AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_hinf_reg_100.orf -o00150_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) Motif number 1 TCAAACCATCTCTCATTTTTAGGATATTTCAAA 1 12 0 TCTCATTTTG 0.969771 -26 ATAAAATACACATAATTTTTTCGCCGCACTTTT 2 17 1 CATAATTTTG 0.923084 -82 AATTTTTTCGCCGCACTTTTGAGCTTCTCAATT 2 30 1 CCGCATTTTG 0.985235 -69 CTTTTGAGCTTCTCAATTTTGTGGCTAATTAAT 2 45 1 TCTCATTTTG 0.969771 -54 CCTTTTTCTTTTTAAGTTCTTTTCTCAAGGTAG 3 32 1 TTTAATTCTT 0.410389 -28 GCCCGTTTTTCTTAACTTTTCCGCCTAAA 4 7 0 CTTAATTTTG 0.86272 -163 GGGCGGATTATAGCCGTTTTTAGCTTTCTACGA 4 36 1 TAGCCTTTTG 0.767271 -134 CCTATAATAACCGCACTTTTCTTATTAAATAGT 4 143 1 CCGCATTTTT 0.958441 -27 AGCAAATCAATCGCACTTTTTGTTTTACAATGA 5 17 0 TCGCATTTTT 0.952985 -58 GCTTATTTAGTCTAACTTTTAAGGACAGAGCAA 5 45 0 TCTAATTTTG 0.957147 -30 CGCTATAATGCCGAAATTCTCTTATTTTC 7 16 1 CCGAATTCTT 0.853729 -19 TATCAATCAACAGAAATTTTAGGA 8 2 0 CAGAATTTTG 0.730912 -299 TGGCGGATTTTATCAGTTTTTTTTCACGGAATA 8 176 1 TATCATTTTT 0.839646 -125 CCTAATTGTATAGAAATTTTGTTTTTACGCTAT 8 208 0 TAGAATTTTT 0.869598 -93 TACAATTAGGCAAAAATTTTAGGGTAGAGAAGA 8 231 1 CAAAATTTTG 0.613962 -70 CTGTGAATTGTTGCAATTCTATGTTTTAGCGTA 9 87 0 TTGCATTCTG 0.840863 -33 GTTTTTCCTTTCAAAATTTTGCGTATTTTTACC 10 16 0 TCAAATTTTG 0.875982 -25 ***** **** * Masking position 7 Map Score: 22.3271 Number of sites scoring better than the average of aligned sites = 1170 Number in coding regions = 872 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 2 CCACAAAATTGAGAAGCTCAAAAGTGCGGCG 2 38 0 GAAAGCTCAA 0.852644 -61 AATTAATATAAATAAGAACAAGCATCAGAGG 2 71 1 AAAAGAACAA 0.701281 -28 AAAAGAACTTAAAAAGAAAAAGGGGCGATTA 3 24 0 AAAAGAAAAA 0.795246 -36 AGGCGGAAAAGTTAAGAAAAACGGGCGGATT 4 14 1 GTAAGAAAAA 0.910349 -156 AGCTTTCTACGAAAGAAAAAATAATATTGTT 4 57 1 GAAGAAAAAA 0.928049 -113 TATTGTTCATGAAAAACTCAATTTGGCATAA 4 81 1 GAAAACTCAA 0.803878 -89 TAAATTCATTGTAAAACAAAAAGTGCGATTG 5 12 1 GTAAACAAAA 0.944729 -63 GTCCTTAAAAGTTAGACTAAATAAGCAACAA 5 52 1 GTAGACTAAA 0.847875 -23 TCTGTTGATTGATAGACAAAATAAAGGGCAT 8 21 1 GAAGACAAAA 0.968404 -280 GTTGATTTCGGTGAGACACAACCGAAAGTAA 8 94 1 GTAGACACAA 0.926231 -207 GCTATATTCCGTGAAAAAAAACTGATAAAAT 8 182 0 GTAAAAAAAA 0.877947 -119 GAATATAGCGTAAAAACAAAATTTCTATACA 8 204 1 TAAAACAAAA 0.665228 -97 TTTCTATACAATTAGGCAAAAATTTTAGGGT 8 225 1 ATAGGCAAAA 0.883745 -76 GTGCGGTAAAAATACGCAAAATTTTGAAAGG 10 12 1 AAACGCAAAA 0.683178 -29 GCAAAATTTTGAAAGGAAAAACAA 10 27 1 GAAGGAAAAA 0.94794 -14 ** ******** Masking position 4 Map Score: 15.471 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 774 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 TCAAAAGTGCGGCGAAAAAATTATGTGTAT 2 22 0 GGCGAAAAAA 0.806918 -77 TCAATTTTGTGGCTAATTAATATAAATAAG 2 57 1 GGCTAATTAA 0.828439 -42 TTCTACGAAAGAAAAAATAATATTGTTCAT 4 61 1 GAAAAAATAA 0.890395 -109 TTAAGGACAGAGCAAATCAATCGCACTTTT 5 30 0 AGCAAATCAA 0.608847 -45 TTAAAAGTTAGACTAAATAAGCAACAATT 5 56 1 GACTAAATAA 0.746392 -19 TGTAAAAATTGGAAAATAAA 6 19 1 GGAAAATAAA 0.90103 -10 TTGATTGATAGACAAAATAAAGGGCATCAA 8 25 1 GACAAAATAA 0.892218 -276 ATTGACAAAAGTATAAAAAATCGGCATATT 8 53 0 GTATAAAAAA 0.663614 -248 GAAAGAGCTTGTAAAAATAACGATACTTAC 8 121 0 GTAAAAATAA 0.890394 -180 CTATATTCCGTGAAAAAAAACTGATAAAAT 8 182 0 TGAAAAAAAA 0.607769 -119 GGAATATAGCGTAAAAACAAAATTTCTATA 8 203 1 GTAAAAACAA 0.870142 -98 GCTGAAAGTGAGAAAATTAAATATCACCTT 9 51 0 AGAAAATTAA 0.649356 -69 AATTTTGAAAGGAAAAACAA 10 31 1 GGAAAAACAA 0.959593 -10 ********** Masking position 5 Map Score: 8.62303 Number of sites scoring better than the average of aligned sites = 1168 Number in coding regions = 938 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 AAAATTATGTGTATTTTATCGGATC 2 6 0 GTATTTTATC 0.90203 -93 AAAAACGGGCGGATTATAGCCGTTTTTAGC 4 30 1 GGATTATAGC 0.991447 -140 GAGAATTTCGGCATTATAGCGAGAAG 7 7 0 GCATTATAGC 0.975215 -28 GATGTGTGGCGGATTTTATCAGTTTTTTTT 8 170 1 GGATTTTATC 0.97339 -131 TTTTTTTCACGGAATATAGCGTAAAAACAA 8 193 1 GGAATATAGC 0.970267 -108 ********** Masking position 5 Map Score: 3.87727 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 14 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TTCAAACCATCTCTCATTTTTAGGATATTTC 1 15 0 CTCTCTTTTT 0.900913 -23 GGCGAGTAATCGCCCCTTTTTCTTTTTAAGT 3 18 1 CGCCCTTTTT 0.996123 -42 GGCTATAATCCGCCCGTTTTTCTTAACTTTT 4 20 0 CGCCCTTTTT 0.996123 -150 CTATAATAACCGCACTTTTCTTATTAAATAG 4 144 1 CGCACTTTCT 0.949026 -26 GCAAATCAATCGCACTTTTTGTTTTACAATG 5 18 0 CGCACTTTTG 0.949026 -57 TTTATTTTCCAATTTTTACATTTTAAA 6 12 0 TTCCATTTTT 0.748735 -17 GGCATATTGATGCCCTTTATTTTGTCTATCA 8 30 0 TGCCCTTATT 0.947368 -271 GGCATCAATATGCCGATTTTTTATACTTTTG 8 47 1 TGCCGTTTTT 0.950762 -254 ***** ***** Masking position 7 Map Score: 7.27863 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 298 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 TTTGAGCTTCTCAATTTTGTGGCTAATTAA 2 47 1 TCAATTTTGT 0.865829 -52 CATGAAAAACTCAATTTGGCATAACCTAAC 4 88 1 TCAATTTGGC 0.981511 -82 ATAAAGGGCATCAATATGCCGATTTTTTAT 8 41 1 TCAATATGCC 0.981308 -260 ACAAGCTCTTTCAATATGGGCTCACACAAA 8 139 1 TCAATATGGG 0.972465 -162 GTATTAATCAATATGCTGTCACCTTCT 9 8 1 TCAATATGCT 0.971462 -112 ********** Masking position 5 Map Score: 2.80601 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 103 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 ATTTGAAATATCCTAAAAATGAGAGAT 1 7 1 AATACCTAAA 0.912244 -31 TTTCTTTCGTAGAAAGCTAAAAACGGCTATA 4 44 0 AGAAGCTAAA 0.940884 -126 ACAATGATTTACAAAGCTAAAACAACCCCTA 4 116 1 ACAAGCTAAA 0.98246 -54 AATATTCTTCTCTACCCTAAAATTTTTGCCT 8 238 0 TCTACCTAAA 0.9199 -63 AGAACTAACAACAATGCTAGATTTTAAAAGT 8 280 0 ACAAGCTAGA 0.945002 -21 TTCAGCAATTTCTACGCTAAAACATAGAATT 9 75 1 TCTAGCTAAA 0.964721 -45 GTGCGGTAAAAATACGCAAAATTTTGAAAGG 10 12 1 AATAGCAAAA 0.836576 -29 **** ****** Masking position 4 Map Score: 2.60176 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 160 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TCAAACCATCTCTCATTTTTAGGATATTTC 1 15 0 TCTCATTTTT 0.934996 -23 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 2 45 1 TCTCAATTTT 0.890794 -54 AGCAAATCAATCGCACTTTTTGTTTTACAA 5 20 0 TCGCACTTTT 0.936278 -55 GCTTATTTAGTCTAACTTTTAAGGACAGAG 5 48 0 TCTAACTTTT 0.890794 -27 GCCGAAATTCTCTTATTTTC 7 25 1 TCTTATTTTC 0.866019 -10 AAATAACGATACTTACTTTCGGTTGTGTCT 8 107 0 ACTTACTTTC 0.81668 -194 ATCAATATGCTGTCACCTTCTTCTAAATGA 9 17 1 TGTCACCTTC 0.909055 -103 GAAAATTAAATATCACCTTCCTCTCATTTA 9 40 0 TATCACCTTC 0.87087 -80 TATTTAATTTTCTCACTTTCAGCAATTTCT 9 58 1 TCTCACTTTC 0.991971 -62 ********** Masking position 5 Map Score: 6.94395 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 163 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 ********** No masking Map Score: 1.21035e-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: 1.21035e-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: 1.21035e-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