AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iargR_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 0.897646 -69 GTTATCAATATTTTAAAGTATTTTTTATTAGG 1 44 0 TTTTAAGATT 0.967739 -55 TACATTCTTTCTTTAAGGATTAGTT 1 84 1 CTTTAAGTTA 0.885876 -15 TCAATTTCAATTTTAGGGGGTTTTGTTTGGTA 2 37 1 TTTTAGGGTT 0.978473 -107 AATTAAAATTATTTATTGAGTTGAATTCAAGG 2 114 1 ATTTATGGTT 0.788747 -30 TAGAAAACTCTTTTTAAGCTTTTTAAATCCC 3 10 0 TTTTTAGTTT 0.979051 -291 CCTAGACCCTTTTTAAAGGGTTTGAATGCCAC 3 45 0 TTTTAAGGTT 0.992433 -256 AGGATTCGTGTTTTTATGTTTTCATATTTCTA 3 92 1 TTTTTAGTTT 0.979051 -209 TTTCATATTTCTATAAGGAGTTTGAAATGCTG 3 111 1 CTATAAGGTT 0.925507 -190 ATCAATGCAACTTTTATGCGTTTAAAGCTTAA 3 215 1 CTTTTAGGTT 0.974202 -86 AGACTTAAAGTTTTTAAGCTTTAAACGCATAA 3 228 0 TTTTTAGTTT 0.979051 -73 ATAAAACGCTTTTTAAAGAATTAAT 4 4 0 TTTTAAGATT 0.967739 -75 TTAGAGTGTATTTTATCGTTTTTTAGATAAAA 4 30 0 TTTTATGTTT 0.948345 -49 TTTTATTTATTTTTAGAGTGTATTTTATCGTT 4 42 0 TTTTAGGGTA 0.895061 -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 0.736203 -71 AATACCAAACAAAACCCCCTAAAATTGAAA 2 41 0 AAAACCCCCT 0.845672 -103 GGGATTTAAAAAGCTTAAAAAGAGTTT 3 8 1 AAAAAGCTTA 0.839676 -293 CCACTATTAGAAAACTCTTTTTAAGCTTTT 3 19 0 AAAACTCTTT 0.960774 -282 TAGTGGCATTCAAACCCTTTAAAAAGGGTC 3 43 1 CAAACCCTTT 0.936203 -258 TTTTTGAAAATAAACTCCTAGACCCTTTTT 3 63 0 TAAACTCCTA 0.951349 -238 TTCAGCATTTCAAACTCCTTATAGAAATAT 3 115 0 CAAACTCCTT 0.967763 -186 AACAAAAGGTAAAACTCCTAGAACATTGTT 3 168 1 AAAACTCCTA 0.951326 -133 TTTTAAGCTTTAAACGCATAAAAGTTGCAT 3 219 0 TAAACGCATA 0.714003 -82 GTTTAAAGCTTAAAAACTTTAAGTCTTAAT 3 234 1 TAAAAACTTT 0.793564 -67 TAGTTTAACCTAAAATCTCTAATTAAGACT 3 255 0 TAAAATCTCT 0.768454 -46 TAAACTACCCTAAAATCTTTATGGGTAAAA 3 278 1 TAAAATCTTT 0.911051 -23 TTTTTTAGATAAAACGCTTTTTAAAGAATT 4 14 0 AAAACGCTTT 0.949266 -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 GTTTTACTCCTTGAATTCAACTCAAT 2 128 0 CTCCTTGAAT 0.950212 -16 TTGAATGCCACTATTAGAAAACTCTTTTTA 3 26 0 CTATTAGAAA 0.871738 -275 TGAAAATAAACTCCTAGACCCTTTTTAAAG 3 59 0 CTCCTAGACC 0.978744 -242 AACACGAATCCTTTTTGAAAATAAACTCCT 3 74 0 CTTTTTGAAA 0.891122 -227 TTTCAAACTCCTTATAGAAATATGAAAACA 3 108 0 CTTATAGAAA 0.923648 -193 AATGCTGAAGCTTCTAGAATGATTCTAGAC 3 136 1 CTTCTAGAAT 0.701564 -165 TTCTAGAATGATTCTAGACAAAACAAAAGG 3 147 1 ATTCTAGACA 0.805226 -154 AAAGGTAAAACTCCTAGAACATTGTTATAA 3 172 1 CTCCTAGAAC 0.982292 -129 ********** Masking position 8 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 TTTGTTTGGTATTTTACTACATTTTGCGCTA 2 58 1 ATTTTACTCA 0.895695 -86 TCAATAAATAATTTTAATTAACCCTACAGCT 2 102 0 ATTTTAATAA 0.703696 -42 TACTCCTTGAATTCAACTCAATAAATAATTT 2 119 0 ATTCAACTAA 0.597762 -25 GTTTTACTCCTTGAATTCAAC 2 133 0 GTTTTACTCT 0.906762 -11 TAATAGTGGCATTCAAACCCTTTAAAAAGGG 3 40 1 ATTCAAACCT 0.387883 -261 TGTTCTAGGAGTTTTACCTTTTGTTTTGTCT 3 162 0 GTTTTACCTT 0.905085 -139 TTATAACATGATTTTACCAATCAATGCAACT 3 196 1 ATTTTACCAT 0.973457 -105 TTTTAGGGTAGTTTAACCTAAAATCTCTAAT 3 262 0 GTTTAACCAA 0.886275 -39 GCATTTTACCCATAAAGATTTTA 3 288 0 ATTTTACCAT 0.973461 -13 TTTAAAAAGCGTTTTATCTAAAAAACGATAA 4 19 1 GTTTTATCAA 0.860818 -60 TTTAGAGTGTATTTTATCGTTTTTTAGATAA 4 32 0 ATTTTATCTT 0.765839 -47 TTTCTCGCATATTTTATTTATTTTTAGAGTG 4 54 0 ATTTTATTAT 0.82409 -25 ******** ** Masking position 6 Map Score: 6.86897 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 806 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 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