AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icarP_hpyl_opreg_100.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0919 98 carbamoyl-phosphate synthase (glutamine-hydrolysing) (pyrAb) #2 HP0920 143 conserved hypothetical integral membrane protein #3 HP1234 300 conserved hypothetical integral membrane protein #4 HP1236 78 H. pylori predicted coding region HP1236 Motif number 1 AAAGTATTTTTTATTAGGTTTTTGCGTGGCGT 1 30 0 TTATTAGTTT 0.894853 -69 GTTATCAATATTTTAAAGTATTTTTTATTAGG 1 44 0 TTTTAAGATT 0.966788 -55 TACATTCTTTCTTTAAGGATTAGTT 1 84 1 CTTTAAGTTA 0.882804 -15 TCAATTTCAATTTTAGGGGGTTTTGTTTGGTA 2 37 1 TTTTAGGGTT 0.977831 -107 AATTAAAATTATTTATTGAGTTGAATTCAAGG 2 114 1 ATTTATGGTT 0.7837 -30 TAGAAAACTCTTTTTAAGCTTTTTAAATCCC 3 10 0 TTTTTAGTTT 0.978426 -291 CCTAGACCCTTTTTAAAGGGTTTGAATGCCAC 3 45 0 TTTTAAGGTT 0.992204 -256 AGGATTCGTGTTTTTATGTTTTCATATTTCTA 3 92 1 TTTTTAGTTT 0.978426 -209 TTTCATATTTCTATAAGGAGTTTGAAATGCTG 3 111 1 CTATAAGGTT 0.92341 -190 ATCAATGCAACTTTTATGCGTTTAAAGCTTAA 3 215 1 CTTTTAGGTT 0.973436 -86 AGACTTAAAGTTTTTAAGCTTTAAACGCATAA 3 228 0 TTTTTAGTTT 0.978426 -73 ATAAAACGCTTTTTAAAGAATTAAT 4 4 0 TTTTAAGATT 0.966788 -75 TTAGAGTGTATTTTATCGTTTTTTAGATAAAA 4 30 0 TTTTATGTTT 0.946854 -49 TTTTATTTATTTTTAGAGTGTATTTTATCGTT 4 42 0 TTTTAGGGTA 0.892207 -37 ****** * *** Masking position 4 Map Score: 24.2308 Number of sites scoring better than the average of aligned sites = 1626 Number in coding regions = 1373 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 GGACGCCACGCAAAAACCTAATAAAAAATA 1 28 1 CAAAAACCTA 0.763775 -71 AATACCAAACAAAACCCCCTAAAATTGAAA 2 41 0 AAAACCCCCT 0.863917 -103 GGGATTTAAAAAGCTTAAAAAGAGTTT 3 8 1 AAAAAGCTTA 0.856457 -293 CCACTATTAGAAAACTCTTTTTAAGCTTTT 3 19 0 AAAACTCTTT 0.965148 -282 TAGTGGCATTCAAACCCTTTAAAAAGGGTC 3 43 1 CAAACCCTTT 0.944447 -258 TTTTTGAAAATAAACTCCTAGACCCTTTTT 3 63 0 TAAACTCCTA 0.957714 -238 TTCAGCATTTCAAACTCCTTATAGAAATAT 3 115 0 CAAACTCCTT 0.97205 -186 AACAAAAGGTAAAACTCCTAGAACATTGTT 3 168 1 AAAACTCCTA 0.957686 -133 TTTTAAGCTTTAAACGCATAAAAGTTGCAT 3 219 0 TAAACGCATA 0.743064 -82 GTTTAAAGCTTAAAAACTTTAAGTCTTAAT 3 234 1 TAAAAACTTT 0.816604 -67 TAGTTTAACCTAAAATCTCTAATTAAGACT 3 255 0 TAAAATCTCT 0.793589 -46 TAAACTACCCTAAAATCTTTATGGGTAAAA 3 278 1 TAAAATCTTT 0.921689 -23 TTTTTTAGATAAAACGCTTTTTAAAGAATT 4 14 0 AAAACGCTTT 0.953915 -65 ********** Masking position 4 Map Score: 15.0027 Number of sites scoring better than the average of aligned sites = 1723 Number in coding regions = 1463 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 ATTGAGTTGAATTCAAGGAGTAAAAC 2 128 1 ATTCAAGGAG 0.94606 -16 TAAAAAGAGTTTTCTAATAGTGGCATTCAA 3 26 1 TTTCTAATAG 0.861668 -275 CTTTAAAAAGGGTCTAGGAGTTTATTTTCA 3 59 1 GGTCTAGGAG 0.976885 -242 AGGAGTTTATTTTCAAAAAGGATTCGTGTT 3 74 1 TTTCAAAAAG 0.882371 -227 TGTTTTCATATTTCTATAAGGAGTTTGAAA 3 108 1 TTTCTATAAG 0.917807 -193 GTCTAGAATCATTCTAGAAGCTTCAGCATT 3 136 0 ATTCTAGAAG 0.710671 -165 CCTTTTGTTTTGTCTAGAATCATTCTAGAA 3 147 0 TGTCTAGAAT 0.796058 -154 TTATAACAATGTTCTAGGAGTTTTACCTTT 3 172 0 GTTCTAGGAG 0.981685 -129 ********** Masking position 6 Map Score: 7.10563 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 84 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TTTGTTTGGTATTTTACTACATTTTGCGCT 2 58 1 ATTTTACTAC 0.843389 -86 TCAATAAATAATTTTAATTAACCCTACAGC 2 103 0 ATTTTAATTA 0.738788 -41 TACTCCTTGAATTCAACTCAATAAATAATT 2 120 0 ATTCAACTCA 0.590025 -24 GTTTTACTCCTTGAATTCAA 2 134 0 GTTTTACTCC 0.929312 -10 TGTTCTAGGAGTTTTACCTTTTGTTTTGTC 3 163 0 GTTTTACCTT 0.886901 -138 TTATAACATGATTTTACCAATCAATGCAAC 3 196 1 ATTTTACCAA 0.946151 -105 TTTTAGGGTAGTTTAACCTAAAATCTCTAA 3 263 0 GTTTAACCTA 0.924035 -38 GCATTTTACCCATAAAGATTTT 3 289 0 ATTTTACCCA 0.975363 -12 TTTAAAAAGCGTTTTATCTAAAAAACGATA 4 19 1 GTTTTATCTA 0.896014 -60 TTTCTCGCATATTTTATTTATTTTTAGAGT 4 55 0 ATTTTATTTA 0.83298 -24 ********** Masking position 6 Map Score: 5.16466 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 335 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 AAATATTGATAACGCTTCGTTTACATTCTT 1 63 1 AACGCTTCGT 0.954158 -36 TTCTTTCTTTAAGGATTAGTT 1 88 1 AAGGATTAGT 0.984199 -11 TATTTTCAAAAAGGATTCGTGTTTTTATGT 3 81 1 AAGGATTCGT 0.982093 -220 TAAAAACTTTAAGTCTTAATTAGAGATTTT 3 244 1 AAGTCTTAAT 0.883531 -57 ACGCTTTTTAAAGAATTAAT 4 1 0 AAGAATTAAT 0.873088 -78 ********** Masking position 6 Map Score: 0.914802 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 110 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ********** No masking Map Score: -9.14168e-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 7 ********** No masking Map Score: -9.14168e-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 8 ********** No masking Map Score: -9.14168e-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