AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_hpyl_reg_100.orf -o00780_hpyl_100.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 Purged sequences: HP0598 22 8-amino-7-oxononanoate synthase (bioF) Input sequences: #1 HP0030 108 H. pylori predicted coding region HP0030 #2 HP0170 74 H. pylori predicted coding region HP0170 #3 HP0171 60 peptide chain release factor RF-2 (prfB) #4 HP0174 300 H. pylori predicted coding region HP0174 #5 HP0599 71 hemolysin secretion protein precursor (hylB) #6 HP0600 163 multidrug resistance protein (spaB) #7 HP0654 296 conserved hypothetical protein #8 HP0655 82 protective surface antigen D15 #9 HP0976 128 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (bioA) #10 HP1010 300 polyphosphate kinase (ppk) #11 HP1011 36 dihydroorotate dehydrogenase (pyrD) #12 HP1406 166 biotin synthetase (bioB) #13 HP1435 70 protease IV (PspA) Motif number 1 CCAATTGGTTTTAAAAAGCGTTTTATAGTAACCAT 2 38 0 TTAAAAATTA 0.947573 -37 TTTTTTCTTTCCAAAAAGAATAAAACTAACACCAA 4 68 0 CCAAAAATAA 0.779562 -233 TAAAGAAGATTCAAAAATTCTCGATGCAATTATGA 4 108 1 TCAAAAATAT 0.897114 -193 ACATGCAATGCTAAAAAACCAAATATAAAGAATAA 4 199 0 CTAAAAAATA 0.72395 -102 TTATCCCATATTAAATAACTTCTATACTCTATTAA 4 233 1 TTAAATATAT 0.726667 -68 TTGTAAATTTTTAAAAATTTTCATACTCTCATTTA 7 73 0 TTAAAAATTA 0.948163 -224 CTAATTCTCATTAAATAGATTTTTATGATAAAATC 7 148 0 TTAAATATTA 0.809752 -149 TATATAATATGTAAAAAGCATTCTTAAATCTAAAA 7 230 1 GTAAAAATTT 0.665511 -67 ATTCTTAAATCTAAAAATGCTACAATGTTTATCTT 7 249 1 CTAAAAATAA 0.820823 -48 CTAATCATTCTTAAAAACGCTAAAAATTA 8 5 0 TTAAAAATAA 0.912638 -78 TCTAATCCCTTTAAAAAATCAAAAATATGAAATTC 9 17 1 TTAAAAAAAA 0.773431 -112 AAATTCAGGTTTAAACAACCTTATAGTAAAATCAA 9 46 1 TTAAACATTA 0.838767 -83 TATAGTAAAATCAAATAACCTTATTTTAACCAAAG 9 67 1 TCAAATATTT 0.782405 -62 GTTAAAAACTCTCTATAATAAGGATA 9 113 0 TTAAAAATAT 0.918636 -16 AAACGCTAAAAAAATTTTAAGCGATCTTTT 10 6 1 CTAAAAATAA 0.818197 -295 GAAGTTTTATTCAAAAAATGAAGTTTTACAAAAAA 10 51 1 TCAAAAAATT 0.8331 -250 TAGTTGTTGTTTAAAAACTCTTTTTTGTAAAACTT 10 71 0 TTAAAAATTT 0.951847 -230 TACTCCGCAATCAAAAAGGGAGATTGTAGCGCGAG 10 112 0 TCAAAAAATT 0.8331 -189 CCATGACTTTTTAAAAAAGCTTCAATGATTATCAT 10 215 1 TTAAAAATAA 0.912614 -86 TATAATCACACCAAACAAACTGATTTTTAAACATG 10 257 1 CCAAACATTT 0.655664 -44 AAACTGATTTTTAAACATGATGATTTAAAGGATTT 10 273 1 TTAAACATTT 0.849053 -28 ATATTATAACTCAAAAATCAAAATAAATCAAATTT 12 46 1 TCAAAAAATA 0.821956 -121 CTTTATTCCATTAAAAAATTTGATTTATTTTGATT 12 61 0 TTAAAAATTT 0.951895 -106 TTCCTTTGTTTTAAAAAAGTTGGTTTTTTGAGACT 12 137 0 TTAAAAATTT 0.951895 -30 ACTCTTATGGTCAAATATTAAGTTTAGGAAAAGCT 13 44 1 TCAAATAATT 0.540226 -27 ******* * ** Masking position 7 Map Score: 29.0765 Number of sites scoring better than the average of aligned sites = 1403 Number in coding regions = 1058 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 2 TTAGGGTTTATTTGGTATAATACCAAAACTTC 1 28 0 TTGTATAATA 0.974042 -81 TCCTTGCCAATTGGTTTTAAAAAGCGTTTTAT 2 47 0 TTGTTTAAAA 0.945037 -28 TTTGGTAATTTTGGGTATAATCCCAAAAGATT 5 26 1 TTGTATAATC 0.89766 -46 GTTGTAACTCCTTGTTATAAAAAACCCAAAGG 6 12 1 CTGTATAAAA 0.879961 -152 TTTAAAGGGCTTTGTTTTAAAAGCAAAATTTA 6 89 1 TTGTTTAAAA 0.944801 -75 AGCATGAAAATGGGCTATAATAAAGAAAATTT 6 125 1 TGGTATAATA 0.927413 -39 GCAATAAGATTTGGTATAAATTTTCTTTATT 6 143 0 TTGTATAAAT 0.741597 -21 TTAATGAGAATTAGGTAAAAAAAGGGGTTGGC 7 169 1 TTGTAAAAAA 0.826093 -128 AAGGGGATATTTTTATATAATATGTAAAAAGC 7 217 1 TTTTATAATA 0.787896 -80 TGTAGCATTTTTAGATTTAAGAATGCTTTTTA 7 241 0 TTGTTTAAGA 0.8007 -56 GCTACAATGTTTATCTTTAAAACGAAAGGGCA 7 267 1 TTTTTTAAAA 0.761941 -30 TTAAGAATGATTAGTTATAATAACGCTACTAA 8 26 1 TTGTATAATA 0.974077 -57 TTAATAACCTTTGGTTAAAATAAGGTTATTTG 9 78 0 TTGTAAAATA 0.84184 -51 GTTAAAAACTCTCTATAATAAGGATAATTT 9 109 0 CTTTATAATA 0.605173 -20 TTTGCTTAGTTGTTGTTTAAAAACTCTTTTTT 10 80 0 TGTTTTAAAA 0.521087 -221 TTTTGATTTTTGAGTTATAATATGCTTACATT 12 37 0 TGGTATAATA 0.927412 -130 CTTCTTTTTCTTTGCTATAATCAGTCTCAAAA 12 115 1 TTGTATAATC 0.897659 -52 AATCATTCCTTTGTTTTAAAAAAGTTGGTTT 12 146 0 TTGTTTAAAA 0.944801 -21 ** * ******* Masking position 6 Map Score: 20.9871 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 244 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 TCAAAGATAAAGCGCTACAATCTCGCTTAG 1 75 1 AGCGCTACAA 0.919587 -34 GTGCGCTAAAATGACAGCCGA 2 2 1 TGCGCTAAAA 0.873291 -73 GGCTTTTAACAATGCTATAATGATAAGTTC 3 14 1 AATGCTATAA 0.907083 -47 GATAACATGCAATGCTAAAAAACCAAATAT 4 208 0 AATGCTAAAA 0.93508 -93 CGAGCGCTTAAAATGTTTGGTA 5 3 1 AGCGCTTAAA 0.954805 -69 TTTAAAACAAAGCCCTTTAAAATTTCAAAC 6 80 0 AGCCCTTTAA 0.887901 -84 CATTATCATTTATGCTATAATTATGGGACA 7 37 0 TATGCTATAA 0.693071 -260 TAAATCTAAAAATGCTACAATGTTTATCTT 7 254 1 AATGCTACAA 0.846815 -43 CATTCTTAAAAACGCTAAAAATTA 8 5 0 AACGCTAAAA 0.970379 -78 AAGAACTCTAATCCCTTTAAAAAATCAAAA 9 11 1 ATCCCTTTAA 0.755865 -118 AAACGCTAAAAAAATTTTAAG 10 2 1 AACGCTAAAA 0.970379 -299 ACCCTAAAAGATCGCTTAAAATTTTTTTAG 10 16 0 ATCGCTTAAA 0.891985 -285 AACTTCATTTAACCCTAAAAGATCGCTTAA 10 27 0 AACCCTAAAA 0.947703 -274 TAGAAATCCTTTAAATCATCATGT 10 287 0 AATCCTTTAA 0.792912 -14 AATGGAATAAAGCCCTTAAAATCAAAAAGC 12 84 1 AGCCCTTAAA 0.921175 -83 CTTCTTTTTCTTTGCTATAATCAGTCTCAA 12 115 1 TTTGCTATAA 0.445313 -52 GATTTAATCCTTAAAACATTTGAAG 13 6 1 AATCCTTAAA 0.849607 -65 ********** Masking position 6 Map Score: 22.8145 Number of sites scoring better than the average of aligned sites = 1794 Number in coding regions = 1601 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 4 GAGATTGTAGCGCTTTATCTTTGAGCTTTCAG 1 67 0 CGCTTTCTTT 0.942538 -42 TGTAATAATATTTATTGTCTTTTTTGGTGTTA 4 45 1 TTTTTTCTTT 0.799503 -256 TTTTTGAATCTTCTTTAACATTTTTTTTCTTT 4 93 0 TTCTTACATT 0.928927 -208 TATTGTTGTATGCATTCTCTTTCCTTGGTTAC 4 159 1 TGCTTTCTTT 0.946061 -142 AGGGTTATTATTCTTTATATTTGGTTTTTTAG 4 192 1 TTCTTTATTT 0.875491 -109 CATTTTCATGCTCCTTTAAATTTTGCTTTTAA 6 105 0 CTCTTAAATT 0.629395 -59 CATTTACTTTTTCATTATCATTTATGCTATAA 7 47 0 TTCTTTCATT 0.973518 -250 TTTTCATACTCTCATTTACTTTTTCATTATCA 7 59 0 CTCTTACTTT 0.943905 -238 TTAGCCGGTGTTCTTTCTCATTTTTGTAAATT 7 99 0 TTCTTTCATT 0.973518 -198 CTTTTTTTACCTAATTCTCATTAAATAGATTT 7 161 0 CTATTTCATT 0.730379 -136 TTAAATCCTTATCTTTTATGATTTGA 11 21 0 ATCTTTCTTT 0.900689 -16 CAAAAAGCGCTTCTTTTTCTTTGCTATAATCA 12 106 1 TTCTTTCTTT 0.980623 -61 *** ** ***** Masking position 6 Map Score: 10.8521 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 471 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 TAAATGAAGTTTTGGTATTATACCAAATAA 1 23 1 TTTGGTATTA 0.927954 -86 CAGCGGGTCATTAGGGTTTATTTGGTATAA 1 40 0 TTAGGGTTTA 0.724421 -69 TTCCTTGCCAATTGGTTTTAAAAAGCGTTT 2 50 0 ATTGGTTTTA 0.793704 -25 TATTGTCTTTTTTGGTGTTAGTTTTATTCT 4 57 1 TTTGGTGTTA 0.932904 -244 ATTCTTTATATTTGGTTTTTTAGCATTGCA 4 201 1 TTTGGTTTTT 0.939435 -100 ATTTGAATCTTTTGGGATTATACCCAAAAT 5 33 0 TTTGGGATTA 0.824088 -39 CAAGGATGCCTTTGGGTTTTTTATAACAAG 6 22 0 TTTGGGTTTT 0.849435 -142 CATCCTTGCTTTTGGTTGGAACTATAATCG 6 44 1 TTTGGTTGGA 0.587433 -120 TCCTTTAAATTTTGCTTTTAAAACAAAGCC 6 96 0 TTTGCTTTTA 0.835906 -68 GCAATAAGATTTGGTATAAATTTTCTTTA 6 145 0 TTTGGTATAA 0.541095 -19 TTGATAAAGCTTAGATTTTATCATAAAAAT 7 135 1 TTAGATTTTA 0.677632 -162 TAAATTGCCCTTTCGTTTTAAAGATAAACA 7 274 0 TTTCGTTTTA 0.778803 -23 ATTTCATATTTTTGATTTTTTAAAGGGATT 9 20 0 TTTGATTTTT 0.818556 -109 AATAAGGTTATTTGATTTTACTATAAGGTT 9 62 0 TTTGATTTTA 0.933029 -67 AATCAGTTTGTTTGGTGTGATTATATAATG 10 252 0 TTTGGTGTGA 0.776377 -49 TTTGATTTATTTTGATTTTTGAGTTATAAT 12 48 0 TTTGATTTTT 0.818556 -119 AGAAGCGCTTTTTGATTTTAAGGGCTTTAT 12 90 0 TTTGATTTTA 0.933029 -77 ********** Masking position 2 Map Score: 18.7239 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 772 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 GCCGATAAATTATGGTTACTATAAAACGCTTT 2 27 1 TAGTTACTAT 0.94151 -48 CAACAATAATTACGAATATTATATTCATAATT 4 135 0 TAGATATTAT 0.91233 -166 CCTTGGTTACCAGGGTTATTATTCTTTATATT 4 181 1 CAGTTATTAT 0.88498 -120 CTCATATTGATAAGCTTACTATGTAAGATTAA 4 273 1 TAGTTACTAT 0.94151 -28 TGGTATAAATTTTCTTTATTATAGCCCATTTT 6 131 0 TTCTTATTAT 0.807361 -33 GTGTTGTTAGTAGCGTTATTATAACTAATCAT 8 32 0 TACTTATTAT 0.96375 -51 TAAAATCAAATAACCTTATTTTAACCAAAGGT 9 72 1 TACTTATTTT 0.807361 -57 TTATTAAAATTATCCTTATTATAGAGAGTTTT 9 103 1 TACTTATTAT 0.96375 -26 CCATTGAATGTAAGCATATTATAACTCAAAAA 12 31 1 TAGATATTAT 0.91233 -136 ** * ******* Masking position 7 Map Score: 5.35915 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 13 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CAAAACTTCATTTAAGGTTGGTTCTT 1 4 0 TTTAAGTGGT 0.937426 -105 AGCTTATCAATATGAGATTGATTAATAGAGTAT 4 256 0 TATGAGTGAT 0.834282 -45 GCATTCCTTATTTAAATTTGAATCTTTTGGGAT 5 45 0 TTTAAATGAT 0.948659 -27 CATTTTTAGATTTAAGAATGCTTTTTACATATT 7 235 0 TTTAAGTGCT 0.937427 -62 TTTTAGCGTTTTTAAGAATGATTAGTTATAATA 8 15 1 TTTAAGTGAT 0.982579 -68 CCTTAATAGATTTTAGCTTGAGTGTTGTTAGTA 8 52 0 TTTTAGTGAT 0.92132 -31 TATAAGGTTGTTTAAACCTGAATTTCATATTTT 9 38 0 TTTAAATGAT 0.948613 -91 AATCATCATGTTTAAAAATCAGTTTGTTTGGTG 10 265 0 TTTAAATCAT 0.728701 -36 AAGTTGGTTTTTTGAGACTGATTATAGCAAAGA 12 123 0 TTTGAGTGAT 0.969573 -44 ****** *** * Masking position 5 Map Score: 5.77366 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 115 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 CAACCTTAAATGAAGTTTTGGTATTATACC 1 17 1 TGAAGTTTTG 0.919095 -92 GGTTAAAGTTTGAAATTTTAAAGGGCTTTG 6 73 1 TGAAATTTTA 0.861233 -91 CTCATTTTTGTAAATTTTTAAAAATTTTCA 7 85 0 TAAATTTTTA 0.718592 -212 TTCATATTTTTGATTTTTTAAAGGGATTAG 9 18 0 TGATTTTTTA 0.852843 -111 TAGGGTTAAATGAAGTTTTATTCAAAAAAT 10 40 1 TGAAGTTTTA 0.971554 -261 ATTCAAAAAATGAAGTTTTACAAAAAAGAG 10 59 1 TGAAGTTTTA 0.971554 -242 ACTCCGACCATGACTTTTTAAAAAAGCTTC 10 208 1 TGACTTTTTA 0.895696 -93 ********** Masking position 3 Map Score: 4.41369 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 127 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TGTCTTTTTTGGTGTTAGTTTTATTCTTTT 4 60 1 GGTGTTAGTT 0.897082 -241 AACTTTAACCGATTATAGTTCCAACCAAAA 6 53 0 GATTATAGTT 0.946956 -111 AACTATAATCGGTTAAAGTTTGAAATTTTA 6 63 1 GGTTAAAGTT 0.951848 -101 CCTTTGTGTTGGTTTAAGTTGTCCCATAAT 7 18 1 GGTTTAAGTT 0.938204 -279 TTCCTTAATAGATTTTAGCTTGAGTGTTGT 8 57 0 GATTTTAGCT 0.808423 -26 TTTTTAAAGGGATTAGAGTTCTT 9 4 0 GATTAGAGTT 0.889446 -125 GGGTTATCGTTCAAATCATAA 11 2 1 GGTTATCGTT 0.919026 -35 ********** Masking position 3 Map Score: 1.14463 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 55 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ATAGAAGTTATTTAATATGGGATAACATGCA 4 227 0 TTAATATGGG 0.865856 -74 TAGTAAGCTTATCAATATGAGATTGATTAAT 4 263 0 ATAATATGAG 0.779278 -38 CTTACTATGTAAGATTAAGGGACT 4 287 1 AAATTAAGGG 0.658437 -14 TTAAAGGAGCATGAAAATGGGCTATAATAAA 6 118 1 ATAAAATGGG 0.966926 -46 CATTTATGCTATAATTATGGGACAACTTAAA 7 30 0 ATATTATGGG 0.919236 -267 AGAATTAGGTAAAAAAAGGGGTTGGCATCAA 7 175 1 AAAAAAGGGG 0.917738 -122 AGGGGTTGGCATCAATAGGGGGTTAAAAGGG 7 191 1 ATAATAGGGG 0.977526 -106 TCAATAGGGGGTTAAAAGGGGATATTTTTAT 7 202 1 GTAAAAGGGG 0.903632 -95 ATACTCCGCAATCAAAAAGGGAGATTGTAGC 10 117 0 ATAAAAAGGG 0.940008 -184 ** ******** Masking position 7 Map Score: 4.80512 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 247 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 AAACAGAACCTTTATGAGTGGGGTTT 3 45 0 AACCTTTATG 0.71032 -16 AATATTTATTGTCTTTTTTGGTGTTAGTTT 4 51 1 GTCTTTTTTG 0.845455 -250 TGTTAGTTTTATTCTTTTTGGAAAGAAAAA 4 72 1 ATTCTTTTTG 0.60357 -229 TTAAATTTGAATCTTTTGGGATTATACCCA 5 37 0 ATCTTTTGGG 0.863718 -35 AGTATCTCCTTTGTGTTGGTTTAAG 7 6 1 CTCCTTTGTG 0.92258 -291 CTTTTTCATTATCATTTATGCTATAATTAT 7 43 0 ATCATTTATG 0.88551 -254 GGTGTTCTTTCTCATTTTTGTAAATTTTTA 7 95 0 CTCATTTTTG 0.864492 -202 ATTTTAAGCGATCTTTTAGGGTTAAATGAA 10 24 1 ATCTTTTAGG 0.884322 -277 TGTTTAAAAACTCTTTTTTGTAAAACTTCA 10 69 0 CTCTTTTTTG 0.936163 -232 TTAAATCCTTATCTTTTATGATTTGAACGA 11 17 0 ATCTTTTATG 0.946749 -20 ********** Masking position 5 Map Score: 4.61987 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 263 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 ********** No masking Map Score: 5.50914e-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 13 ********** No masking Map Score: 5.50914e-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 14 ********** No masking Map Score: 5.50914e-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