AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifis_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 HP0281 50 tRNA-guanine transglycosylase (tgt) #2 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #3 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #4 HP1058 148 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) #5 HP1060 67 H. pylori predicted coding region HP1060 #6 HP1550 62 protein-export membrane protein (secD) #7 HP1551 47 conserved hypothetical secreted protein #8 HP1552 23 Na+/H+ antiporter (nhaA) #9 HP1553 248 helicase Motif number 1 ATCGCGCACATAAGAAGTAGAAAATAAAGAAGCA 2 29 1 TAAGAAGAAA 0.948696 -177 TTTTAAAGGATTAAAAAGCTAAAATACTGCTTCT 2 56 0 TTAAAATAAA 0.944562 -150 TTTAATCCTTTAAAAATACTGAAAAATTGAAGTT 2 75 1 TAAAAATAAA 0.987508 -131 CTCCAAATTTTAAAAAACTTCAATTTTTCAGTAT 2 90 0 TAAAAATAAT 0.959702 -116 TAAAACCCCCTAAAAGCCAGAAAAAACTCCAAAT 2 116 0 TAAAAGGAAA 0.95833 -90 TAGAATACCTTAAAAGAATTTAAAACCCCCTAAA 2 136 0 TAAAAGTAAA 0.970554 -70 ATAAAAAAATTAAAAAACTTTAAAACTTATTCTC 3 42 1 TAAAAATAAA 0.987101 -130 ATAAAAAACTTAAGAAAAAGAAAAGTTCAAGTTG 3 92 0 TAAGAAGAAA 0.948696 -80 TCAATTATACTAAAATAATTAAAATGACCGGTTA 4 50 1 TAAAATTAAA 0.955073 -99 AATGACCGGTTAAAATGGAGTAAAATTTTTACCC 4 72 1 TAAAATGAAA 0.936002 -77 TAAAAATCCTAAGTGTTAAATATA 4 135 0 TAAAAATAGT 0.839167 -14 CGATAAAATTTTAAAGGGTGTAAAAGTAGATTGT 5 43 1 TTAAAGGAAA 0.832249 -25 AGCGCGCCAATAAAAACGATTAAACGAGCGTTAA 6 17 0 TAAAAATAAA 0.987401 -46 CTAAAAATGCTATAATTTGAGATTA 7 2 1 TAAAAATTAA 0.856641 -46 AGACAACCTTAAAATTTTTAATT 8 2 0 TTAAAATAAT 0.837063 -22 TAGGTGTTCTTAAGAAAATTAAGAATCAAATGAG 9 52 0 TAAGAATAGA 0.854845 -197 TTGTTCCTATTAAAATGATAGAAAAACGACAAAA 9 127 1 TAAAATAAAA 0.693502 -122 TTACTTAAGCTAAAAAACCTTAATCTTTTGCTAT 9 171 0 TAAAAATAAT 0.959701 -78 ****** * *** Masking position 1 Map Score: 27.9523 Number of sites scoring better than the average of aligned sites = 1352 Number in coding regions = 1066 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 2 TTAAAGGATTAAAAAGCTAAAATACTGCTTCT 2 56 0 AAAAGCTAAA 0.96265 -150 TAATCCTTTAAAAATACTGAAAAATTGAAGTT 2 77 1 AAAAACTGAA 0.93915 -129 TCCAAATTTTAAAAAACTTCAATTTTTCAGTA 2 91 0 AAAAACTTAA 0.988999 -115 TAAAAGCCAGAAAAAACTCCAAATTTTAAAAA 2 108 0 AAAAACTCAA 0.93915 -98 AGAATACCTTAAAAGAATTTAAAACCCCCTAA 2 137 0 AAAAAATTAA 0.971527 -69 TAAAAAAATTAAAAAACTTTAAAACTTATTCT 3 43 1 AAAAACTTAA 0.988998 -129 TTGTATCAATAAAAAACTTAAGAAAAAGAAAA 3 102 0 AAAAACTTAG 0.919364 -70 ATTTAAAAAACAAACGATTTAATTCAAATTTA 3 140 1 CAAAGATTAA 0.893002 -32 AAACTTTTAACAAACAATTCAAGGGATTTGGC 4 15 0 CAAAAATTAA 0.894958 -134 CAATTATACTAAAATAATTAAAATGACCGGTT 4 51 1 AAAAAATTAA 0.971527 -98 CGCGCCAATAAAAACGATTAAACGAGCGTTAA 6 17 0 AAAAGATTAA 0.970951 -46 CTAAAAATGCTATAATTTGAGATTA 7 4 1 AAAAGCTAAA 0.96265 -44 AAGAGAACCAAAATAACTTTAAGGAGAATTCT 9 12 0 AAATACTTAA 0.88496 -237 TGTTCCTATTAAAATGATAGAAAAACGACAAA 9 128 1 AAAAGATAAA 0.907254 -121 TACTTAAGCTAAAAAACCTTAATCTTTTGCTA 9 172 0 AAAAACCTAA 0.919363 -77 GCTTAAGTAAAAAAGGCTTTTAGGTTATAATA 9 195 1 AAAAGCTTTA 0.882473 -54 **** **** ** Masking position 3 Map Score: 28.1921 Number of sites scoring better than the average of aligned sites = 1040 Number in coding regions = 844 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 TTTGTTCCTTAATTTCCTTAAAACTATCTCAA 2 184 0 TATTCTTAAA 0.974629 -22 TTTAACCCAAATGTCATTAAATGGAGGGGGT 3 9 1 AATTCTTAAA 0.966854 -163 TAAAGTTTTTTAATTTTTTTATACCCCCTCCAT 3 31 0 TATTTTTATA 0.571501 -141 CTTTAAAACTTATTCTCATTAATAGAACAAATC 3 59 1 TATTCTTAAT 0.91831 -113 AAATTTGGAATTGTATCAATAAAAAACTTAAGA 3 111 0 TTTTCATAAA 0.741456 -61 AATTTTTCCTTAAATTTGAATTAA 3 158 0 ATTTCTTAAA 0.956802 -14 TGTTTGTTAAAAGTTTCTTTCAATTATACTAAA 4 31 1 AATTCTTCAA 0.90211 -118 ATTGTAGTGTAATTTTCTTTCTAAACAAGA 5 8 0 AATTCTTCTA 0.840157 -60 CCCTTTAAAATTTTATCGTTATTGTAGTGTAAT 5 28 0 TTTTCTTATT 0.829598 -40 TTAATTTCCTTAAAAGATGTTTTA 7 34 0 TATTCTTAAA 0.974629 -14 GAGAATTCTCCTTAAAGTTATTTTGG 9 4 1 AATTCTTAAA 0.966854 -245 TTTGTCGTTTTTCTATCATTTTAATAGGAACAA 9 127 0 TTTTCTTTTA 0.658334 -122 AAAATTCTAATTTTGTCTTTATTATAACCTAAA 9 213 0 TTTTCTTATT 0.829614 -36 TGAGATCTATCCTAAAATTCTAATTTT 9 232 0 ATTTCTAAAA 0.685529 -17 ** * ** ***** Masking position 6 Map Score: 13.9294 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 397 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 AAAATACTGAAAAATTGAAGTTTTTTAAAATT 2 87 1 AAATTAAGTT 0.957716 -119 AAGTTTTTTAAAATTTGGAGTTTTTTCTGGCT 2 104 1 AAATTGAGTT 0.973059 -102 AAGAAAAAGAAAAGTTCAAGTTGGATTTGTTC 3 83 0 AAATTAAGTT 0.957716 -89 TTTGTTTTTTAAATTTGGAATTGTATCAATAA 3 122 0 AAATTGAATT 0.97476 -50 AATTTTTCCTTAAATTTGAATTAAATCGTTTG 3 150 0 TAATTGAATT 0.90558 -22 ACTATATTTAACACTTAGGATTTTTA 4 133 1 ACATTGGATT 0.871901 -16 AAAAATGCTATAATTTGAGATTAAAACATCTT 7 13 1 TAATTAGATT 0.849026 -35 GACAACCTTAAAATTTTTAATT 8 1 0 AAATTTAATT 0.856712 -23 TGTTCTTAAGAAAATTAAGAATCAAATGAGCA 9 50 0 AAATTAGAAT 0.742259 -199 ATTATAGCAAAAGATTAAGGTTTTTTAGCTTA 9 168 1 AAGTTAGGTT 0.798647 -81 TAATAAAGACAAAATTAGAATTTTAGGATAGA 9 222 1 AAATTGAATT 0.974747 -27 *** ** ***** Masking position 6 Map Score: 9.42139 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 146 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TGGCGTAATCATTTTTTAGGAAGT 1 5 0 ATTTTTTAGG 0.944818 -46 ATTTTTCAGTATTTTTAAAGGATTAAAAAG 2 72 0 ATTTTTAAAG 0.836126 -134 AGTTTTTTCTGGCTTTTAGGGGGTTTTAAA 2 122 1 GGCTTTTAGG 0.951782 -84 GGGTTTTAAATTCTTTTAAGGTATTCTAAC 2 142 1 TTCTTTTAAG 0.700287 -64 TCATTGAGATAGTTTTAAGGAAATTAAGGA 2 181 1 AGTTTTAAGG 0.935753 -25 AATGAGAATAAGTTTTAAAGTTTTTTAATT 3 49 0 AGTTTTAAAG 0.846811 -123 GATTTAATTCAAATTTAAGGAAAAATT 3 155 1 AAATTTAAGG 0.809461 -17 AATTGAAAGAAACTTTTAACAAACAATTCA 4 26 0 AACTTTTAAC 0.616778 -123 ATAACGATAAAATTTTAAAGGGTGTAAAAG 5 39 1 AATTTTAAAG 0.836127 -29 ATTGGCGCGCTTCTTTTAGGGGTAGGGTTT 6 40 1 TTCTTTTAGG 0.860264 -23 AGATTAAAACATCTTTTAAGGAAATTAA 7 30 1 ATCTTTTAAG 0.912499 -18 AATTAAAAATTTTAAGGTTGTCT 8 8 1 AATTTTAAGG 0.930765 -16 GAACCAAAATAACTTTAAGGAGAATTCTC 9 10 0 AACTTTAAGG 0.955702 -239 AAAGATTAAGGTTTTTTAGCTTAAGTAAAA 9 177 1 GTTTTTTAGC 0.63665 -72 AAGTAAAAAAGGCTTTTAGGTTATAATAAA 9 199 1 GGCTTTTAGG 0.951782 -50 GACAAAATTAGAATTTTAGGATAGATCTCA 9 229 1 GAATTTTAGG 0.782023 -20 ********** Masking position 5 Map Score: 21.8472 Number of sites scoring better than the average of aligned sites = 1480 Number in coding regions = 1285 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 6 TGATTACGCCATTATATCCAAGATTAAGGC 1 24 1 ATTATATCCA 0.895356 -27 CTTTTAAGGTATTCTAACAAGACTATATCA 2 154 1 ATTCTAACAA 0.8434 -52 TTCTAACAAGACTATATCATTGAGATAGTT 2 165 1 ACTATATCAT 0.833901 -41 TAAATTTGGAATTGTATCAATAAAAAACTT 3 115 0 ATTGTATCAA 0.908332 -57 ATATAGTGGCATTGTAGCATGACTTTATTA 4 110 0 ATTGTAGCAT 0.950103 -39 TTAATCTCAAATTATAGCATTTTTAG 7 7 0 ATTATAGCAT 0.966963 -41 ATAATTTGAGATTAAAACATCTTTTAAGGA 7 22 1 ATTAAAACAT 0.772721 -26 AAACCCTACGATTATAGCAAAAGATTAAGG 9 158 1 ATTATAGCAA 0.964801 -91 TTTTGTCTTTATTATAACCTAAAAGCCTTT 9 206 0 ATTATAACCT 0.913344 -43 ********** Masking position 6 Map Score: 6.29259 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 50 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 AGCCTTAATCTTGGATATAATGGCGTAATC 1 25 0 TTGGATATAA 0.701892 -26 CTGGCTTTTAGGGGGTTTTAAATTCTTTTA 2 130 1 GGGGGTTTTA 0.874912 -76 TTAATGACATTTGGGTTAAA 3 1 0 TTGGGTTAAA 0.911378 -171 ATTAAATGGAGGGGGTATAAAAAAATTAAA 3 26 1 GGGGGTATAA 0.987252 -146 CCGGTTAAAATGGAGTAAAATTTTTACCCA 4 77 1 TGGAGTAAAA 0.883086 -72 CTTTATTAGGGTGGGTAAAAATTTTACTCC 4 88 0 GTGGGTAAAA 0.97993 -61 AAATTTTAAAGGGTGTAAAAGTAGATTGTT 5 48 1 GGGTGTAAAA 0.93976 -20 ********** Masking position 10 Map Score: 2.78349 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 478 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ********** No masking Map Score: 9.90086e-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 9 ********** No masking Map Score: 9.90086e-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: 9.90086e-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