AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -irpoE_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 HP1010 300 polyphosphate kinase (ppk) #2 HP1011 36 dihydroorotate dehydrogenase (pyrD) #3 HP1015 111 H. pylori predicted coding region HP1015 #4 HP1017 97 amino acid permease (rocE) #5 HP1018 47 H. pylori predicted coding region HP1018 Motif number 1 CGCTAAAAAAATTTTAAGCGATCTTTTAGGG 1 14 1 ATTTTAACGA 0.832949 -287 AAACTTCATTTTTTGAATAAAACTTCATTTA 1 46 0 TTTTGAAAAA 0.929333 -255 AAAAATGAAGTTTTACAAAAAAGAGTTTTTA 1 64 1 TTTTACAAAA 0.685032 -237 CAAAAAAGAGTTTTTAAACAACAACTAAGCA 1 79 1 TTTTTAACAA 0.96923 -222 CGACCATGACTTTTTAAAAAAGCTTCAATGA 1 212 1 TTTTTAAAAA 0.710925 -89 AACAAACTGATTTTTAAACATGATGATTTAA 1 270 1 TTTTTAACAT 0.957646 -31 AAACATGATGATTTAAAGGATTTCTA 1 285 1 ATTTAAAGAT 0.869245 -16 ATCTTTTATGATTTGAACGATAACCC 2 6 0 ATTTGAAGAT 0.912689 -31 GTGGATAATGTTTTGCAAGAAATATCT 3 7 0 TTTTGCAGAA 0.934422 -105 CAACAAGCATTTTTTAATGAATTGCAACTCT 3 52 0 TTTTTAAGAA 0.98939 -60 TATTTTAAAAGAAGTTTTTAGCG 4 3 1 TTTTAAAGAA 0.971105 -95 TTTTAAGGTTTTTTTAAAGAACGCTAAAAAC 4 24 0 TTTTTAAGAA 0.97884 -74 AAGCGATAGTTTTTTAAGCGTTTTAAGGTTT 4 44 0 TTTTTAACGT 0.870783 -54 TTTTTAAAGATTAAATAGTAA 4 87 0 TTTTTAAGAT 0.975906 -11 AGTTTAGCAAATTTTAAGGAAGTAACCATG 5 28 1 ATTTTAAGAA 0.973081 -20 ******* *** Masking position 7 Map Score: 27.6218 Number of sites scoring better than the average of aligned sites = 1449 Number in coding regions = 1163 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 AAAGATCGCTTAAAATTTTTTTAGCGTTT 1 9 0 TAAAATTTTT 0.758758 -292 ATTTTTTGAATAAAACTTCATTTAACCCTAA 1 39 0 TAAAACTCAT 0.98609 -262 CTCTTTTTTGTAAAACTTCATTTTTTGAATA 1 58 0 TAAAACTCAT 0.98609 -243 AGTTGTTGTTTAAAAACTCTTTTTTGTAAAA 1 74 0 TAAAAATCTT 0.943479 -227 GAAGCTTTTTTAAAAAGTCATGGTCGGAGTA 1 207 0 TAAAAATCAT 0.981421 -94 AGAAATCCTTTAAATCATCATGTTTAAAAAT 1 279 0 TAAATCTCAT 0.935395 -22 TTAAATCCTTATCTTTTATGAT 2 25 0 TAAATCTTAT 0.883889 -12 ATATTTCTTGCAAAACATTATCCACATCCAC 3 13 1 CAAAACTTAT 0.85462 -99 TGCAATTCATTAAAAAATGCTTGTTGGGCTA 3 57 1 TAAAAATGCT 0.945881 -55 TAAAGAACGCTAAAAACTTCTTTTAAAATA 4 10 0 TAAAAATTCT 0.962926 -88 TAGCGTTCTTTAAAAAAACCTTAAAACGCTT 4 29 1 TAAAAAACCT 0.851234 -69 TTAAAACGCTTAAAAAACTATCGCTTGATCA 4 49 1 TAAAAACTAT 0.826625 -49 GTTACTTCCTTAAAATTTGCTAAACTTCAAA 5 23 0 TAAAATTGCT 0.864834 -25 ****** **** Masking position 4 Map Score: 16.8264 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 588 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 3 ATTTAACCCTAAAAGATCGCTTAAAATTTT 1 21 0 AAAAGATCGC 0.944727 -280 ACAACTAAGCAAACTCGCGCTACAATCTCC 1 99 1 AAACTCGCGC 0.971208 -202 AACTCGCGCTACAATCTCCCTTTTTGATTG 1 110 1 ACAATCTCCC 0.844588 -191 TGGCGCAGCCTGATTAGCGCGCACCCTTGG 1 147 1 TGATTAGCGC 0.885176 -154 GTCGTGGGTTTGAATCCCGCTACTCCGACC 1 187 1 TGAATCCCGC 0.896895 -114 AAGGGGCGAAAAAATAGCCCAACAAGCATT 3 72 0 AAAATAGCCC 0.973834 -40 TAACAGAATAGCCCCACACAAAGG 3 98 0 AGAATAGCCC 0.973313 -14 AAGGTTTTTTTAAAGAACGCTAAAAACTTC 4 21 0 TAAAGAACGC 0.780146 -77 AACGCTTAAAAAACTATCGCTTGATCAAGC 4 53 1 AAACTATCGC 0.951925 -45 ********** Masking position 3 Map Score: 5.11494 Number of sites scoring better than the average of aligned sites = 1132 Number in coding regions = 1064 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 TACAATCTCCCTTTTTGATTGCGGAGTATGGCG 1 119 1 CTTTGTTGCG 0.990848 -182 TTAGCGCGCACCCTTGGGGTGGGTGAGGTCGTG 1 160 1 CTTGGGTGGG 0.994616 -141 GTTTAAAAATCAGTTTGTTTGGTGTGATTATAT 1 256 0 CTTTGTTGGT 0.986496 -45 TGAATTGCAACTCTTTGTTTTGGTGGATGTGGA 3 33 0 CTTTGTTTGG 0.986495 -79 ATTTTTTCGCCCCTTTGTGTGGGGCTATTCTGT 3 87 1 CTTTGGTGGG 0.997557 -25 * **** ***** Masking position 5 Map Score: 4.50428 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 55 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 AAGGGAGATTGTAGCGCGAGTTTGCTTAGT 1 102 0 GTAGCGCGAG 0.977533 -199 CGCTAATCAGGCTGCGCCATACTCCGCAAT 1 136 0 GCTGCGCCAT 0.954818 -165 CCACCCCAAGGGTGCGCGCTAATCAGGCTG 1 152 0 GGTGCGCGCT 0.976738 -149 GCACCCTTGGGGTGGGTGAGGTCGTGGGTT 1 167 1 GGTGGGTGAG 0.916073 -134 CATGGTCGGAGTAGCGGGATTCAAACCCAC 1 190 0 GTAGCGGGAT 0.953146 -111 AAAAATGCTTGTTGGGCTATTTTTTCGCCC 3 69 1 GTTGGGCTAT 0.976975 -43 GCCCCTTTGTGTGGGGCTATTCTGTTA 3 95 1 GTGGGGCTAT 0.949643 -17 ********** Masking position 6 Map Score: 3.35329 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 289 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 CTTAAAATTTTTTTAGCGTTT 1 1 0 TTTTACGTTT 0.97586 -300 TTAAGCGATCTTTTAGGGTTAAATGAAGTTT 1 27 1 TTTTAGGTTA 0.937897 -274 AACATGATGATTTAAAGGATTTCTA 1 286 1 TTTAAGGATT 0.923422 -15 AATCCTTATCTTTTATGATTTGAACGATAAC 2 13 0 TTTTAGATTT 0.964325 -24 ACAAGCATTTTTTAATGAATTGCAACTCTTT 3 50 0 TTTAAGAATT 0.772851 -62 TAAAAGAAGTTTTTAGCGTTCTTTAAAAAAA 4 16 1 TTTTACGTTC 0.904261 -82 TTTTTAAGCGTTTTAAGGTTTTTTTAAAGAA 4 34 0 TTTTAGGTTT 0.98967 -64 GATCAAGCTCTTTTACTATTTAATCTTTAAA 4 75 1 TTTTATATTT 0.807015 -23 TTTTTAAAGATTAAATAGTAAA 4 86 0 TTTTAAGATT 0.92208 -12 CTTTTCTTAATTTTGAAGTTTAGCAAATTTT 5 12 1 TTTTGAGTTT 0.844967 -36 ***** ***** Masking position 3 Map Score: 11.2354 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 847 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 7 ********** No masking Map Score: -1.17707e-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 8 ********** No masking Map Score: -1.17707e-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 9 ********** No masking Map Score: -1.17707e-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