AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_hinf_reg_100.orf -o00440_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 HI0949 300 aminotransferase #6 HI0961 74 hit-related protein #7 HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) #8 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #9 HI0964 300 virulence factor (mviN) #10 HI0976 119 conserved hypothetical protein #11 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #12 HI1166 87 histidinol-phosphate aminotransferase (hisH) #13 HI1167 190 phosphoserine aminotransferase (serC) Motif number 1 TCGCCCCTTTTTCTTTTTAAGTTCTTTTCTCAA 3 27 1 TTCTTTTTAT 0.667495 -33 ATCCGCCCGTTTTTCTTAACTTTTCCGCCTAAA 4 11 0 TTTTCTTACT 0.704413 -159 ATGAACAATATTATTTTTTCTTTCGTAGAAAGC 4 58 0 TTATTTTTCT 0.860827 -112 ATTATAGGGGTTGTTTTAGCTTTGTAAATCATT 4 118 0 TTGTTTTACT 0.953384 -52 ACGTTTGCTTTTTATTTAGCCGTTTGACTCGTA 5 26 1 TTTATTTACT 0.890302 -275 CAATTGTATATTTTTTTTGCAATATGAAAAGTA 5 71 0 TTTTTTTTCT 0.970555 -230 TTCAGCTTTTTTGTTTTTACCCTAGTTTGCCCA 5 159 0 TTGTTTTTCT 0.96434 -142 CTGAAACGCTTTTTTTAATAAGTAGCGAGTCAA 5 187 1 TTTTTTAAAT 0.705602 -114 ACCCGACTTATTTTTTTTCACCTCTTTTAGAAG 5 265 1 TTTTTTTTAT 0.927155 -36 TTTTGATTAAAACCTTCTAAAAGAG 5 286 0 TTGATTAAAT 0.390313 -15 ATCGCACTTTTTGTTTTACAATGAATTTAA 6 8 0 TTGTTTTAAG 0.75722 -67 TTTATTTTCCAATTTTTACATTT 7 16 0 TTTATTTTCT 0.914757 -13 AATATGCCGATTTTTTATACTTTTGTCAATGGA 9 53 1 TTTTTTATCT 0.891387 -248 GTAAGTATCGTTATTTTTACAAGCTCTTTCAAT 9 121 1 TTATTTTTCG 0.709536 -180 ATTTTATCAGTTTTTTTTCACGGAATATAGCGT 9 182 1 TTTTTTTTAG 0.83407 -119 TATAGAAATTTTGTTTTTACGCTATATTCCGTG 9 200 0 TTGTTTTTCT 0.96434 -101 TTGTTTTTCCTTTCAAAATTTTG 11 28 0 TTGTTTTTCT 0.96434 -13 TACGCCCAAATTTATTTAAAAATACATACTAAC 12 39 1 TTTATTTAAT 0.758079 -49 AGTCATTTTATTTATTTTAAAGGGAGTTGTT 13 9 0 TTTATTTTAG 0.620711 -182 AATTTAGCTTTTTTTTAATCAATCGTCAAAATT 13 49 1 TTTTTTAACT 0.861244 -142 ATAATGATGTCTTTTTTATCACTACAAAAATCG 13 144 0 CTTTTTTACT 0.704413 -47 ******** * * Masking position 6 Map Score: 21.2369 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 736 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 2 TTTCAAACCATCTCTCATTTTTAGGATATT 1 17 0 TCTCTCATTT 0.945453 -21 AATTTTTTCGCCGCACTTTTGAGCTTCTCA 2 30 1 CCGCACTTTT 0.969686 -69 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 2 45 1 TCTCAATTTT 0.906508 -54 CCTATAATAACCGCACTTTTCTTATTAAAT 4 143 1 CCGCACTTTT 0.969686 -27 AGCAAATCAATCGCACTTTTTGTTTTACAA 6 20 0 TCGCACTTTT 0.952229 -55 GCTTATTTAGTCTAACTTTTAAGGACAGAG 6 48 0 TCTAACTTTT 0.914133 -27 ATGCCGAAATTCTCTTATTTTC 8 23 1 TCTCTTATTT 0.749769 -12 TCCTAAAATTTCTGTTGATTG 9 2 1 CCTAAAATTT 0.807107 -299 CATCAATATGCCGATTTTTTATACTTTTGT 9 49 1 CCGATTTTTT 0.59791 -252 TCTTCTCTACCCTAAAATTTTTGCCTAATT 9 234 0 CCTAAAATTT 0.807107 -67 ATATCACCTTCCTCTCATTTAGAAGAAGGT 10 31 0 CCTCTCATTT 0.965296 -89 TATTTAATTTTCTCACTTTCAGCAATTTCT 10 58 1 TCTCACTTTC 0.89718 -62 CAAAATTTACCCTCTATTTTATGAATGATA 13 75 1 CCTCTATTTT 0.921968 -116 AAAAATTCTTTCTATCATTCATAAAATAGA 13 87 0 TCTATCATTC 0.640506 -104 ********** Masking position 8 Map Score: 13.7206 Number of sites scoring better than the average of aligned sites = 1303 Number in coding regions = 892 Number in noncoding regions = 411 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 3 AAAGTGCGGCGAAAAAATTATGTGTATTTTATCGGATC 2 11 0 GAATTTTATT 0.958549 -88 CGTCAAAACGGGGACAATTGTATATTTTTTTTGCAATA 5 80 0 GAATTTTTTT 0.974221 -221 CGAGTCAAATGCCCTATGTGTCTGTTTTATAAACAGTA 5 212 1 GATGTTTTTT 0.721312 -89 CGGGTGCCTTGCGATAAATTTACTGTTTATAAAACAGA 5 232 0 GAAATTGTTT 0.843432 -69 TTTATTTTCCAATTTTTACATTTTAAAA 7 5 0 TATTTTTTTT 0.731832 -24 TCGCTATAATGCCGAAATTCTCTTATTTTC 8 15 1 GAATTTATTT 0.827641 -20 TTTTGTCAATGGAAAATTTGTGTTGATTTCGGTGAGAC 9 73 1 GATTTTGATT 0.899183 -228 AACGATGTGTGGCGGATTTTATCAGTTTTTTTTCACGG 9 167 1 GATTTAGTTT 0.701709 -134 TGCCTAATTGTATAGAAATTTTGTTTTTACGCTATATT 9 205 0 TAAATTTTTT 0.502191 -96 CCTGTGAATTGTTGCAATTCTATGTTTTAGCGTAGAAA 10 83 0 GAATTTTTTT 0.974221 -37 TGTTTTTCCTTTCAAAATTTTGCGTATTTTTACCGCAC 11 12 0 TAATTTTATT 0.780581 -29 AGTTGTATTTATAAATATTGATATGGGTT 12 69 0 GATTTTTATT 0.915678 -19 AAATGACTGTGCCGTAATTTAGCTTTTTTTTAATCAAT 13 34 1 GAATTATTTT 0.859166 -157 ATAAAATAGAGGGTAAATTTTGACGATTGATTAAAAAA 13 59 0 GAATTTGATT 0.949992 -132 ATGAATGATAGAAAGAATTTTTTTGATTTCAGTAAAAA 13 95 1 GAATTTGATT 0.949987 -96 TCAGTAAAAAGCATTGATTATCGATTTTTGTAGTGATA 13 123 1 GGATTTTTTT 0.827368 -68 * **** * **** Masking position 9 Map Score: 13.1595 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 451 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 ATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 3 26 1 TTTCTTTTTA 0.770997 -34 TAGCCGTTTTTAGCTTTCTACGAAAGAAAA 4 46 1 TAGCTTTCTA 0.899099 -124 GGGGTTGTTTTAGCTTTGTAAATCATTGTT 4 115 0 TAGCTTTGTA 0.899102 -55 TTAGAAACGTTTGCTTTTTATTTAGCCGTT 5 20 1 TTGCTTTTTA 0.977132 -281 AAAGTAAATTTAGCTTCTTACGAGTCAAAC 5 47 0 TAGCTTCTTA 0.899102 -254 AAAAGCGTTTCAGCTTTTTTGTTTTTACCC 5 170 0 CAGCTTTTTT 0.854782 -131 AAAAGCTGAAACGCTTTTTTTAATAAGTAG 5 182 1 ACGCTTTTTT 0.719154 -119 AATTGTTGCTTATTTAGTCTAACTT 6 60 0 TTGCTTATTT 0.779973 -15 TGCCGTAATTTAGCTTTTTTTTAATCAATC 13 43 1 TAGCTTTTTT 0.961822 -148 TCGATAATCAATGCTTTTTACTGAAATCAA 13 117 0 ATGCTTTTTA 0.922346 -74 TGTATTTCCTTGCTTTTTATGAAAATAAT 13 172 0 TTGCTTTTTA 0.977132 -19 ********** Masking position 5 Map Score: 10.2791 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 198 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TTGGGCGAGTAATCGCCCCTTTTTCTTTTTAAG 3 15 1 ATCCCCTTTT 0.890242 -45 AAACGGCTATAATCCGCCCGTTTTTCTTAACTT 4 22 0 ATGCCCGTTT 0.970892 -148 TTTGCTTTTTATTTAGCCGTTTGACTCGTAAGA 5 29 1 ATGCCGTTTG 0.94888 -272 AAAATATACAATTGTCCCCGTTTTGACGTAACC 5 90 1 ATCCCCGTTT 0.897563 -211 TTTTTACCCTAGTTTGCCCATTGGACGGGCTAG 5 146 0 ATGCCCATTG 0.983799 -155 AAAGGGCATCAATATGCCGATTTTTTATACTTT 9 43 1 ATGCCGATTT 0.974142 -258 ACATCGTTTGTGTGAGCCCATATTGAAAGAGCT 9 142 0 TTGCCCATAT 0.766694 -159 GGGCGTAGTAAATACGCCCATTGGAAATGTTTT 12 13 0 ATGCCCATTG 0.983724 -75 GGGCGTATTTACTACGCCCAAATTTATTTAAAA 12 27 1 ATGCCCAAAT 0.862236 -61 AAATAAAATGACTGTGCCGTAATTTAGCTTTTT 13 29 1 ATGCCGTAAT 0.662345 -162 TAGAGGGTAAATTTTGACGATTGATTAAAAAAA 13 58 0 ATGACGATTG 0.736026 -133 * * ******** Masking position 3 Map Score: 8.27318 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 226 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 TTTTTTCGCCGCACTTTTGAGCTTCTCAAT 2 32 1 GCACTTTTGA 0.717775 -67 CGAGTAATCGCCCCTTTTTCTTTTTAAGTT 3 20 1 CCCCTTTTTC 0.847395 -40 CTATAATCCGCCCGTTTTTCTTAACTTTTC 4 19 0 CCCGTTTTTC 0.891344 -151 GCGGATTATAGCCGTTTTTAGCTTTCTACG 4 38 1 GCCGTTTTTA 0.955556 -132 GTTAGGTTATGCCAAATTGAGTTTTTCATG 4 88 0 GCCAAATTGA 0.73177 -82 TTTTTATTTAGCCGTTTGACTCGTAAGAAG 5 34 1 GCCGTTTGAC 0.47224 -267 TACAATTGTCCCCGTTTTGACGTAACCCTA 5 96 1 CCCGTTTTGA 0.957356 -205 ACCCTAGTTTGCCCATTGGACGGGCTAGGT 5 144 0 GCCCATTGGA 0.874427 -157 TTTATTTTCCAATTTTTACATTTTAAAA 7 11 0 CCAATTTTTA 0.467355 -18 GCATCAATATGCCGATTTTTTATACTTTTG 9 48 1 GCCGATTTTT 0.674733 -253 TTTGTGTGAGCCCATATTGAAAGAGCTTGT 9 139 0 CCCATATTGA 0.737011 -162 ACGATGTGTGGCGGATTTTATCAGTTTTTT 9 168 1 GCGGATTTTA 0.634529 -133 TAGTAAATACGCCCATTGGAAATGTTTTTC 12 11 0 GCCCATTGGA 0.874427 -77 ATTTACTACGCCCAAATTTATTTAAAAATA 12 33 1 CCCAAATTTA 0.606466 -55 ********** Masking position 7 Map Score: 3.43347 Number of sites scoring better than the average of aligned sites = 982 Number in coding regions = 867 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 7 CATAATTTTTTCGCCGCACTTTTGAGCTTC 2 27 1 TCGCCGCACT 0.979325 -72 ACCCCTATAATAACCGCACTTTTCTTATTA 4 140 1 TAACCGCACT 0.989699 -30 CAGAGCAAATCAATCGCACTTTTTGTTTTA 6 23 0 CAATCGCACT 0.934142 -52 TTGCGTATTTTTACCGCACT 11 1 0 TTACCGCACT 0.981977 -40 ********** Masking position 8 Map Score: 0.3347 Number of sites scoring better than the average of aligned sites = 1225 Number in coding regions = 793 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 8 AGCCACAAAATTGAGAAGCTCAAAAGTGCGGC 2 39 0 TTGAGAAGCA 0.835198 -60 AAATCCTACCTTGAGAAAAGAACTTAAAAAGA 3 38 0 TTGAGAAAAA 0.977961 -22 CCTTAAAAGTTAGACTAAATAAGCAACAATT 6 54 1 TAGACTAAAA 0.882384 -21 TGTTGATTGATAGACAAAATAAAGGGCATCAA 9 23 1 TAGACAAAAA 0.934671 -278 AAATTTTCCATTGACAAAAGTATAAAAAATCG 9 60 0 TTGACAAAAA 0.964632 -241 AATTTTAGGGTAGAGAAGAATATTTTGAGTAA 9 245 1 TAGAGAAGAA 0.919212 -56 GAAGAATATTTTGAGTAAACGACTTTTAAAAT 9 259 1 TTGAGTAAAA 0.958801 -42 ATTGCTGAAAGTGAGAAAATTAAATATCACCT 10 52 0 GTGAGAAAAA 0.912033 -68 ATTTTGACGATTGATTAAAAAAAAGCTAAATT 13 49 0 TTGATTAAAA 0.782588 -142 ********* * Masking position 7 Map Score: 4.30599 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 95 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 ********** No masking Map Score: 2.07722e-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: 2.07722e-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: 2.07722e-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