AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 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 = 0 Input sequences: #1 HI0229 298 polynucleotide phosphorylase (pnp) #2 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #3 HI0964 300 virulence factor (mviN) #4 HI1282 300 conserved hypothetical protein #5 HI1288 300 ribosome binding factor A (rbfA) #6 HI1324 96 lon protease, putative #7 HI1325 168 3-hydroxydecanoyl-(acyl carrier-protein) dehydratase (fabA) #8 HI1326 233 H. influenzae predicted coding region HI1326 #9 HI1328 135 ribosomal protein S15 (rpS15) Motif number 1 TGGGCGTTTAAAAATTTCTTTTGATAGCCGCACG 1 184 0 AAATTTTTTA 0.982644 -115 TGTTTTCCTTAAAATTTATATTAAAAACAATGCC 1 273 0 AAATTTTTTA 0.982642 -26 TCCTAAAATTTCTGTTGATTGATAGACA 3 5 1 AAATTTTTTA 0.982644 -296 TTGTCAATGGAAAATTTGTGTTGATTTCGGTGAG 3 75 1 AAATTTTTTA 0.982644 -226 AATTGTATAGAAATTTTGTTTTTACGCTATATTC 3 204 0 AAATTTTTTA 0.982644 -97 TCTCTACCCTAAAATTTTTGCCTAATTGTATAGA 3 227 0 AAATTTTCCA 0.948323 -74 GAGATTTAATAAACTATCTTTTTACTATTACTAA 4 162 1 AAATATTTTA 0.867688 -139 TAACCTTATGAAACCTTATCCTAAACAATACTTA 4 206 0 AAACTTTCTA 0.90089 -95 TTCTTGTAAATTTTGTTCTAATGTAGCCAAT 4 280 0 AAATTTTCTA 0.981464 -21 AAGTGCGGTGAAAGTTTTTCCTAGATTTTCACCG 8 34 1 AAATTTTCTG 0.90089 -200 AGATATTTTAAAAATTTATTACAATTTAATAAGT 8 75 0 AAATTTTACA 0.778587 -159 AGTGGTAAATAAAGTTTATTTTAAAGTTTTTAAT 8 139 1 AAATTTTTTA 0.982644 -95 *** *** * ** * Masking position 3 Map Score: 17.5195 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 53 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TTTCTTTTGATAGCCGCACGCTAATGTAGAAA 1 172 0 TGCCGCACCT 0.978638 -127 TTCGAAAAAATGACCGCACTTTGGGCGTTTAA 1 207 0 TACCGCACTT 0.99755 -92 AGGGTGTAATTCACCGCACTATATCATAACCT 4 234 0 TACCGCACAT 0.990143 -67 ATTATCGCATATTTAATAGCCTT 6 84 0 TATCGCATTT 0.872624 -13 GGAAAAACTTTCACCGCACTTTTGTATGAATT 8 23 0 TACCGCACTT 0.99755 -211 TCCTAGATTTTCACCGCACCTTTACTTATTAA 8 52 1 TACCGCACTT 0.99755 -182 AAGATTAAAGTTACCGCACTTTTCATTA 9 7 0 TACCGCACTT 0.99755 -129 * ******* ** Masking position 8 Map Score: 14.3085 Number of sites scoring better than the average of aligned sites = 793 Number in coding regions = 461 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 3 TTAATTATCATTGTTTCGACAGTATTTTCCT 1 77 0 TTGTTTCGAA 0.864991 -222 GCACGGGCTTTATTTTCTACATTAGCGTGCG 1 159 1 TATTTTCTAA 0.822646 -140 AGTGCGGTCATTTTTTCGAAAGATTTCTTTT 1 219 1 TTTTTTCGAA 0.964817 -80 TAAGGCATTGTTTTTAATATAAATTTTAAGG 1 270 1 TTTTTAATAA 0.789917 -29 AATATGCCGATTTTTTATACTTTTGTCAATG 3 53 1 TTTTTTATAT 0.665965 -248 AGAAATTTTGTTTTTACGCTATATTCCGTGA 3 199 0 TTTTTACGCA 0.859368 -102 GTTTTGGGGTTTTTTTCTATAAGAAATTTAG 4 86 1 TTTTTTCTAA 0.968491 -215 ATAAACTATCTTTTTACTATTACTAAAATAG 4 170 1 TTTTTACTAT 0.859009 -131 AATGTGTGATTTTTATCGACAATCTTGGTCG 5 89 1 TTTTATCGAA 0.805523 -212 TCAGGTGTCATTTTATCGAAAAACAGTATTA 5 204 1 TTTTATCGAA 0.805521 -97 AAAGCGAGCATTTTTTCGCTTTTCTTTTTTT 7 17 1 TTTTTTCGCT 0.763772 -152 TCGCTTTTCTTTTTTTCTATAATTTCTAAGA 7 32 1 TTTTTTCTAA 0.968491 -137 GCGGTGAAAGTTTTTCCTAGATTTTCACCGC 8 38 1 TTTTTCCTAA 0.852712 -196 TATTTTAAAGTTTTTAATAAACGTTATTATA 8 155 1 TTTTTAATAA 0.787904 -79 ATTAATTTAATATTTTCTATAATAACGTTTA 8 172 0 TATTTTCTAA 0.822642 -62 AAAGGTAGTGTTGTTAATACATCATTCGCCG 9 103 0 TTGTTAATAA 0.467918 -33 TTTTTACTCCTAAAAGGTAGT 9 125 0 TTTTTACTCT 0.689053 -11 ********* * Masking position 4 Map Score: 13.7591 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 524 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 4 AATTAGGTTCTTTTATATGAAATATAATGTAATGA 1 17 0 TTTTAAGTAT 0.930186 -282 AGCCCGTGCATTATACAGGATGTTTGGCTTTAATG 1 133 0 TTATAAGTTT 0.958067 -166 GTATCGTTATTTTTACAAGCTCTTTCAATATGGGC 3 125 1 TTTTAAGTTT 0.970973 -176 GTGTGGCGGATTTTATCAGTTTTTTTTCACGGAAT 3 173 1 TTTTACGTTT 0.969023 -128 CAATGCTAGATTTTAAAAGTCGTTTACTCAAAATA 3 265 0 TTTTAAGTTT 0.970973 -36 TGGGGTTTTTTTCTATAAGAAATTTAGTAACTGGG 4 90 1 TTCTAAGTTT 0.911446 -211 AACCCTTTTTTTATGCCTGAGATTTAATAAACTAT 4 144 1 TTATGCGTTT 0.80093 -157 CAACAAGCATTTTTAAATGATTAGACGAAAAACT 5 53 0 TTTTAAGTAG 0.715028 -248 GTAAAGTGATTTTTATCGGAAGTTTGAATATTCAA 5 161 1 TTTTACGTTT 0.969024 -140 GTAACTGCATTAATATACGTGTTTTTATGCCGATT 6 32 1 TAATAAGTTT 0.743792 -65 TAAATCCAGTTTATAACTGATATATTTATTTTAAA 7 123 0 TTATACGTAT 0.888673 -46 ***** * * *** Masking position 4 Map Score: 7.06612 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 143 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 CGCTAATGTAGAAAATAAAGCCCGTGCATT 1 156 0 GAAAATAAAG 0.757239 -143 GTGCGGCTATCAAAAGAAATTTTTAAACGC 1 185 1 CAAAAGAAAT 0.958711 -114 TTGCGACTAGCAAAAGAAATCTTTCGAAAA 1 231 0 CAAAAGAAAT 0.958711 -68 GTCTATCAATCAACAGAAATTTTAGGA 3 8 0 CAACAGAAAT 0.957911 -293 GATTGATAGACAAAATAAAGGGCATCAATA 3 27 1 CAAAATAAAG 0.949614 -274 TCACCGAAATCAACACAAATTTTCCATTGA 3 78 0 CAACACAAAT 0.866021 -223 CGGTGAGACACAACCGAAAGTAAGTATCGT 3 102 1 CAACCGAAAG 0.872547 -199 GCGTTCCTTTTAAAATAAATATATCAGTTA 7 115 1 TAAAATAAAT 0.620453 -54 AGTTCAAATGCAAGATAAAGATTAAAGTTA 9 26 0 CAAGATAAAG 0.873277 -110 ********** Masking position 7 Map Score: 3.62135 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 223 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 6 TTTCATATAAAAGAACCTAATTTCAGAGAG 1 30 1 AAGAACCTAA 0.981181 -269 AGTTCAGTAAAAGAACCCCAGTTTTGGGGT 4 66 1 AAGAACCCCA 0.983808 -235 TCTTATAGAAAAAAACCCCAAAACTGGGGT 4 80 0 AAAAACCCCA 0.920902 -221 TTAGGTTCATAAGAACCTAAGCCCAGTTAC 4 116 0 AAGAACCTAA 0.981181 -185 TTAGGTTCTTATGAACCTAACCCTTTTTTT 4 126 1 ATGAACCTAA 0.940642 -175 ********** Masking position 5 Map Score: 3.03038 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ACTTTATTTCACATTACCAACTTAATTATCATTGTTTCG 1 90 0 ATTACAATTT 0.970269 -209 TTTTAAAAGTCGTTTACTCAAAATATTCTTCTCTACCCT 3 251 0 CTTACAATTT 0.981048 -50 AACTGGGGTTCTTTTACTGAACTTATTATTGGTTGCGGG 4 50 0 CTTACAATTT 0.981048 -251 AACCTAAGCCCAGTTACTAAATTTCTTATAGAAAAAAAC 4 94 0 CTTACACTTT 0.967012 -207 TAAAAATCACACATTACAACAAGCATTTTTAAATGATT 5 65 0 ATTACCATTT 0.948589 -236 GATAAAAATCACTTTACAGAGGGCATAATTTATGCAAGC 5 139 0 ATTACAATAT 0.853974 -162 AGCTATTTACAGTTTACTGCGTTCCTTTTAAAATAAATA 7 97 1 ATTACCCTTT 0.91278 -72 TTTCACCGCACCTTTACTTATTAAATTGTAATAAATTTT 8 60 1 CTTACAATTT 0.981049 -174 * **** * *** * Masking position 6 Map Score: 3.0889 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 36 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ACAAAAGTATAAAAAATCGGCATATTGATG 3 49 0 AAAAAATCGG 0.810389 -252 GGCATAATTTATGCAAGCGAGACGAGACGA 5 127 0 ATGCAAGCGA 0.749093 -174 TTCCTTATTTATAAAAGCGCCTCATTCTAC 5 276 0 ATAAAAGCGC 0.939634 -25 AAAATCCACTAGAAAATCGGCATAAAAACA 6 51 0 AGAAAATCGG 0.957089 -46 TAGAGAAAAGCGAGCATTTTTTC 7 4 1 AGAAAAGCGA 0.977102 -165 ATAGAAAAAAAGAAAAGCGAAAAAATGCTC 7 22 0 AGAAAAGCGA 0.977102 -147 AGCGATGACAAGGAAATCGCATTCTAACGA 9 62 0 AGGAAATCGC 0.937533 -74 ********** Masking position 5 Map Score: 2.10187 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 90 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 ********** No masking Map Score: 2.41828e-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 TTGATTGTTCTCTCTGAAATTAGGTTCTTTTA 1 37 0 TCTGAAATTA 0.96389 -262 CTAGTCGCAATCTGGGAAATAAGGCATTGTTT 1 251 1 TCTGAAATAA 0.86817 -48 CGGTTGTGTCTCACCGAAATCAACACAAATTT 3 86 0 TCAGAAATCA 0.927057 -215 CAGTTTTTTTTCACGGAATATAGCGTAAAAAC 3 189 1 TCAGAATATA 0.758409 -112 GTTTGAATATTCAAACAAATTATCAGGTGTCA 5 182 1 TCACAAATTA 0.869828 -119 CTACTGGAAATCATTGAATTTAGCACGCAAAA 5 248 0 TCAGAATTTA 0.937904 -53 GAGCAGTCACTCTTAGAAATTATAGAAAAAAA 7 41 0 TCTGAAATTA 0.963891 -128 *** ******* Masking position 7 Map Score: 0.300739 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 85 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 ********** No masking Map Score: 2.41828e-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 AAACAATGATAATTAAGTTGGTAATGTGAA 1 92 1 AATTAAGTTG 0.9157 -207 GGTAATGTGAAATAAAGTTAGCCATTAAAG 1 111 1 AATAAAGTTA 0.899951 -188 CGAAAAACAGTATTAAGTTGAAAGGGATTT 5 220 1 TATTAAGTTG 0.850703 -81 CACCTTTACTTATTAAATTGTAATAAATTT 8 68 1 TATTAAATTG 0.743602 -166 ATTTACCACTAATAAAATTAAAAAATAACA 8 119 0 AATAAAATTA 0.820735 -115 ATTAGTGGTAAATAAAGTTTATTTTAAAGT 8 136 1 AATAAAGTTT 0.689357 -98 TTATAGAAAATATTAAATTAATTTCTATTT 8 181 1 TATTAAATTA 0.747399 -53 ATTAATTTCTATTTAAATTATAAATAATAT 8 197 1 ATTTAAATTA 0.640605 -37 CAAGATAAAGATTAAAGTTACCGCACTTTT 9 16 0 ATTAAAGTTA 0.739752 -120 ********** Masking position 5 Map Score: 1.46895 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 135 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: 2.41828e-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: 2.41828e-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 15 ********** No masking Map Score: 2.41828e-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