * ****** Masking position 11 Map Score: 14.7958 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 451 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 7 AAAAAAAGCCACCTAAGGTCGCTTTTTATA 2 68 1 ACCTAAGGTC 0.931175 -207 TACACAGAATCCCTAAAATAGATGCTAACG 2 120 0 CCCTAAAATA 0.845487 -155 TCCTGTACCTAGGGTAGTATACTCTA 4 7 1 ACCTAGGGTA 0.983103 -78 TGAAGAACTAACCTAGAGTATACTACCCTA 4 20 0 ACCTAGAGTA 0.973685 -65 ATAGGACTGAACCTAGGATATACTTACCTA 4 50 1 ACCTAGGATA 0.973686 -35 CCCTTTCGGCACCTAAAATAGCCGCCACAA 9 77 1 ACCTAAAATA 0.937364 -56 ********** Masking position 5 Map Score: 3.52596 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 = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 TTCAGATAACTGTCAATTACAGATTTAAAAAAA 1 133 1 TGTCAAACGA 0.806396 -168 ATAACTATGGTTTCAATTCCTATCCGCACCTGA 2 217 0 TTTCAACCAT 0.971416 -58 AGAATATGACTTTCAAACCCTATTT 6 3 0 TTTCAACCAT 0.971416 -124 CTTTATTCAGTTTCAAAGCAGGTAATTAG 9 114 1 TTTCAACAGT 0.929318 -19 TCTTGGGTGGGTTCAACTCCCATTCCCCTCCGC 10 53 0 GTTCAACCAT 0.888146 -153 GGTGGCAGGATTTCAAATCCTGTTGAGGACGCC 10 91 0 TTTCAACCGT 0.985244 -115 GTGACCGCAATTTCAACCACGGAGGGGCGTCAT 10 133 0 TTTCAAACGA 0.946885 -73 TGAAGTATTTTTTCACCTACTGAAATATGGTAG 11 64 0 TTTCACACGA 0.806396 -89 TTTTCTTTCCTTTCAATAAAAATATGCTTAAAA 11 130 0 TTTCAAAAAT 0.773042 -23 ****** ** ** Masking position 5 Map Score: 3.43567 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 167 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CGCATTCGCTGTTATTGGTGCGCATTTTAC 1 98 1 GTTATTGGTG 0.843681 -203 TTTAAAAAAAGTTCATTTTGTTCAAATAAA 1 177 1 GTTCATTTTG 0.877762 -124 TATCATCAGAGATAATTTAGAATAAACCAT 2 39 0 GATAATTTAG 0.681205 -236 TGAAACCATAGTTATTTTTGCCCTATAAGT 2 235 1 GTTATTTTTG 0.965524 -40 CCGCACTTTTGTTCTTGTTGAAGGATTTTA 7 13 0 GTTCTTGTTG 0.918642 -96 CAAAAGTGCGGTTATTTTAGTGGATAAATC 7 32 1 GTTATTTTAG 0.957861 -77 TTTTGTGGCGGCTATTTTAGGTGCCGAAAG 9 79 0 GCTATTTTAG 0.857906 -54 GCAATTCAACGTTATTTTAAACGGATTCAA 10 184 1 GTTATTTTAA 0.690255 -22 GTTGGACTTCGTTAATGTTGGTTTATTTAT 12 65 0 GTTAATGTTG 0.923765 -34 ********** Masking position 6 Map Score: 3.81496 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 127 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 ATTAGGCAATGGAAAAAATAAAGAGAAAAC 2 169 0 GGAAAAAATA 0.952706 -106 TAACTTATAGGGCAAAAATAACTATGGTTT 2 237 0 GGCAAAAATA 0.90074 -38 ATTTAGATTAGGGAAAAATA 3 17 1 GGGAAAAATA 0.90074 -10 GCAAAAGTGCGGTTAAAATTAATTACATTT 5 23 1 GGTTAAAATT 0.891281 -24 AAGAAATGGAAGAAAAAATTCGGCTGACGC 6 63 1 AGAAAAAATT 0.743011 -64 TAAAAAGTGCGGTAAAAAATCTCAACAAAT 9 19 1 GGTAAAAAAT 0.805816 -114 ATAAAAGTGCGGTAAAAATTTGTTGAGATT 9 36 0 GGTAAAAATT 0.967204 -97 GCCCCTCCGTGGTTGAAATTGCGGTCACTT 10 138 1 GGTTGAAATT 0.630954 -68 TTTCAGTAGGTGAAAAAATACTTCAAAGTG 11 72 1 TGAAAAAATA 0.663845 -81 TCCAACGAAAGGAAAATATT 12 89 1 GGAAAATATT 0.805816 -10 ********** Masking position 6 Map Score: 3.76647 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 323 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 11 TTGGTGCGCATTTTACGGAAATTCAGATAA 1 112 1 TTTTACGGAA 0.758925 -189 TAGGTGGCTTTTTTTATCATCAGAGATAAT 2 53 0 TTTTTATCAT 0.596019 -222 TCATCTGCGGTATTAGGCAATGGAAAAAAT 2 180 0 TATTAGGCAA 0.790956 -95 GTGCGGTCTGTTTTAAGCATATTTTTATTG 11 120 1 TTTTAAGCAT 0.946294 -33 ATAACTATTTTTTTAATCAAAAGTGCGGTA 12 33 1 TTTTAATCAA 0.866045 -66 AATCAGGTCATTTTACGCAAA 13 2 0 TTTTACGCAA 0.950052 -40 ACCGCTTGCTTATTAAGCAAAAATGCGTAT 14 12 1 TATTAAGCAA 0.911878 -73 ATTATTCTCTTTTTTAGCATACAAAAATTG 15 81 0 TTTTTAGCAT 0.865779 -22 ********** Masking position 9 Map Score: 1.37916 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 293 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 ********** No masking Map Score: 4.74175e-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 13 ********** No masking Map Score: 4.74175e-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 14 ********** No masking Map Score: 4.74175e-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