AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_hinf_reg_300.orf -o00440_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 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 HI0974.1 300 conserved hypothetical protein #11 HI0976 119 conserved hypothetical protein #12 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #13 HI1166 87 histidinol-phosphate aminotransferase (hisH) #14 HI1167 190 phosphoserine aminotransferase (serC) Motif number 1 ATTTGAAATATCCTAAAAATGAGAGATGGT 1 11 1 TCCTAAAAAT 0.855099 -27 GGCGGAAAAGTTAAGAAAAACGGGCGGATT 4 15 1 TTAAGAAAAA 0.787139 -155 ATAATATTGTTCATGAAAAACTCAATTTGG 4 77 1 TCATGAAAAA 0.807562 -93 CTTTTCATATTGCAAAAAAAATATACAATT 5 73 1 TGCAAAAAAA 0.916116 -228 TCGCTACTTATTAAAAAAAGCGTTTCAGCT 5 185 0 TTAAAAAAAG 0.928748 -116 CTAAAAGAGGTGAAAAAAAATAAGTCGGGT 5 265 0 TGAAAAAAAA 0.955082 -36 CTATATTCCGTGAAAAAAAACTGATAAAAT 9 182 0 TGAAAAAAAA 0.955082 -119 TCGGTATTCGTCAAAAAAATAAGGAATATG 10 21 1 TCAAAAAAAT 0.941876 -280 TTTATCATATTCATAAAAAGGATGATTACT 10 134 0 TCATAAAAAG 0.936677 -167 TTTATGAATATGATAAAAATCGAATTTACG 10 147 1 TGATAAAAAT 0.905956 -154 TTTTGAATTATTCAAAAAAGTTGTAAGATT 10 194 1 TTCAAAAAAG 0.870044 -107 CCTTATACCATTCAAAAAATATACTTTCAC 10 256 1 TTCAAAAAAT 0.838714 -45 ATACTTTCACTTATAAAAAATTTTAAGGAA 10 276 1 TTATAAAAAA 0.91826 -25 TGACGATTGATTAAAAAAAAGCTAAATTAC 14 47 0 TTAAAAAAAA 0.940633 -144 TTTACTGAAATCAAAAAAATTCTTTCTATC 14 101 0 TCAAAAAAAT 0.941876 -90 ATTTTTGTAGTGATAAAAAAGACATCATTA 14 146 1 TGATAAAAAA 0.937795 -45 ATCATTATTTTCATAAAAAGCAAGGAAATA 14 169 1 TCATAAAAAG 0.936677 -22 ********** Masking position 6 Map Score: 21.6898 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 330 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 2 GATCCGATAAAATACACATAATTTTTTCGCCGCAC 2 10 1 AAAACAATTT 0.89674 -89 TATTTATATTAATTAGCCACAAAATTGAGAAGCTCA 2 49 0 AATACAAATT 0.652429 -50 TAAAAACGGCTATAATCCGCCCGTTTTTCTTAACTT 4 22 0 TATACCCTTT 0.650957 -148 ACAACCCCTATAATAACCGCACTTTTCTTATTAAAT 4 137 1 TAAACACTTT 0.853409 -33 AACGGCTAAATAAAAAGCAAACGTTTCTAATAAGAA 5 14 0 TAAACACTTT 0.853414 -287 TTTTTTGCAATATGAAAAGTAAATTTAGCTTCTTAC 5 56 0 TATAAAATTT 0.798209 -245 GTGTCTGTTTTATAAACAGTAAATTTATCGCAAGGC 5 229 1 TATAAAATTT 0.798209 -72 GGACAGAGCAAATCAATCGCACTTTTTGTTTTACAA 6 20 0 AATACACTTT 0.96258 -55 ATTGTTGCTTATTTAGTCTAACTTTTAAGGACAGAG 6 48 0 ATTACACTTT 0.660672 -27 CTTCTCGCTATAATGCCGAAATTCTCTTATTTTC 8 9 1 TATACAATTC 0.789098 -26 TTTGTCTATCAATCAACAGAAATTTTAGGA 9 5 0 AATAAAATTT 0.859548 -296 GTCTCACCGAAATCAACACAAATTTTCCATTGACAA 9 75 0 AATAAAATTT 0.859553 -226 TTGTAAAAATAACGATACTTACTTTCGGTTGTGTCT 9 107 0 AACACACTTC 0.635417 -194 ATTTCTATACAATTAGGCAAAAATTTTAGGGTAGAG 9 224 1 AATACAATTT 0.961246 -77 ATATTTGGGGAATTACACCGAAATTATCTTGGTCGT 10 84 1 AATACAATTA 0.679727 -217 TTTACGTAGAAATCAGCAAAACCTTTTGAATTATTC 10 171 1 AATAAACTTT 0.863907 -130 AGTGCGGTAAAAATACGCAAAATTTTGAAAGGAAAA 12 11 1 AAAACAATTT 0.89674 -30 TGGGCGTATTTACTACGCCCAAATTTATTTAAAAAT 13 26 1 TACACAATTT 0.823114 -62 *** * * ** *** Masking position 15 Map Score: 14.6826 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 374 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 3 GGCGAAAAAATTATGTGTATTTTATCGGATC 2 10 0 TTTTGTATTT 0.937892 -89 CCTCTGATGCTTGTTCTTATTTATATTAATTA 2 70 0 TTTCTTATTT 0.962902 -29 TAATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 3 24 1 TTTCTTTTTA 0.652367 -36 TTGTTCTTATTAGAAACGTTTG 5 1 1 TTTCTTATTA 0.874673 -300 TAGAAACGTTTGCTTTTTATTTAGCCGTTTGA 5 21 1 TGTTTTATTT 0.853131 -280 GCGTTTCAGCTTTTTTGTTTTTACCCTAGTTT 5 164 0 TTTTGTTTTT 0.802392 -137 AATTGTTGCTTATTTAGTCTAACTT 6 60 0 TGTCTTATTT 0.891306 -15 AATGGAAAATTTGTGTTGATTTCGGTGAGACA 9 80 1 TTTTTGATTT 0.886025 -221 GACTGATGCATATTCCTTATTTTTTTGACGAA 10 27 0 TATCTTATTT 0.841297 -274 ATTCAAAAGGTTTTGCTGATTTCTACGTAAAT 10 170 0 TTTCTGATTT 0.916487 -131 ATTGTTGCAATTCTATGTTTTAGCGTAGAAAT 11 82 0 TTTTGTTTTA 0.521947 -38 CCTTTCAAAATTTTGCGTATTTTTACCGCACT 12 11 0 TTTCGTATTT 0.955193 -30 TGATATGGGTTAGTATGTATTTTTAAATAAAT 13 48 0 TATTGTATTT 0.755149 -40 GGCACAGTCATTTTATTTATTTTAAAGGGAGT 14 15 0 TTTTTTATTT 0.948417 -176 ATAGAAAGAATTTTTTTGATTTCAGTAAAAAG 14 102 1 TTTTTGATTT 0.886025 -89 ** * ******* Masking position 4 Map Score: 14.2273 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 247 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 4 TTGAGAAAAGAACTTAAAAAGAAAAAGGGGCGA 3 27 0 AATAAAAGAA 0.60979 -33 GCTTTCTACGAAAGAAAAAATAATATTGTTCAT 4 58 1 AAGAAAATAA 0.955583 -112 AATGATTTACAAAGCTAAAACAACCCCTATAAT 4 118 1 AAGAAAACAA 0.966523 -52 TTACGAGTCAAACGGCTAAATAAAAAGCAAACG 5 27 0 AAGTAAATAA 0.788753 -274 TACTTTTCATATTGCAAAAAAAATATACAATTG 5 71 1 ATGAAAAAAA 0.818021 -230 TGGGCAAACTAGGGTAAAAACAAAAAAGCTGAA 5 159 1 AGGAAAACAA 0.959598 -142 CTTCTAAAAGAGGTGAAAAAAAATAAGTCGGGT 5 265 0 AGTAAAAAAA 0.686685 -36 TTAAATTCATTGTAAAACAAAAAGTGCGAT 6 8 1 CATAAAACAA 0.646604 -67 AAAATGTAAAAATTGGAAAATAAA 7 15 1 AATAAAATAA 0.835492 -14 CTGTTGATTGATAGACAAAATAAAGGGCATCAA 9 22 1 ATGAAAATAA 0.895499 -279 TCCATTGACAAAAGTATAAAAAATCGGCATATT 9 53 0 AAGTAAAAAA 0.662005 -248 ATTGAAAGAGCTTGTAAAAATAACGATACTTAC 9 121 0 CTGAAAATAA 0.697014 -180 CACGGAATATAGCGTAAAAACAAAATTTCTATA 9 200 1 AGGAAAACAA 0.959598 -101 AATTGCTGAAAGTGAGAAAATTAAATATCACCT 11 52 0 AGGAAAATTA 0.618351 -68 CAAAATTTTGAAAGGAAAAACAA 12 28 1 AAGAAAACAA 0.966523 -13 ** * ******* Masking position 8 Map Score: 11.231 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 364 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 AGGGGCGATTACTCGCCCAAAAAA 3 5 0 ACTCGCCCAA 0.883972 -55 TTGGGCGAGTAATCGCCCCTTTTTCTTTTT 3 15 1 AATCGCCCCT 0.868731 -45 AACGGCTATAATCCGCCCGTTTTTCTTAAC 4 24 0 ATCCGCCCGT 0.927902 -146 AACTGATAAAATCCGCCACACATCGTTTGT 9 164 0 ATCCGCCACA 0.886804 -137 TCTTATCGGTATTCGTCAAAAAAATAAGGA 10 16 1 ATTCGTCAAA 0.526066 -285 TTACCTTTTGATACGACCAAGATAATTTCG 10 102 0 ATACGACCAA 0.853834 -199 CGTATATTTCATACGTCCCTTGTGTTTGCT 10 224 0 ATACGTCCCT 0.929882 -77 CGTATGAAATATACGCCCCTTATACCATTC 10 239 1 ATACGCCCCT 0.985368 -62 GGCGTAGTAAATACGCCCATTGGAAATGTT 13 15 0 ATACGCCCAT 0.981218 -73 GGCGTATTTACTACGCCCAAATTTATTTAA 13 28 1 CTACGCCCAA 0.916032 -60 ********** Masking position 4 Map Score: 6.08041 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 223 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 TTTTCTTAACTTTTCCGCCTAAA 4 1 0 TTCGCCTAAA 0.738729 -169 TATTATTTTTTCTTTCGTAGAAAGCTAAAAACG 4 50 0 TTCGTAGAAA 0.970564 -120 CTTCTCGCTATAATGCCGAAATTCTCTTATT 8 9 1 TTTGCCGAAA 0.81629 -26 CTTTCGGTTGTGTCTCACCGAAATCAACACAAA 9 89 0 TTCACCGAAA 0.938112 -212 TTTCACGGAATATAGCGTAAAAACAAAATTTCT 9 197 1 TTCGTAAAAA 0.850762 -104 ATTTTTGCCTAATTGTATAGAAATTTTGTTTTT 9 215 0 ATTATAGAAA 0.611639 -86 GTCCTTACTATCTGGCATAGAAACTTTCATATT 10 56 1 TTCATAGAAA 0.945469 -245 ATATTTGGGGAATTACACCGAAATTATCTTGGT 10 84 1 ATCACCGAAA 0.899405 -217 TAAAAATCGAATTTACGTAGAAATCAGCAAAAC 10 160 1 ATCGTAGAAA 0.951085 -141 AATTCTATGTTTTAGCGTAGAAATTGCTGAAAG 11 73 0 TTCGTAGAAA 0.97049 -47 AGACATCATTATTTTCATAAAAAGCAAGGAAAT 14 165 1 ATCATAAAAA 0.638624 -26 * * ******** Masking position 11 Map Score: 5.86885 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 238 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 AAAACGGGCGGATTATAGCCGTTTTTAGCTTTCTA 4 31 1 GATTATAGTT 0.853578 -139 AAAGTGCGGTTATTATAGGGGTTGTTTTAGCTTTG 4 127 0 TATTATAGTT 0.808409 -43 GACAATTGTATATTTTTTTTGCAATATGAAAAGTA 5 71 0 TATTTTTGCT 0.835158 -230 TTTTTTCACCTCTTTTAGAAGGTTTTAATCAAAA 5 277 1 TCTTTTAGGT 0.555667 -24 ATGTGTGGCGGATTTTATCAGTTTTTTTTCACGGA 9 171 1 GATTTTAGTT 0.96615 -130 AACAATGCTAGATTTTAAAAGTCGTTTACTCAAAA 9 267 0 GATTTTAGTT 0.96615 -34 AAAGATCTTATCGGTATTCGTCAAAAAA 10 4 1 GATCTTAGTT 0.818241 -297 ACGTAAATTCGATTTTTATCATATTCATAAAAAGG 10 143 0 GATTTTTATT 0.784064 -158 AGTGAAAGTATATTTTTTGAATGGTATAAGGGGCG 10 252 0 TATTTTTATT 0.724375 -49 AAATTTTGCGTATTTTTACCGCACT 12 1 0 TATTTTTGCT 0.835158 -40 TCATTTTATTTATTTTAAAGGGAGTTGTT 14 5 0 TATTTTAGGT 0.888003 -186 ATTTACCCTCTATTTTATGAATGATAGAAAGAATT 14 79 1 TATTTTAATT 0.804418 -112 ATTGATTATCGATTTTTGTAGTGATAAAAAAGACA 14 135 1 GATTTTTGTT 0.94802 -56 ******* ** * Masking position 6 Map Score: 6.25547 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 291 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 ATTTACTTTTCATATTGCAAAAAAAATATA 5 68 1 CATATTGCAA 0.908143 -233 AAAAAATCGGCATATTGATGCCCTTTATTT 9 39 0 CATATTGATG 0.938285 -262 TGTGTGAGCCCATATTGAAAGAGCTTGTAA 9 137 0 CATATTGAAA 0.936273 -164 AGGACTGATGCATATTCCTTATTTTTTTGA 10 31 0 CATATTCCTT 0.837124 -270 CGATTTTTATCATATTCATAAAAAGGATGA 10 139 0 CATATTCATA 0.934429 -162 AAGGTGACAGCATATTGATTAATAC 11 6 0 CATATTGATT 0.947641 -114 TGTATTTATAAATATTGATATGGGTTAGTA 13 65 0 AATATTGATA 0.814147 -23 ********** Masking position 4 Map Score: 2.21737 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 129 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ********** No masking Map Score: 1.37378e-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: 1.37378e-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: 1.37378e-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