AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_hinf_reg_300.orf -o00150_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 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 HI0974.1 300 conserved hypothetical protein #10 HI0976 119 conserved hypothetical protein #11 HI0978 40 ribosomal protein L11 methyltransferase (prmA) Motif number 1 ATTTGAAATATCCTAAAAATGAGAGATGGT 1 6 1 AAATACTAAT 0.872221 -32 GATCCGATAAAATACACATAATTTTTTCGCCGCA 2 10 1 AAATACAAAT 0.982942 -89 TATTTATATTAATTAGCCACAAAATTGAGAAGCTC 2 50 0 AATTACAAAT 0.975575 -49 TGAAAAACTCAATTTGGCATAACCTAACAATGATT 4 90 1 AATTTCAAAT 0.84892 -80 AGGACAGAGCAAATCAATCGCACTTTTTGTTTTAC 5 22 0 AAATCTCCAT 0.61545 -53 AAGTTAGACTAAATAAGCAACAATT 5 60 1 AAATACACAT 0.972459 -15 TTTTGTCTATCAATCAACAGAAATTTTAGGA 8 7 0 CAATCCAAAT 0.879092 -294 TGTCTCACCGAAATCAACACAAATTTTCCATTGAC 8 77 0 AAATCCAAAT 0.981434 -224 AAAACTGATAAAATCCGCCACACATCGTTTGTGTG 8 161 0 AAATCCCCAT 0.937147 -140 ATTTCTATACAATTAGGCAAAAATTTTAGGGTAGA 8 224 1 AATTACAAAT 0.974582 -77 ATATTTGGGGAATTACACCGAAATTATCTTGGTCG 9 84 1 AATTACCAAT 0.948161 -217 ATTTACGTAGAAATCAGCAAAACCTTTTGAATTAT 9 170 1 AAATCCAAAT 0.981685 -131 AAACCTTTTGAATTATTCAAAAAAGTTGTAAGATT 9 189 1 AATTACAAAG 0.844219 -112 AAAGTGAGAAAATTAAATATCACCTTCCTCTCATT 10 42 0 AATTATACAT 0.72157 -78 AGTGCGGTAAAAATACGCAAAATTTTGAAAGGAAA 11 11 1 AAATACAAAT 0.981838 -30 ***** ** ** * Masking position 12 Map Score: 19.0199 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 296 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 GTAATCGCCCCTTTTTCTTTTTAAGTTCTTTTCT 3 23 1 CTTTCTTTAA 0.887363 -37 ATATTATTTTTTCTTTCGTAGAAAGCTAAAAACG 4 50 0 TTCTCTAAAA 0.966479 -120 ATAGGGGTTGTTTTAGCTTTGTAAATCATTGTTA 4 114 0 TTTTCTTTAA 0.905418 -56 GATTGATTTGCTCTGTCCTTAAAAGTTAGACTAA 5 38 1 CTCTCTTAAA 0.954681 -37 TATTTTCCAATTTTTACATTTTAAAA 6 3 0 TTTTCTTTAA 0.903637 -26 ATCAACACAAATTTTCCATTGACAAAAGTATAAA 8 66 0 ATTTCTTACA 0.728786 -235 TTTTCACGGAATATAGCGTAAAAACAAAATTTCT 8 196 1 ATATCTAAAA 0.736073 -105 AAATATTCTTCTCTACCCTAAAATTTTTGCCTAA 8 236 0 CTCTCTAAAT 0.806059 -65 AGTCCTTACTATCTGGCATAGAAACTTTCATATT 9 55 1 ATCTCTAAAA 0.920604 -246 TAAATTCGATTTTTATCATATTCATAAAAAGGAT 9 141 0 TTTTCTATCA 0.745063 -160 TATACGCCCCTTATACCATTCAAAAAATATACTT 9 248 1 TTATCTTAAA 0.87473 -53 AAAAAATATACTTTCACTTATAAAAAATTTTAAG 9 269 1 CTTTCTAAAA 0.95918 -32 ATTTCTTCCTTAAAATTTTTTATAAG 9 285 0 TTCTCTAAAT 0.834705 -16 CAATTCTATGTTTTAGCGTAGAAATTGCTGAAAG 10 73 0 TTTTCTAAAA 0.956429 -47 TTGTTTTTCCTTTCAAAATTTTGCGTA 11 24 0 TTTTCTTAAA 0.961589 -17 **** * ** *** Masking position 9 Map Score: 15.3642 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 303 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TAATTAATATAAATAAGAACAAGCATCAGAG 2 70 1 AAATAGAACA 0.863019 -29 TAGGCGGAAAAGTTAAGAAAAACGGGCGGAT 4 13 1 AGTTAGAAAA 0.789818 -157 TGAAAAACTCAATTTGGCATAACCTAACAAT 4 90 1 AATTGGCATA 0.80299 -80 AAGTACTATTTAATAAGAAAAGTGCGGTTAT 4 149 0 TAATAGAAAA 0.780712 -21 AAGTTAGACTAAATAAGCAACAATT 5 60 1 AAATAGCAAC 0.907493 -15 TAAAATGTAAAAATTGGAAAATAAA 6 14 1 AAATGGAAAA 0.96494 -15 GAAAATAAGAGAATTTCGGCATT 7 22 0 AAATAGAGAA 0.84068 -13 AAAGTATAAAAAATCGGCATATTGATGCCCT 8 45 0 AAATGGCATA 0.91977 -256 ATTTCTATACAATTAGGCAAAAATTTTAGGG 8 224 1 AATTGGCAAA 0.947894 -77 ATTTACGTAGAAATCAGCAAAACCTTTTGAA 9 170 1 AAATAGCAAA 0.984177 -131 AAAAGTTGTAAGATTAGCAAACACAAGGGAC 9 209 1 AGATAGCAAA 0.951574 -92 AAATTGCTGAAAGTGAGAAAATTAAATATCA 10 55 0 AAGTAGAAAA 0.87464 -65 AGTGCGGTAAAAATACGCAAAATTTTGAAAG 11 11 1 AAATCGCAAA 0.935617 -30 **** ****** Masking position 4 Map Score: 10.92 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 375 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 AAAGTGCGGCGAAAAAATTATGTGTATTTT 2 19 0 GAAAAAATTA 0.902067 -80 ATCCTACCTTGAGAAAAGAACTTAAAAAGA 3 38 0 GAGAAAAGAA 0.925445 -22 TTCTACGAAAGAAAAAATAATATTGTTCAT 4 61 1 GAAAAAATAA 0.962836 -109 TTAAAAGTTAGACTAAATAAGCAACAATT 5 56 1 GACTAAATAA 0.794382 -19 TTGATTGATAGACAAAATAAAGGGCATCAA 8 25 1 GACAAAATAA 0.970892 -276 ATTTTCCATTGACAAAAGTATAAAAAATCG 8 60 0 GACAAAAGTA 0.852868 -241 GAAAGAGCTTGTAAAAATAACGATACTTAC 8 121 0 GTAAAAATAA 0.949545 -180 GCTATATTCCGTGAAAAAAAACTGATAAAA 8 183 0 GTGAAAAAAA 0.85357 -118 GGAATATAGCGTAAAAACAAAATTTCTATA 8 203 1 GTAAAAACAA 0.833294 -98 ATCGGTATTCGTCAAAAAAATAAGGAATAT 9 20 1 GTCAAAAAAA 0.88448 -281 TGCTGAAAGTGAGAAAATTAAATATCACCT 10 52 0 GAGAAAATTA 0.900284 -68 AGTGCGGTAAAAATACGCAAAATTTT 11 7 1 GTAAAAATAC 0.76363 -34 ********** Masking position 5 Map Score: 11.7983 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 230 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 5 ATTTTTTCGCCGCACTTTTGAGCTTCTCAA 2 31 1 CGCACTTTTG 0.927146 -68 GGCGAGTAATCGCCCCTTTTTCTTTTTAAG 3 18 1 CGCCCCTTTT 0.99307 -42 GGCTATAATCCGCCCGTTTTTCTTAACTTT 4 21 0 CGCCCGTTTT 0.981636 -149 CTATAATAACCGCACTTTTCTTATTAAATA 4 144 1 CGCACTTTTC 0.927146 -26 GCAAATCAATCGCACTTTTTGTTTTACAAT 5 19 0 CGCACTTTTT 0.979556 -56 GGCATATTGATGCCCTTTATTTTGTCTATC 8 31 0 TGCCCTTTAT 0.839917 -270 AACAAGTAATCATCCTTTTTATGAATATGA 9 130 1 CATCCTTTTT 0.738369 -171 ATATTTCATACGTCCCTTGTGTTTGCTAAT 9 221 0 CGTCCCTTGT 0.896719 -80 ATGAAATATACGCCCCTTATACCATTCAAA 9 242 1 CGCCCCTTAT 0.981294 -59 ********** Masking position 7 Map Score: 10.3767 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 369 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 GATCCGATAAAATACACATAATTTT 2 6 1 GATAAAATAC 0.883043 -93 GCTAAAAACGGCTATAATCCGCCCGTTTTT 4 30 0 GCTATAATCC 0.989651 -140 CTTCTCGCTATAATGCCGAAATTCTC 7 7 1 GCTATAATGC 0.97095 -28 AAAAAAAACTGATAAAATCCGCCACACATC 8 170 0 GATAAAATCC 0.967738 -131 TTGTTTTTACGCTATATTCCGTGAAAAAAA 8 193 0 GCTATATTCC 0.964998 -108 ********** Masking position 6 Map Score: 2.41912 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 7 CATAATTTTTTCGCCGCACTTTTGAGCTTC 2 27 1 TCGCCGCACT 0.987383 -72 ACCCCTATAATAACCGCACTTTTCTTATTA 4 140 1 TAACCGCACT 0.977641 -30 CGGTTGTGTCTCACCGAAATCAACACAAAT 8 88 0 TCACCGAAAT 0.971606 -213 TTGGGGAATTACACCGAAATTATCTTGGTC 9 88 1 ACACCGAAAT 0.912281 -213 TTGCGTATTTTTACCGCACT 11 1 0 TTACCGCACT 0.97764 -40 ********** Masking position 8 Map Score: 2.36028 Number of sites scoring better than the average of aligned sites = 1167 Number in coding regions = 751 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 8 TTTTAAAATGTAAAAATTGG 6 1 1 TTTTAAAATG 0.709163 -28 AAATAAAGGGCATCAATATGCCGATTTTTT 8 39 1 CATCAATATG 0.917653 -262 TTACAAGCTCTTTCAATATGGGCTCACACA 8 137 1 TTTCAATATG 0.919708 -164 ATCTTGGTCGTATCAAAAGGTAACAAGTAA 9 109 1 TATCAAAAGG 0.935977 -192 TTATCATATTCATAAAAAGGATGATTACTT 9 133 0 CATAAAAAGG 0.663154 -168 TTTTTGAATAATTCAAAAGGTTTTGCTGAT 9 182 0 ATTCAAAAGG 0.906135 -119 GTATTAATCAATATGCTGTCACCTT 10 6 1 AATCAATATG 0.832812 -114 CTGTCACCTTCTTCTAAATGAGAGGAAGGT 10 26 1 CTTCTAAATG 0.805356 -94 TTGTTTTTCCTTTCAAAATTTTGCGTATTT 11 21 0 TTTCAAAATT 0.681603 -20 ********** Masking position 6 Map Score: 1.55381 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 509 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 TTATAGGGGTTGTTTTAGCTTTGTAAATCA 4 120 0 TGTTTTAGCT 0.97403 -50 ATAGAAATTTTGTTTTTACGCTATATTCCG 8 202 0 TGTTTTTACG 0.935919 -99 ATACGTCCCTTGTGTTTGCTAATCTTACAA 9 214 0 TGTGTTTGCT 0.960349 -87 TGCAATTCTATGTTTTAGCGTAGAAATTGC 10 79 0 TGTTTTAGCG 0.975896 -41 TTGTTTTTCCTTTCAAAATTT 11 30 0 TGTTTTTCCT 0.952508 -11 ********** Masking position 5 Map Score: 1.98292 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 53 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: -3.45081e-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: -3.45081e-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 ********** No masking Map Score: -3.45081e-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