AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_hpyl_reg_300.orf -o00630_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -x5 -e 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0026 198 citrate synthase (gltA) #2 HP0577 73 methylene-tetrahydrofolate dehydrogenase (folD) #3 HP0584 81 flagellar switch protein (fliN) #4 HP0585 228 endonuclease III (nth) #5 HP0779 127 aconitase B (acnB) #6 HP0795 111 trigger factor (tig) #7 HP0796 28 H. pylori predicted coding region HP0796 #8 HP0797 118 flagellar sheath adhesin hpaA #9 HP0801 72 molybdopterin converting factor, subunit 1 (moaD) #10 HP0802 88 GTP cyclohydrolase II (ribA) #11 HP0803 88 H. pylori predicted coding region HP0803 #12 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #13 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) #14 HP1100 65 6-phosphogluconate dehydratase #15 HP1435 70 protease IV (PspA) Motif number 1 GCATTCAAAAAAAGATTTTTAAGGGTTATA 1 62 0 AAAGATTTTT 0.708158 -137 TCTTTTTTTGAATGCGTGTTTAAAAGTAGC 1 77 1 AATGCGTGTT 0.95172 -122 GTGTTTAAAAGTAGCGGTTGGAAATAACTT 1 92 1 GTAGCGGTTG 0.720085 -107 TTTTAAAAACATTGCGTTTTTTCAAGTTAT 1 115 0 ATTGCGTTTT 0.96237 -84 TCTTGAAAGAGTAGAGTTTT 3 72 1 GTAGAGTTTT 0.89079 -10 CAAAAGAGAGAAAGCGTTTTTTAAGGGCTT 4 76 0 AAAGCGTTTT 0.96215 -153 AAGCCACTTGAATGCGGTTGATTTTAACCG 4 166 0 AATGCGGTTG 0.916374 -63 CTAAAAGTAAAAAGAGTTTTGTTATCATGG 5 61 1 AAAGAGTTTT 0.978513 -67 ATTAGTCAATAATGCGATTTAAAAAGGAGA 5 107 1 AATGCGATTT 0.891274 -21 CAGTTTATAAAAAGCGGTTTTAATTCTAGT 6 29 0 AAAGCGGTTT 0.955359 -83 TTTGACAACAAAAGCGTGTTGGTTGCTTCG 8 52 1 AAAGCGTGTT 0.96444 -67 TGAGTGCTTTAAAGAGGTTTTAAAAATATT 9 17 1 AAAGAGGTTT 0.963103 -56 AGAAAATTATAAAGAGTTTTGATAGAATAC 10 25 1 AAAGAGTTTT 0.978513 -64 TTTTTTAAAAGATGCGTTTTAAAACTAATT 10 57 1 GATGCGTTTT 0.975913 -32 CTTGACTTAAAAAGAGTTTATTATACCTTA 11 50 0 AAAGAGTTTA 0.817807 -39 ATTCAATAATATTGAGTTTTATAGAAAAAA 12 134 0 ATTGAGTTTT 0.91843 -37 GATGCGTATTTTACTAAAAT 13 1 1 GATGCGTATT 0.788036 -81 ********** Masking position 9 Map Score: 24.4303 Number of sites scoring better than the average of aligned sites = 1670 Number in coding regions = 1490 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 2 TAACCCTTAAAAATCTTTTTTTGAATGCGTG 1 64 1 AAATCTTTTT 0.956031 -135 TTTTTAAAAGAAATCATTTAATTTTTTGGCT 1 136 1 AAATCATTAA 0.72509 -63 GATAGCATTCAACTCCTAATTATAAGCCAAA 1 160 0 AACTCCTATT 0.676823 -39 TATATAATTAAAATCCTATTATTGTAGCAAA 2 45 0 AAATCCTATA 0.900962 -29 ATTTTACTATAAATTTTATAACAAATAAAGC 3 13 0 AAATTTTAAA 0.718883 -69 TTTGATTATAAAATCTTAATTTTACTATAAA 3 31 0 AAATCTTATT 0.936227 -51 AATCAAAGTCAAATCATTCTTGAAAGAGTAG 3 55 1 AAATCATTTT 0.766628 -27 TTAAAATCCTTTTTTGTATCGCAT 5 4 1 AAATCCTTTT 0.880971 -124 ATGATAACAAAACTCTTTTTACTTTTAGTTA 5 58 0 AACTCTTTTA 0.943235 -70 TTTTTTAAATTTTTGAAAACTAGAATT 6 7 1 AAATTTTTAA 0.791152 -105 CTAAAAAATTAAATTTTTGTATCATTATAGC 6 76 0 AAATTTTTTA 0.895734 -36 TTTGTTGTCAAAATGTTATTTTACCCTAACA 8 33 0 AAATGTTATT 0.722492 -86 TAGAAGTCTAAAATATTACAATCAAGGATAG 8 94 1 AAATATTAAA 0.578163 -25 GCATGATTTTAAATATTTTTAAAACCTCTTT 9 27 0 AAATATTTTA 0.82152 -46 CCCTTATATTAAATCTTTTAAAGCATGATTT 9 49 0 AAATCTTTAA 0.94589 -24 ATTCTATCAAAACTCTTTATAATTTTCTTAA 10 22 0 AACTCTTTTA 0.943235 -67 AGGTATAATAAACTCTTTTTAAGTCAAGCAA 11 52 1 AACTCTTTTA 0.943235 -37 ATTCTAGCGCAAATTTTAGTAAAATACGCAT 13 12 0 AAATTTTATA 0.852907 -70 ATTATATATTAAATCTTAATTAAAGGGGTAT 14 43 1 AAATCTTATT 0.936227 -23 ATTATACTTCAAATGTTTTAAGGATTAAATC 15 11 0 AAATGTTTAA 0.758486 -60 ******** ** Masking position 7 Map Score: 20.3868 Number of sites scoring better than the average of aligned sites = 989 Number in coding regions = 834 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 GTAACTATACTAGCGCAAAAATACTATATAAC 1 36 1 TGGCAAAAAT 0.733995 -163 CTCCTAATTATAAGCCAAAAAATTAAATGATT 1 147 0 TACCAAAAAA 0.723984 -52 ATCATGCGTTTAATGGAATAAAAACCTAGTTT 2 12 0 TAGGAATAAA 0.960491 -62 ATCCTATTATTGTAGCAAAAATCATGCGTTTA 2 32 0 TTGCAAAAAT 0.650562 -42 GTGGCTTTTTTCATGGAATAATGCAAAAGAAT 4 129 0 TAGGAATAAT 0.946984 -100 GATTAGGGCATTAGTCAATAATGCGATTTAAA 5 98 1 TATCAATAAT 0.835617 -30 TTAAAACAAATTAAGCTATAATGATACAAAAA 6 62 1 TAGCTATAAT 0.914639 -50 TTTTTAGCCATTAAGGAAAAAA 6 100 1 TAGGAAAAAA 0.940165 -12 AGACAAATAACGCATAAAAAAAGAACGC 7 8 1 TAGCATAAAA 0.87171 -21 TCTAAAGATGTTAGGGTAAAATAACATTTTGA 8 25 1 TAGGTAAAAT 0.76471 -94 ATATTTAAAATCATGCTTTAAAAGATTTAATA 9 42 1 TAGCTTTAAA 0.747447 -31 TGTAATGTTTTTAAGGTATAATAAACTCTTTT 11 39 1 TAGGTATAAT 0.834121 -50 TCTTTTTAAGTCAAGCAATAAAGTTTGCAACC 11 65 1 TAGCAATAAA 0.981062 -24 ACTCCCCCTATCATGCAAGAAATGCTCAAAGA 12 17 0 TAGCAAGAAA 0.898917 -154 AGGGGGAGTTTCATTCAATTAATTTAGAGGCT 12 40 1 TATCAATTAA 0.480051 -131 TGTATCTAAATAAAGCAATAAAGTAATAATCG 12 81 1 TAGCAATAAA 0.981062 -90 CTCCCTAGTTTTATTCAATAATATTGAGTTTT 12 144 0 TATCAATAAT 0.835617 -27 CCTTAATTCTTAATGCAAATAAAATCAATATC 13 55 0 TAGCAAATAA 0.81712 -27 TTCAAATGTTTTAAGGATTAAATC 15 3 0 TAGGATTAAA 0.831471 -68 * * ******** Masking position 1 Map Score: 19.0818 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 780 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 TTAAAAATCTTTTTTTGAATGCGTGTTTAA 1 70 1 TTTTTTGAAT 0.897193 -129 ATCATTTAATTTTTTGGCTTATAATTAGGA 1 148 1 TTTTTGGCTT 0.834061 -51 AAACTAGGTTTTTATTCCATTAAACGCATG 2 12 1 TTTATTCCAT 0.909311 -62 AACTTTGTCTTTAATGGCTTCATTGAGCGT 4 15 0 TTAATGGCTT 0.630195 -214 TTCAATGCATTCTTTTGCATTATTCCATGA 4 121 1 TCTTTTGCAT 0.815797 -108 TTAAAATCCTTTTTTGTATCGCATGGTAG 5 10 1 TTTTTTGTAT 0.726215 -118 TTTTTTCCTTAATGGCTAAA 6 102 0 TTTTTTCCTT 0.831549 -10 CTCGTTAAGTTTTATTGAATGTGTTGTAAT 11 15 1 TTTATTGAAT 0.909991 -74 GGTTGCAAACTTTATTGCTTGACTTAAAAA 11 67 0 TTTATTGCTT 0.952518 -22 TCTTTGAGCATTTCTTGCATGATAGGGGGA 12 17 1 TTTCTTGCAT 0.903306 -154 AGCCTCTAAATTAATTGAATGAAACTCCCC 12 42 0 TTAATTGAAT 0.747398 -129 CGATTATTACTTTATTGCTTTATTTAGATA 12 83 0 TTTATTGCTT 0.952518 -88 ACTCCCTAGTTTTATTCAATAATATTGAGT 12 147 0 TTTATTCAAT 0.742408 -24 GATATTGATTTTATTTGCATTAAGAATTAA 13 55 1 TTATTTGCAT 0.89884 -27 ********** Masking position 5 Map Score: 14.0618 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 608 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 TAGTTACTCAAACTTTAGAAAAAGGATAAACA 1 11 0 AATTTAAAAA 0.949361 -188 GGTTGGAAATAACTTGAAAAAACGCAATGTTT 1 107 1 AATTGAAAAA 0.690578 -92 TTTTACTATAAATTTTATAACAAATAAAGCCA 3 11 0 AATTTAAACA 0.747264 -71 ATAAAATCTTAATTTTACTATAAATTTTATAA 3 23 0 AATTTATATA 0.901898 -59 ATTAAAGACAAAGTTTATGAAATCGTAGAAAT 4 30 1 AATTTAGAAA 0.930308 -199 AGTTTCTTACAACTTAACTAAAAGTAAAAAGA 5 44 1 AATTAATAAA 0.631246 -84 TAGTTTTCAAAAATTTAAAAAA 6 1 0 AATTTAAAAA 0.949362 -111 GTTTTAATTCCAGTTTATAAAAAGCGGTTTTA 6 37 0 CATTTAAAAA 0.690578 -75 GTTGTTATAGAAGTCTAAAATATTACAATCAA 8 87 1 AATCTAAATA 0.475487 -32 ATGCTTTAAAAGATTTAATATAAGGGTAA 9 54 1 AGTTTATATA 0.853992 -19 GAGCTTAAAATTTAAGAAAATTATAAAGA 10 8 1 AATTTAGAAA 0.930308 -81 AGGCTCGTTAAGTTTTATTGAATGTGTTGTAA 11 12 1 AGTTTATGAA 0.759881 -77 GACTTAAAAAGAGTTTATTATACCTTAAAAAC 11 45 0 GATTTATATA 0.52254 -44 AATAATATTGAGTTTTATAGAAAAAAGAAATA 12 128 0 AGTTTAAGAA 0.735714 -43 CTAACTCCCTAGTTTTATTCAATAATATTGAG 12 148 0 AGTTTATCAA 0.632296 -23 TTCTAGCGCAAATTTTAGTAAAATACGCATC 13 10 0 AATTTATAAA 0.955183 -72 CCTTTAATTAAGATTTAATATATAATAATAAC 14 37 0 AGTTTATATA 0.853992 -29 GTCAAATATTAAGTTTAGGAAAAGCTGC 15 53 1 AATTTAGAAA 0.930308 -18 ** **** **** Masking position 4 Map Score: 14.0897 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 319 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 ATGCGTGTTTAAAAGTAGCGGTTGGAAATAA 1 88 1 AAAGTAGCGG 0.730931 -111 ATACCAAAAGAGAGAAAGCGTTTTTTAAGGG 4 79 0 AAGAAAGCGT 0.986839 -150 GAATAATGCAAAAGAATGCATTGAACCCCTT 4 115 0 AAGAATGCAT 0.754016 -114 GTTGATTTTAACCGAAAGCGTGGCTTTTTTC 4 149 0 ACGAAAGCGT 0.97699 -80 CCTTGTCATCAAAGAAAGCGT 4 218 1 AAGAAAGCGT 0.986839 -11 ATTCCAGTTTATAAAAAGCGGTTTTAATTCT 6 32 0 AAAAAAGCGG 0.963989 -80 ACATTTTGACAACAAAAGCGTGTTGGTTGCT 8 48 1 ACAAAAGCGT 0.963989 -71 ACCTTTTTTTAAAAGATGCGTTTTAAAACTA 10 53 1 AAAGATGCGT 0.907406 -36 * ********* Masking position 1 Map Score: 5.89294 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 355 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TACTTTTAAACACGCATTCAAAAAAAGATT 1 75 0 CACGCATTCA 0.8946 -124 GCCCTTAAAAAACGCTTTCTCTCTTTTGGT 4 78 1 AACGCTTTCT 0.955483 -151 GAATGCATTGAACCCCTTCATGGATACCAA 4 103 0 AACCCCTTCA 0.786612 -126 GAAGGGGTTCAATGCATTCTTTTGCATTAT 4 114 1 AATGCATTCT 0.336735 -115 TGAAAAAAGCCACGCTTTCGGTTAAAATCA 4 148 1 CACGCTTTCG 0.897226 -81 GTTAAAATCAACCGCATTCAAGTGGCTTTA 4 168 1 ACCGCATTCA 0.920211 -61 ATGATAACAAAACTCTTTTTACTTTTAGTT 5 59 0 AACTCTTTTT 0.706448 -69 TAGAATTAAAACCGCTTTTTATAAACTGGA 6 31 1 ACCGCTTTTT 0.875081 -81 AAGCAACCAACACGCTTTTGTTGTCAAAAT 8 50 0 CACGCTTTTG 0.776243 -69 TATTTTTAAAACCTCTTTAAAGCACTCATA 9 15 0 ACCTCTTTAA 0.573681 -58 AAAACATTACAACACATTCAATAAAACTTA 11 20 0 AACACATTCA 0.6106 -69 AGGTATAATAAACTCTTTTTAAGTCAAGCA 11 52 1 AACTCTTTTT 0.706448 -37 GAATGAAACTCCCCCTATCATGCAAGAAAT 12 26 0 CCCCCTATCA 0.470791 -145 CAATAACCCTTTTAGAGTGTTTTT 14 5 1 AACCCTTTTA 0.886085 -61 GAATACCCCTTTAATTAAGATTTA 14 52 0 ACCCCTTTAA 0.735398 -14 ********** Masking position 8 Map Score: 5.1842 Number of sites scoring better than the average of aligned sites = 2044 Number in coding regions = 1860 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 8 TAAGGGTTATATAGTATTTTTGCGCTAGTAT 1 42 0 ATAGTATTTT 0.414877 -157 TCTTTTTTTGAATGCGTGTTTAAAAGTAGCG 1 77 1 AATGCGTGTT 0.787329 -122 AACTTGAAAAAACGCAATGTTTTTAAAAGAA 1 117 1 AACGCAATTT 0.900322 -82 TATTCCATTAAACGCATGATTTTTGCTACAA 2 24 1 AACGCATGTT 0.980854 -50 AATCAAAGTCAAATCATTCTTGAAAGAGTAG 3 55 1 AAATCATTTT 0.746329 -27 CAAAAGAGAGAAAGCGTTTTTTAAGGGCTTC 4 75 0 AAAGCGTTTT 0.880187 -154 GAAGGGGTTCAATGCATTCTTTTGCATTATT 4 114 1 AATGCATTTT 0.910038 -115 CCTTTTTTGTATCGCATGGTAGCTAAAGTTT 5 18 1 ATCGCATGTA 0.716231 -110 TCCTTTTTAAATCGCATTATTGACTAATGCC 5 104 0 ATCGCATTTT 0.953434 -24 TAAATCTTTTAAAGCATGATTTTAAATATTT 9 40 0 AAAGCATGTT 0.964204 -33 TTAGTTTTAAAACGCATCTTTTAAAAAAAGG 10 54 0 AACGCATCTT 0.921484 -35 AAAAAGAAATATAGCATGTTTAATAACGATT 12 108 0 ATAGCATGTT 0.925762 -63 TTTTCTATAAAACTCAATATTATTGAATAAA 12 136 1 AACTCAATTT 0.533345 -35 ******** ** Masking position 1 Map Score: 10.7495 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 733 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 ATTTTATAACAAATAAAGCCA 3 2 0 AAATAAAGCC 0.932978 -80 AATGACGCTCAATGAAGCCATTAAAGACA 4 10 1 CAATGAAGCC 0.984797 -219 TCGCTAACTGCGATGAAGCCCTTAAAAAAC 4 61 1 CGATGAAGCC 0.985897 -168 CTTTAAGATCCCATGAAGCACAATACCTTG 4 193 1 CCATGAAGCA 0.927743 -36 AGATACAAATCGCTAAAGCCTCTAAATTAA 12 58 0 CGCTAAAGCC 0.941921 -113 ATTTGTATCTAAATAAAGCAATAAAGTAAT 12 78 1 AAATAAAGCA 0.824676 -93 ********** Masking position 6 Map Score: 2.76902 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 151 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ********** No masking Map Score: -2.44894e-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 11 ********** No masking Map Score: -2.44894e-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 12 ********** No masking Map Score: -2.44894e-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