AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iargR_hpyl_opreg_300.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 ACGCCACGCAAAAACCTAATAAAAAATACTTT 1 30 1 AACCTAATAA 0.964571 -69 CCTAATAAAAAATACTTTAAAATATTGATAAC 1 44 1 AACTTTAAAA 0.987813 -55 AACTAATCCTTAAAGAAAGAATGTAA 1 83 0 AACTTAAAGA 0.970187 -16 TACCAAACAAAACCCCCTAAAATTGAAATTGA 2 37 0 AACCCTAAAA 0.888972 -107 GGGATTTAAAAAGCTTAAAAAGAGTTTTCTA 3 10 1 AACTTAAAAA 0.989462 -291 GTGGCATTCAAACCCTTTAAAAAGGGTCTAGG 3 45 1 AACTTTAAAA 0.987813 -256 TAGAAATATGAAAACATAAAAACACGAATCCT 3 92 0 AACATAAAAA 0.963101 -209 CAGCATTTCAAACTCCTTATAGAAATATGAAA 3 111 0 AACCTTATAG 0.922263 -190 TTAAGCTTTAAACGCATAAAAGTTGCATTGAT 3 215 0 AACATAAAAG 0.929461 -86 TTATGCGTTTAAAGCTTAAAAACTTTAAGTCT 3 228 1 AACTTAAAAA 0.989462 -73 TAAAAACTTTAAGTCTTAATTAGAGATTTTAG 3 244 1 AACTTAATTA 0.846701 -57 AACTACCCTAAAATCTTTATGGGTAAAATGC 3 280 1 AACTTTATGG 0.867809 -21 ATTAATTCTTTAAAAAGCGTTTTAT 4 4 1 AACTTTAAAA 0.987813 -75 ** ******** Masking position 9 Map Score: 23.4112 Number of sites scoring better than the average of aligned sites = 1261 Number in coding regions = 1078 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 TATTTTTTATTAGGTTTTTGCGTGGCGTCC 1 28 0 TAGGTTTTTG 0.749544 -71 TTTCAATTTTAGGGGGTTTTGTTTGGTATT 2 41 1 AGGGGGTTTT 0.85457 -103 AAACTCTTTTTAAGCTTTTTAAATCCC 3 8 0 TAAGCTTTTT 0.847903 -293 AAAAGCTTAAAAAGAGTTTTCTAATAGTGG 3 19 1 AAAGAGTTTT 0.962941 -282 GACCCTTTTTAAAGGGTTTGAATGCCACTA 3 43 0 AAAGGGTTTG 0.94025 -258 AAAAAGGGTCTAGGAGTTTATTTTCAAAAA 3 63 1 TAGGAGTTTA 0.954477 -238 ATATTTCTATAAGGAGTTTGAAATGCTGAA 3 115 1 AAGGAGTTTG 0.969872 -186 AACAATGTTCTAGGAGTTTTACCTTTTGTT 3 168 0 TAGGAGTTTT 0.954452 -133 ATGCAACTTTTATGCGTTTAAAGCTTAAAA 3 219 1 TATGCGTTTA 0.728042 -82 ATTAAGACTTAAAGTTTTTAAGCTTTAAAC 3 234 0 AAAGTTTTTA 0.804759 -67 AGTCTTAATTAGAGATTTTAGGTTAAACTA 3 255 1 AGAGATTTTA 0.780645 -46 TTTTACCCATAAAGATTTTAGGGTAGTTTA 3 278 0 AAAGATTTTA 0.916276 -23 AATTCTTTAAAAAGCGTTTTATCTAAAAAA 4 14 1 AAAGCGTTTT 0.95159 -65 ********** Masking position 7 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 0.947434 -16 TAAAAAGAGTTTTCTAATAGTGGCATTCAA 3 26 1 TTTCTAATAG 0.864982 -275 CTTTAAAAAGGGTCTAGGAGTTTATTTTCA 3 59 1 GGTCTAGGAG 0.977501 -242 AGGAGTTTATTTTCAAAAAGGATTCGTGTT 3 74 1 TTTCAAAAAG 0.885254 -227 TGTTTTCATATTTCTATAAGGAGTTTGAAA 3 108 1 TTTCTATAAG 0.919741 -193 GTCTAGAATCATTCTAGAAGCTTCAGCATT 3 136 0 ATTCTAGAAG 0.707745 -165 CCTTTTGTTTTGTCTAGAATCATTCTAGAA 3 147 0 TGTCTAGAAT 0.799113 -154 TTATAACAATGTTCTAGGAGTTTTACCTTT 3 172 0 GTTCTAGGAG 0.981895 -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 ATATTTTAAAGTATTTTTTATTAGGTTTTT 1 39 0 GTATTTTTTA 0.885901 -60 GGGTTTTGTTTGGTATTTTACTACATTTTG 2 54 1 TGGTATTTTA 0.957276 -90 AAAGATTTTAGGGTAGTTTAACCTAAAATC 3 268 0 GGGTAGTTTA 0.960393 -33 GTGTATTTTATCGTTTTTTAGATAAAACGC 4 27 0 TCGTTTTTTA 0.923136 -52 TATTTTTAGAGTGTATTTTATCGTTTTTTA 4 37 0 GTGTATTTTA 0.977206 -42 GATTTTTCTCGCATATTTTATTTATTTTTA 4 59 0 GCATATTTTA 0.957276 -20 ********** Masking position 4 Map Score: 3.27947 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 404 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 CGTCCCCCCCTATTTTTTCAAA 1 3 0 TATTTTTTCA 0.965213 -96 TATTTTAAAGTATTTTTTATTAGGTTTTTG 1 38 0 TATTTTTTAT 0.788312 -61 ACTATTATCCTATTTTCAGACTTCAATTTC 2 15 1 TATTTTCAGA 0.954297 -129 TAATTAAAATTATTTATTGAGTTGAATTCA 2 113 1 TATTTATTGA 0.893508 -31 TCTAGGAGTTTATTTTCAAAAAGGATTCGT 3 71 1 TATTTTCAAA 0.902616 -230 TTCGTGTTTTTATGTTTTCATATTTCTATA 3 96 1 TATGTTTTCA 0.895149 -205 ATATTTTATTTATTTTTAGAGTGTATTTTA 4 47 0 TATTTTTAGA 0.968785 -32 ********** Masking position 2 Map Score: 3.52744 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 273 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 GTCCCCCCCTATTTTTTCAAA 1 2 0 ATTTTTTCAA 0.729503 -97 TTTGTTTGGTATTTTACTACATTTTGCGCT 2 58 1 ATTTTACTAC 0.948942 -86 GTTTTACTCCTTGAATTCAA 2 134 0 GTTTTACTCC 0.873512 -10 GCTTAAAAAGAGTTTTCTAATAGTGGCATT 3 23 1 AGTTTTCTAA 0.841215 -278 TTATAACATGATTTTACCAATCAATGCAAC 3 196 1 ATTTTACCAA 0.964379 -105 GCATTTTACCCATAAAGATTTT 3 289 0 ATTTTACCCA 0.970321 -12 GATTTTTCTCGCATATTTTAT 4 68 0 ATTTTTCTCG 0.903534 -11 ********** Masking position 5 Map Score: 1.4406 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 398 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 CCTATTTTCAGACTTCAATTTCAATTTTAG 2 23 1 GACTTCAATT 0.915142 -121 TTTACTCCTTGAATTCAACTCAATAAATAA 2 122 0 GAATTCAACT 0.986498 -22 TAAAGGGTTTGAATGCCACTATTAGAAAAC 3 34 0 GAATGCCACT 0.985138 -267 TTTTACCAATCAATGCAACTTTTATGCGTT 3 207 1 CAATGCAACT 0.976777 -94 ********** Masking position 4 Map Score: 0.373998 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 17 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 AAGAATGTAAACGAAGCGTTATCAATATTT 1 63 0 ACGAAGCGTT 0.990886 -36 AACTAATCCTTAAAGAAAGAA 1 88 0 ACTAATCCTT 0.962399 -11 ACATAAAAACACGAATCCTTTTTGAAAATA 3 81 0 ACGAATCCTT 0.981942 -220 TTAATTCTTTAAAAAGCGTTTTATCTAAAA 4 12 1 AAAAAGCGTT 0.909567 -67 ********** Masking position 5 Map Score: 0.517225 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 66 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ********** 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 10 ********** 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 11 ********** 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