AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_hinf_reg_100.orf -o00950_hinf_100.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 HI0329 37 conserved hypothetical protein #2 HI0330 98 opacity associated protein (oapA) #3 HI0331 59 opacity associated protein (oapB) #4 HI0549 169 dimethyladenosine transferase (ksgA) #5 HI0961 74 hit-related protein #6 HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) #7 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #8 HI0964 300 virulence factor (mviN) #9 HI0976 119 conserved hypothetical protein #10 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #11 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #12 HI1064 56 conserved hypothetical protein #13 HI1560 22 H. influenzae predicted coding region HI1560 #14 HI1561 106 peptide chain release factor 1 (prfA) #15 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 GATCCGATAAAATACACATAATTTTTTCGCCGCAC 2 11 1 AATCCATTTT 0.991834 -88 AAACGGCTATAATCCGCCCGTTTTTCTTAACTTTT 4 20 0 AATCCGTTTT 0.950442 -150 CAACCCCTATAATAACCGCACTTTTCTTATTAAAT 4 138 1 AATACATTTT 0.987049 -32 TTTATTTTCCAATTTTTACATTTTAAA 6 12 0 TATTCATTTT 0.834917 -17 ATAATGCCGAAATTCTCTTATTTTC 7 20 1 AATCCATTTC 0.976817 -15 TTTGTCTATCAATCAACAGAAATTTTAGGA 8 6 0 AATACAATTT 0.939646 -295 AAAGGGCATCAATATGCCGATTTTTTATACTTTTG 8 43 1 AATTCATTTT 0.978376 -258 GTCTCACCGAAATCAACACAAATTTTCCATTGACA 8 76 0 AATACAATTT 0.939662 -225 GGTGATATTTAATTTTCTCACTTTCAGCAATTTCT 9 53 1 AATTCATTTC 0.942767 -67 GTGCGGTAAAAATACGCAAAATTTTGAAAGGAAAA 10 12 1 AATCCATTTT 0.991834 -29 TATTTTATAGAATAAGCCAATTTTTTAAGCCAGAA 12 21 0 AATACATTTT 0.98704 -36 AATCGGCTAGAATACGCCGATTTTATTTTCGGTGA 14 75 1 AATCCATTTA 0.939106 -32 TGTAAAAAATGACCGCACTTTTTGATGAATAT 15 8 1 AATACATTTT 0.987055 -131 *** * * * **** Masking position 2 Map Score: 24.4858 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 141 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 TTTTTTCGCCGCACTTTTGAGCTTCTCAATTTTG 2 32 1 GCACTTTGTT 0.929644 -67 GCGAGTAATCGCCCCTTTTTCTTTTTAAGTTCTT 3 19 1 GCCCTTTTTT 0.994235 -41 GCTATAATCCGCCCGTTTTTCTTAACTTTTCCGC 4 16 0 GCCCTTTTTA 0.990261 -154 GCGGATTATAGCCGTTTTTAGCTTTCTACGAAAG 4 38 1 GCCGTTTTTT 0.990147 -132 TATAATAACCGCACTTTTCTTATTAAATAGTACT 4 145 1 GCACTTTCTT 0.929644 -25 CAAATCAATCGCACTTTTTGTTTTACAATGAATT 5 14 0 GCACTTTTTT 0.984462 -61 GCATATTGATGCCCTTTATTTTGTCTATCAATCA 8 26 0 GCCCTTATGT 0.932083 -275 GCATCAATATGCCGATTTTTTATACTTTTGTCAA 8 48 1 GCCGTTTTTA 0.983403 -253 GCGTATTCTAGCCGATTTTAGGGAAAATTGACAG 14 58 0 GCCGTTTTGA 0.973761 -49 GCTAGAATACGCCGATTTTATTTTCGGTGACTTA 14 80 1 GCCGTTTTTT 0.990147 -27 AAAAATGACCGCACTTTTTGATGAATATTTAAAA 15 15 1 GCACTTTTGA 0.959012 -124 **** **** ** Masking position 7 Map Score: 18.7546 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 146 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 GCTTTCTACGAAAGAAAAAATAATATTGTTCA 4 58 1 AAGAAAAATA 0.955482 -112 AATGATTTACAAAGCTAAAACAACCCCTATAA 4 118 1 AAGTAAAACA 0.909744 -52 TTAGACTAAATAAGCAACAATT 5 63 1 TAGAACAATT 0.703913 -12 TTTTAAAATGTAAAAATTGGAAAATAAA 6 7 1 AAGAAAAATT 0.955156 -22 TACTTTTGTCAATGGAAAATTTGTGTTGATTT 8 70 1 AAGAAAATTT 0.814216 -231 CACGGAATATAGCGTAAAAACAAAATTTCTAT 8 200 1 AGGAAAAACA 0.834003 -101 TCTATACAATTAGGCAAAAATTTTAGGGTAGA 8 227 1 TAGAAAAATT 0.942189 -74 CAGCAATTTCTACGCTAAAACATAGAATTGCA 9 77 1 TAGTAAAACA 0.884446 -43 GCGGTAAAAATACGCAAAATTTTGAAAGGAAA 10 14 1 TAGAAAATTT 0.768983 -27 CAAAATTTTGAAAGGAAAAACAA 10 28 1 AAGAAAAACA 0.971786 -13 TTTAAGCCAGAAGGAAAAAACA 12 1 0 AAGAAAAACA 0.971787 -56 TTTTGATGAATATTTAAAAATATCAAAGCGTG 15 30 1 TATAAAAATA 0.646704 -109 AAAATGACTGAAGTATAAAACTATTCATCACA 15 94 1 AATTAAAACT 0.539304 -45 AACACATACATAAGGAAAAGCT 15 127 1 TAGAAAAGCT 0.817846 -12 ** * ******* Masking position 7 Map Score: 10.1917 Number of sites scoring better than the average of aligned sites = 664 Number in coding regions = 533 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 AAATATCCTAAAAATGAGAGATGGTTTGAA 1 16 1 AAAATGAGAG 0.963272 -22 ATTAGCCACAAAATTGAGAAGCTCAAAAGT 2 44 0 AAATTGAGAA 0.912451 -55 CTAATTAATATAAATAAGAACAAGCATCAG 2 69 1 TAAATAAGAA 0.716108 -30 TTAGGCGGAAAAGTTAAGAAAAACGGGCGG 4 12 1 AAGTTAAGAA 0.618083 -158 AAAGTTAGACTAAATAAGCAACAATT 5 59 1 TAAATAAGCA 0.625831 -16 GAAAATAAGAGAATTTCGGCA 7 24 0 AAAATAAGAG 0.942232 -11 GACACAACCGAAAGTAAGTATCGTTATTTT 8 108 1 AAAGTAAGTA 0.587356 -193 CATTTAGAAGAAGGTGACAGCATATTGATT 9 16 0 AAGGTGACAG 0.713601 -104 CACCTTCTTCTAAATGAGAGGAAGGTGATA 9 30 1 TAAATGAGAG 0.867064 -90 GAAATTGCTGAAAGTGAGAAAATTAAATAT 9 57 0 AAAGTGAGAA 0.910839 -63 CTTATTCTATAAAATAACCGCTCAAGA 12 40 1 AAAATAACCG 0.867895 -17 AGCGAAAAGGAAATTAAGAATCTCAGACGC 14 30 0 AAATTAAGAA 0.866335 -77 ATTTTAGGGAAAATTGACAGCGAAAAGGAA 14 48 0 AAATTGACAG 0.910558 -59 TGTAAAAAATGACCGCACTTTTTGA 15 6 1 AAAATGACCG 0.913526 -133 GATTTTATAAAAATTAACCACGCTTTGATA 15 50 0 AAATTAACCA 0.723041 -89 TTGATAAAATAAAATGACTGAAGTATAAAA 15 84 1 AAAATGACTG 0.781166 -55 ********** Masking position 5 Map Score: 14.5422 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 450 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 5 ATTTGAAATATCCTAAAAATGAGAGATGG 1 6 1 AAAACAAAAA 0.956589 -32 GATCCGATAAAATACACATAATTTTTTCGCCG 2 9 1 AAATCATAAT 0.52953 -90 TATTTATATTAATTAGCCACAAAATTGAGAAGCT 2 51 0 AATACCAAAA 0.773181 -48 TACCTTGAGAAAAGAACTTAAAAAGAAAAAGGGG 3 30 0 AAAACAAAAA 0.956589 -30 GCTTTCTACGAAAGAAAAAATAATATTGTTCATG 4 58 1 AAAAAATAAT 0.583022 -112 TACAAAGCTAAAACAACCCCTATAATAACCGCAC 4 125 1 AAAACCTATA 0.752219 -45 TTTAAAATGTAAAAATTGGAAAATAAA 6 12 1 AAAATAAAAT 0.529847 -17 TTTGTCTATCAATCAACAGAAATTTTAGGA 8 7 0 AATACAAATT 0.423795 -294 GTCTCACCGAAATCAACACAAATTTTCCATTGAC 8 77 0 AATACAAATT 0.423795 -224 GCCCATATTGAAAGAGCTTGTAAAAATAACGATA 8 126 0 AAAACGTAAA 0.799519 -175 ATTCCGTGAAAAAAAACTGATAAAATCCGCCACA 8 174 0 AAAACATAAA 0.964713 -127 TTTTCACGGAATATAGCGTAAAAACAAAATTTCT 8 196 1 ATAACAAAAA 0.625133 -105 AGTGCGGTAAAAATACGCAAAATTTTGAAAGG 10 9 1 AAAAACAAAA 0.530349 -32 TTTTAGCTATAAATATCGTATAATCCGATAGATT 11 32 1 AAAACATAAT 0.933392 -54 CCTTACAAAAAATAAACAAATAAAATCTATCGGA 11 55 0 AATACATAAA 0.891706 -31 TTATTCTATAAAATAACCGCTCAAGA 12 41 1 AAAACCTCAA 0.611651 -16 TGGGTAAATCACAAATAAAGCGTCTGAGA 14 6 1 AAACCATAAA 0.764953 -101 TTTTATCAAGAAAGATTTTATAAAAATTAACCAC 15 59 0 AAAATATAAA 0.73174 -80 *** * * ***** Masking position 1 Map Score: 9.55491 Number of sites scoring better than the average of aligned sites = 1435 Number in coding regions = 1106 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 6 ATAATTTTTTCGCCGCACTTTTGAGCTTCT 2 28 1 CGCCGCACTT 0.99155 -71 CCCCTATAATAACCGCACTTTTCTTATTAA 4 141 1 AACCGCACTT 0.990225 -29 AGAGCAAATCAATCGCACTTTTTGTTTTAC 5 22 0 AATCGCACTT 0.934225 -53 TGATAAAATCCGCCACACATCGTTTGTGTG 8 161 0 CGCCACACAT 0.961125 -140 TGTAAAAAATGACCGCACTTTTTGATGAAT 15 11 1 GACCGCACTT 0.984829 -128 TATAAAAATTAACCACGCTTTGATATTTTT 15 45 0 AACCACGCTT 0.942256 -94 CTATTCATCACACAACACATACATAAGGAA 15 114 1 CACAACACAT 0.82656 -25 ********** Masking position 10 Map Score: 5.07021 Number of sites scoring better than the average of aligned sites = 1728 Number in coding regions = 1194 Number in noncoding regions = 534 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 7 GATCCGATAAAATACACATAATT 2 4 1 CCGATAAAAT 0.753665 -95 CCGCACTTTTCTTATTAAATAGTACTT 4 153 1 CTTATTAAAT 0.66891 -17 TTTTAAAATGTAAAAATTGGAAAATAA 6 8 1 ATGTAAAAAT 0.586562 -21 TTGAAAGAGCTTGTAAAAATAACGATACTT 8 123 0 TTGTAAAAAT 0.728173 -178 TGAAAAAAAACTGATAAAATCCGCCACACA 8 172 0 CTGATAAAAT 0.950942 -129 GAGTAAACGACTTTTAAAATCTAGCATTGT 8 271 1 CTTTTAAAAT 0.874518 -30 TTGTTTTTCCTTTCAAAATTTTGCGTATT 10 22 0 CTTTCAAAAT 0.854732 -19 GTTGATACCTTACAAAAAATAAACAAAT 11 68 0 CTTACAAAAA 0.497507 -18 TTCCTTCTGGCTTAAAAAATTGGCTTATTC 12 17 1 CTTAAAAAAT 0.918045 -40 GAGCGGTTATTTTATAGAATAAGCCAATTT 12 33 0 TTTATAGAAT 0.524318 -24 TTTGATGAATATTTAAAAATATCAAAGCGT 15 31 1 ATTTAAAAAT 0.497163 -108 GTGGTTAATTTTTATAAAATCTTTCTTGAT 15 59 1 TTTATAAAAT 0.869366 -80 AAAATCTTTCTTGATAAAATAAAATGACTG 15 74 1 TTGATAAAAT 0.87682 -65 ********** Masking position 8 Map Score: 5.56691 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 371 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 8 ATTTGAAATATCCTAAAAATGAGAGATG 1 8 1 ATACCTAAAA 0.961044 -30 CCTTGAGAAAAGAACTTAAAAAGAAAAAGGG 3 31 0 AGACTTAAAA 0.943709 -29 TCTTTCGTAGAAAGCTAAAAACGGCTATAAT 4 42 0 AAACTAAAAA 0.661413 -128 TCAATTTGGCATAACCTAACAATGATTTACA 4 98 1 ATACCTAACA 0.795547 -72 TTCACGGAATATAGCGTAAAAACAAAATTTC 8 198 1 ATACGTAAAA 0.875103 -103 ATATTCTTCTCTACCCTAAAATTTTTGCCTA 8 237 0 CTACCTAAAA 0.925674 -64 CAACAATGCTAGATTTTAAAAGTCGTTTACT 8 272 0 AGATTTAAAA 0.69964 -29 AGAACTAACAACAATGCTAGA 8 290 0 AGACTAACAA 0.710312 -11 TCAGCAATTTCTACGCTAAAACATAGAATTG 9 76 1 CTAGCTAAAA 0.59257 -44 TACGATATTTATAGCTAAAAATAAAACGCAC 11 21 0 ATACTAAAAA 0.932809 -65 GTTGATACCTTACAAAAAATAAACA 11 71 0 ATACTTACAA 0.904527 -15 TTTTTTCCTTCTGGCTTAAAAAATTGGCTTA 12 13 1 CTGCTTAAAA 0.70482 -44 TTTTTGATGAATATTTAAAAATATCAAAGCG 15 29 1 ATATTAAAAA 0.658575 -110 *** ******* Masking position 8 Map Score: 5.04356 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 313 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 AGTTTTTCATGAACAATATTATTTTTTCTT 4 69 0 GAACAATATT 0.935746 -101 TTAGGGTAGAGAAGAATATTTTGAGTAAAC 8 249 1 GAAGAATATT 0.975024 -52 CGCACTTTTTGATGAATATTTAAAAATATC 15 24 1 GATGAATATT 0.975022 -115 TGTGTTGTGTGATGAATAGTTTTATACTTC 15 103 0 GATGAATAGT 0.958158 -36 ********** Masking position 5 Map Score: 0.86977 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 39 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** No masking Map Score: 3.09329e-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: 3.09329e-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: 3.09329e-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