AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_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 HI0033 53 conserved hypothetical protein #2 HI0034 124 conserved hypothetical protein #3 HI0035 205 conserved hypothetical protein #4 HI0266 82 conserved hypothetical protein #5 HI0267 41 nitrate/nitrite sensor protein (narQ) #6 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #7 HI1129 201 conserved hypothetical protein #8 HI1130 30 conserved hypothetical protein #9 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #10 HI1137 21 cell division protein (ftsW) #11 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #12 HI1140 71 D-alanine--D-alanine ligase (ddlB) #13 HI1143 83 cell division protein (ftsZ) Motif number 1 ATTTTAGTAAAGTGCGGTAAAAAATAA 1 8 1 TAAAGTGCGG 0.985965 -46 TCCTTATCTAAAAAGTGCGGTTATTTTTTA 1 28 0 AAAAGTGCGG 0.998195 -26 TTTAGACATAAAAAGCGCGGTTAATTTCGC 2 26 1 AAAAGCGCGG 0.995309 -99 CACGCAAAAAATAAGCGCGAAATTAACCGC 2 42 0 ATAAGCGCGA 0.866504 -83 ACTTAGCAATAAAGGTGCGGAATTCTATCA 2 96 0 AAAGGTGCGG 0.988662 -29 CATCCGAGATAAAAGTGCGGTGAAAAATAA 3 19 1 AAAAGTGCGG 0.998195 -187 CCCTTTTACAAAAAGTGCGGTTATTTTTCA 3 39 0 AAAAGTGCGG 0.998195 -167 GGAAATTTAGAAAAGTGCGGTAAAATTT 5 9 0 AAAAGTGCGG 0.998195 -33 AGAAGTGGAGAAAAGTGGTGTTTTGTGGAG 7 136 1 AAAAGTGGTG 0.872267 -66 TTTCAAAAGTGAAAGAGCGAACCTAGCTAT 9 16 0 GAAAGAGCGA 0.931815 -107 TTTCACTTTTGAAAGAGCGACCTTTTTTAC 9 32 1 GAAAGAGCGA 0.931815 -91 TTTTATATCCAAAAGTGCTAATATTAGAAA 11 51 1 AAAAGTGCTA 0.952624 -87 AAACTCAACTAAAAGTGCGGTTAAAATTCG 11 92 0 AAAAGTGCGG 0.998195 -46 ********** Masking position 3 Map Score: 39.4814 Number of sites scoring better than the average of aligned sites = 1473 Number in coding regions = 972 Number in noncoding regions = 501 Number of orfs with sites within 600 bp upstream = 323 Fraction of orfs with sites within 600 bp upstream = 0.0518792 Motif number 2 GCGGTTATTTTTTACCGCACTTTACTAAAAT 1 11 0 TTACCGCACT 0.998857 -43 GCGGTAAAAAATAACCGCACTTTTTAGATAA 1 24 1 ATACCGCACT 0.996883 -30 AAGCGCGAAATTAACCGCGCTTTTTATGTCT 2 29 0 TTACCGCGCT 0.99571 -96 GCGGTTATTTTTCACCGCACTTTTATCTCGG 3 22 0 TTACCGCACT 0.998857 -184 GCGGTGAAAAATAACCGCACTTTTTGTAAAA 3 35 1 ATACCGCACT 0.996883 -171 TTTGAAAACCTTAACCAAACTCAAAAAATGA 3 132 0 TTACCAAACT 0.915938 -74 AAATTTTACCGCACTTTTCTAAATT 5 5 1 TTACCGCACT 0.998857 -37 GTTGCGAATTTTAACCGCACTTTTAGTTGAG 11 88 1 TTACCGCACT 0.998857 -50 ** ******** Masking position 4 Map Score: 27.5039 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 496 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 CGGTAAAAAATAACCGCACTTTTTAGATAAGG 1 25 1 TACGCACTTT 0.957399 -29 TAAAAATAATTTCAATTTAGACATAAAA 2 7 1 TATTCAATTT 0.977732 -118 CGGTGAAAAATAACCGCACTTTTTGTAAAAGG 3 36 1 TACGCACTTT 0.957399 -170 TTGTAGAGGCTATGCTCAATTTCGCAAGAAAA 3 85 1 TACTCAATTT 0.968192 -121 CCGAAGGAGTTAAATTTCATTTTTAAGGGGTC 3 181 1 TATTTCATTT 0.923641 -25 TAAAAATCTTTAAATTCAATTTTGATTTGACG 6 101 1 TATTCAATTT 0.978641 -81 GGCATATAAATACTTTTACTTTATTTT 6 165 1 TATTTACTTT 0.966969 -17 TTTCTAAAAATAAGTTCAATTTTTAAGGCGTA 7 178 1 TATTCAATTT 0.97716 -24 GTAGTACTTTTATCTTAAATTT 8 19 1 TATTAAATTT 0.818196 -12 GATGGAAATATAAATTTCCTTTACTAACGTAA 9 58 0 TATTTCCTTT 0.951009 -65 TTGCGAATTTTAACCGCACTTTTAGTTGAGTT 11 89 1 TACGCACTTT 0.957399 -49 TTATTTTTCCTTTTCTCCCAATG 11 125 0 TATTTCCTTT 0.951009 -13 TTATTTTAATTTTTCATCTACA 13 1 1 TTTTTAATTT 0.642276 -83 ATATAAAATATAAATTCCCTTTATTGTAGATG 13 25 0 TATTCCCTTT 0.979938 -59 ** ******** Masking position 10 Map Score: 20.7403 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 300 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 TAAAAAGTGCGGTTATTTTTTACCGCACTTT 1 19 0 GGTTTTTTTT 0.665312 -35 TCTAAATTGAAATTATTTTTA 2 1 0 AATTTTTTTA 0.853042 -124 TTAATTTCGCGCTTATTTTTTGCGTGGATTT 2 46 1 GCTTTTTTTT 0.867133 -79 ATTATATCCAAGTTGTTTTTTGAAAACCTTA 3 150 0 AGTTTTTTTT 0.872586 -56 CTATTCAATTACTTATTTATTAGCATTTTAA 6 25 1 ACTTTTTATT 0.903838 -157 AATTGAATTTAAAGATTTTTATAAGATTTGT 6 91 0 AAAGTTTTTA 0.377626 -91 AATAAAGTAAAAGTATTTATATGCCCTAAAC 6 159 0 AAGTTTTATA 0.712039 -23 AACAATTCAAACGGCTTTTTTCATAAAATTT 7 17 0 ACGGTTTTTT 0.938241 -185 AAGCCGTTTGAATTGTTTATTCAAACGGCTT 7 31 1 AATTTTTATT 0.809687 -171 GTTTATTCAAACGGCTTTTTTATTTTGATAA 7 45 1 ACGGTTTTTT 0.938241 -157 CATTAAAGCAACTGATTTTTATCAAAATAAA 7 63 0 ACTGTTTTTA 0.894773 -139 TAAAAATTGAACTTATTTTTAGAAAATCTCT 7 172 0 ACTTTTTTTA 0.927662 -30 CCTCAGTCATAAGTATTTTTTATATCCAAAA 11 34 1 AAGTTTTTTT 0.912054 -104 AAAATTCGCAACGTTTTTATTTCTAATATTA 11 69 0 ACGTTTTATT 0.905463 -69 **** ****** Masking position 6 Map Score: 10.9041 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 313 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 5 TATTTTTTGCGTGGATTTTGCGCAAGAGGG 2 59 1 GTGGATTTTG 0.853062 -66 TTATATCCAAGTTGTTTTTTGAAAACCTTA 3 150 0 GTTGTTTTTT 0.813597 -56 GGAAACTCCAGTGGAAATTTAGAAAAGTGC 5 21 0 GTGGAAATTT 0.888667 -21 GTGGAGAAAAGTGGTGTTTTGTGGAGATTT 7 140 1 GTGGTGTTTT 0.971486 -62 GTGGTGTTTTGTGGAGATTTTTAGAGATTT 7 150 1 GTGGAGATTT 0.980987 -52 GGGTTGTGGCGTTTTATAAATAGCC 11 6 1 GTGGCGTTTT 0.987141 -132 ACTTATGACTGAGGCTATTTATAAAACGCC 11 18 0 GAGGCTATTT 0.793364 -120 AAATAAAAACGTTGCGAATTTTAACCGCAC 11 78 1 GTTGCGAATT 0.762986 -60 CGCACTTTTAGTTGAGTTTTGTCATTGGGA 11 103 1 GTTGAGTTTT 0.954199 -35 ********** Masking position 9 Map Score: 5.85209 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 353 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 TACAATACCGAAAATTTTTGACCCTTTTAC 3 60 0 AAAATTTTTG 0.824309 -146 CCAAACTCAAAAAATGATACGTTCGTCACA 3 119 0 AAAATGATAC 0.786188 -87 GGTTTCCTCTAAAATTATTGTAGGCGTATG 4 13 1 AAAATTATTG 0.899444 -70 ATTCTACCCAAAATTGATAGCATACGCCTA 4 33 0 AAATTGATAG 0.893754 -50 CTTTTTTCATAAAATTTTATTGA 7 4 0 AAAATTTTAT 0.853006 -198 TTAGTAAAGGAAATTTATATTTCCATCAAT 9 63 1 AAATTTATAT 0.853006 -60 TATAAATTTTAAAATTATATCATTGATGGA 9 84 0 AAAATTATAT 0.917102 -39 TATAATTTTAAAATTTATAGCAATTAAGAA 9 95 1 AAATTTATAG 0.936928 -28 GGATTGATTGAAAATCTTAGTATTAGAAAA 12 19 1 AAAATCTTAG 0.820499 -53 ********** Masking position 5 Map Score: 3.30226 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 207 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 TTCGTCACATTTTTTCTTGCGAAATTGAGC 3 98 0 TTTTTCTTGC 0.96612 -108 TAACGAACAGTTTTTCTTGCTGGAGTGCAA 4 62 1 TTTTTCTTGC 0.96612 -21 TCAAACGGCTTTTTTCATAAAATTTTATTG 7 12 0 TTTTTCATAA 0.843641 -190 ATGTAGTACTTTTATCTTAAATTT 8 17 1 TTTATCTTAA 0.843641 -14 TTTCTTTCTTCTTAATTGCTATAAA 9 108 0 TTCTTCTTAA 0.947732 -15 TATCCTGTTTTTCTTCTTACTGATGATACT 12 48 0 TTCTTCTTAC 0.966119 -24 ********** Masking position 5 Map Score: 2.97468 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 115 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ACCGCGCTTTTTATGTCTAAATTGAAATTA 2 17 0 TTATGTCTAA 0.945468 -108 TTCCGCACCTTTATTGCTAAGTGAGAACAA 2 104 1 TTATTGCTAA 0.907861 -21 CTCCTTCGGATTATATCCAAGTTGTTTTTT 3 160 0 TTATATCCAA 0.956943 -46 TAAGTATTTTTTATATCCAAAAGTGCTAAT 11 43 1 TTATATCCAA 0.956943 -95 CGCAACGTTTTTATTTCTAATATTAGCACT 11 64 0 TTATTTCTAA 0.953275 -74 ********** Masking position 4 Map Score: 2.08567 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 33 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 TTGCGCAAGAGGGTATTCAATGATAGAATT 2 76 1 GGGTATTCAA 0.923261 -49 AATAAAGGTGCGGAATTCTATCATTGAATA 2 89 0 CGGAATTCTA 0.931508 -36 CAAAAATTTTCGGTATTGTAGAGGCTATGC 3 70 1 CGGTATTGTA 0.965114 -136 AAAAACTGTTCGTTATTCTACCCAAAATTG 4 47 0 CGTTATTCTA 0.96946 -36 AAACAAGCGGCTGTATTCTATTTCAAATTA 6 133 0 CTGTATTCTA 0.969443 -49 CGTTTGAATTGTTTATTCAAACGGCTTTTT 7 35 1 GTTTATTCAA 0.73831 -167 TATAAATTCCCTTTATTGTAGATGAAAAAT 13 19 0 CTTTATTGTA 0.866409 -65 ********** Masking position 5 Map Score: 3.58063 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 63 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 AACCTTAACCAAACTCAAAAAATGATACGT 3 127 0 AAACTCAAAA 0.895424 -79 TCACATTTGTAAAATCTAAAACATCCATTA 6 53 0 AAAATCTAAA 0.943037 -129 ATCTTATAAAAATCTTTAAATTCAATTTTG 6 95 1 AATCTTTAAA 0.561158 -87 CAAATTACGTCAAATCAAAATTGAATTTAA 6 110 0 CAAATCAAAA 0.714933 -72 GATTTTTATCAAAATAAAAAAGCCGTTTGA 7 51 0 AAAATAAAAA 0.903296 -151 TTGAGCGAACAAATTATAAACTTGCCAGAA 7 110 1 AAATTATAAA 0.802509 -92 ATTTTTAGAAAATCTCTAAAAATCTCCACA 7 159 0 AATCTCTAAA 0.725351 -43 ATCATTGATGGAAATATAAATTTCCTTTAC 9 66 0 GAAATATAAA 0.831516 -57 TAATTGCTATAAATTTTAAAATTATATCAT 9 91 0 AAATTTTAAA 0.716955 -32 GCTAATATTAGAAATAAAAACGTTGCGAAT 11 67 1 GAAATAAAAA 0.781897 -71 TTGTAGATGAAAAATTAAAATAA 13 4 0 AAAATTAAAA 0.853429 -80 CTAAATATATAAAATATAAATTCCCTTTAT 13 33 0 AAAATATAAA 0.927845 -51 ********** Masking position 8 Map Score: 7.51176 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 416 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 11 ********** No masking Map Score: 2.51122e-13 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 TAACCGCGCTTTTTATGTCTAAATTGAAATTA 2 17 0 TTTTATGCAA 0.686065 -108 ATTTTCGGTATTGTAGAGGCTATGCTCAATTT 3 75 1 TTGTAGAGTA 0.810878 -131 AAATTTCATTTTTAAGGGGTCAAT 3 192 1 TTTAAGGGCA 0.720956 -14 CCTACAATAATTTTAGAGGAAACCTT 4 5 0 TTTTAGAGAA 0.955115 -78 TCTAAAATTATTGTAGGCGTATGCTATCAATT 4 20 1 TTGTAGGGAT 0.79527 -63 AAATAAGTAATTGAATAGGTATAAAAGCAAAT 6 11 0 TTGAATAGAT 0.60285 -171 TTAATGGATGTTTTAGATTTTACAAATGTGAT 6 52 1 TTTTAGATTA 0.310918 -130 ATTTAAAGATTTTTATAAGATTTGTGACTTGT 6 84 0 TTTTATAGTT 0.409784 -98 TCAATAAAATTTTATGAAAAAAGCCGTTTGA 7 10 1 TTTTATGAAA 0.668304 -192 AAAAAGCCGTTTGAATAAACAATTCAAACGGC 7 33 0 TTGAATAAAA 0.542392 -169 AATCAGTTGCTTTAATGTGGAATTACTTGCAA 7 77 1 TTTAATGGAA 0.888688 -125 AAGTTCAATTTTTAAGGCGTAAT 7 189 1 TTTAAGGGAA 0.942466 -13 AAATTTAAGATAAAAGTACTACATT 8 16 0 TTTAAGAAAA 0.751109 -15 ATTTATAGCAATTAAGAAGAAAGAAA 9 107 1 ATTAAGAGAA 0.58862 -16 CATAAGTATTTTTTATATCCAAAAGTGCTAAT 11 41 1 TTTTATACAA 0.658945 -97 ATTCCCTTTATTGTAGATGAAAAATTAAAATA 13 12 0 TTGTAGAGAA 0.939049 -72 ******* * ** Masking position 5 Map Score: 3.28092 Number of sites scoring better than the average of aligned sites = 1087 Number in coding regions = 890 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 13 ********** No masking Map Score: 2.51122e-13 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: 2.51122e-13 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: 2.51122e-13 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