AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ilexA_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 HP0153 98 recombinase (recA) #2 HP0705 182 excinuclease ABC subunit A (uvrA) #3 HP0883 25 Holliday junction DNA helicase (ruvA) #4 HP0884 167 H. pylori predicted coding region HP0884 #5 HP1058 148 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) #6 HP1085 66 H. pylori predicted coding region HP1085 #7 HP1088 46 transketolase A (tktA) #8 HP1114 69 excinuclease ABC subunit B (uvrB) #9 HP1116 300 H. pylori predicted coding region HP1116 #10 HP1394 187 conserved hypothetical protein #11 HP1483 26 gerC2 protein (gerC2) #12 HP1490 103 hemolysin #13 HP1491 138 phosphate permease Motif number 1 AGTCCTTTTATTATAATAGATTTTAGGCTAGGAT 1 36 1 TTATATATTT 0.720096 -63 CAAGCAAATATTTTTAACTCTTATGAATAAGAAA 2 70 1 TTTTAACTTT 0.969567 -113 AATGGTTTTATTATCATTTCTTATTCATAAGAGT 2 86 0 TTATATCTTT 0.92817 -97 TAATAGCTCCTTTTAATCCATTTTCTTATTTTAA 2 133 1 TTTTATATTT 0.893465 -50 TTTTATCCCTTTTTTATTTCTTGTT 3 2 0 TTTTATCTTT 0.976812 -24 AAGCTGTTGGTTAAAAATATTTTTTTTAGCATAC 4 54 1 TTAAAATTTT 0.497314 -114 TATTACCTAATTTTCAGTGTTTTTTTGTTAGCAT 4 98 1 TTTTAGTTTT 0.788159 -70 ATATTTCTTTTTTCAAATTCTTATATTATACCAT 4 130 1 TTTCAACTTT 0.7716 -38 TTTTTAATCCTTAAATGGTATAAT 4 154 0 TTTTAACTTA 0.907172 -14 TAACCGGTCATTTTAATTATTTTAGTATAATTGA 5 50 0 TTTTATTTTA 0.878583 -99 AATTTTTCCATTTTTAAGGTTTTTGAGAGTCATT 7 21 0 TTTTAATTTT 0.946922 -26 TTTAGGGGTATTATAGTGGTTTTTTAACACGCCT 8 29 0 TTATGTTTTT 0.560063 -41 TAGCGTCGTTTTTAAAAAGCTTGTGAAAACCGCT 9 134 0 TTTAAACTTT 0.852056 -167 TAAAAATAATTTTTTGTTACTTGAAAAGAATACC 10 22 1 TTTTGTCTTA 0.694508 -166 ATTTAATCGTTTTTAATTATTTTTTGGGTATTCT 10 48 0 TTTTATTTTT 0.959331 -140 GTTTTTATTTTTATTAATGTTTCATTATTTAATC 10 74 0 TTATAATTTA 0.626695 -114 AAATAAAAACTTTTCATGAATTTTACATAAGATG 10 98 1 TTTTATATTT 0.893465 -90 AAAAAGGGGGTTTTAATTGCTTTTTTATCATCTT 10 126 0 TTTTATCTTT 0.976812 -62 AAACCCCCTTTTTTAAAATTTTGTTTCAAGCTTT 10 147 1 TTTTAATTTT 0.946922 -41 GACTTTTCTTTTTTCATGGCTTGTCT 11 3 0 TTTTATCTTT 0.976812 -24 GGTTTTTGAAGGCTTGATTTTTAAAGT 12 4 1 TTTTAACTTA 0.907175 -100 ATTCTGAGATTTTATATATTTTATATTTATCGTT 12 61 1 TTTAATTTTT 0.810018 -43 **** ** *** * Masking position 11 Map Score: 29.4307 Number of sites scoring better than the average of aligned sites = 1254 Number in coding regions = 1003 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 2 TATCTTTAAAATTGTCTCATAAAATAATAGCAT 2 24 1 ATTTCCAAAA 0.895807 -159 AAAAGGAGCTATTATACTTCAAAAAAGAATGGT 2 114 0 ATTTATTAAA 0.756677 -69 AAAAAGAAATATGCTAACAAAAAAACACTGAAA 4 109 0 ATGTACAAAA 0.944524 -59 TTGAAAGAAACTTTTAACAAACAATTCAAGGGA 5 21 0 CTTTACAACA 0.821552 -128 TAAAATCTATATTATAACTAAAAGGGGGTTTT 6 10 0 ATTTACTAAA 0.982316 -57 TATAGATTTTATTTTAGCTAAAAATGGCATGGG 6 32 1 ATTTACTAAA 0.982316 -35 TTTGAGAGTCATTTTAACACAAA 7 1 0 ATTTACAAAA 0.984027 -46 AACACGCCTTATTCAATCTCAAAAAAA 8 5 0 ATTAACTAAA 0.90634 -65 GTGGCTTTCTACCAAAAACTTTAGTCAG 9 6 1 TTTTACAAAA 0.928258 -295 AAACAGCAAAATTATAGCAAGCAATGTTTTCTG 9 36 0 ATTTACAGCA 0.784431 -265 ACATACTATTGTAGCTTAAAGCTTGAAACA 10 168 0 ATTTACTAAA 0.982316 -20 AAATCTCAGAATTTTAACATAAAAGATTAAGCC 12 40 0 ATTTACAAAA 0.984027 -64 AACTTTAAACCTAAAACCTAACGATA 12 88 0 TTTAACTAAA 0.736642 -16 GGCTCATTATATGGTATCTTAAAGTAAAATTTT 13 28 0 ATGTACTAAA 0.937419 -111 TAATGAGCCATTTTTATCAAACAACGCTTTTTA 13 52 1 TTTTACAACA 0.886586 -87 *** ** ** *** Masking position 13 Map Score: 19.6397 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 145 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 ACATTCCTATCTTTAAAATTGTCTCATAAA 2 17 1 CTTTAAAATT 0.8776 -166 TATTCATAAGAGTTAAAAATATTTGCTTGA 2 69 0 AGTTAAAAAT 0.771262 -114 GCAAGAGTTTCCTTAAAATAAGAAAATGGA 2 149 0 CCTTAAAATA 0.633909 -34 CAAATCCCGTAAAAAGCCAAAAATCC 4 7 1 CCGTAAAAAG 0.68139 -161 CTAAGCTGTTGGTTAAAAATATTTTTTTTA 4 52 1 GGTTAAAAAT 0.930548 -116 TTGAATTGTTTGTTAAAAGTTTCTTTCAAT 5 25 1 TGTTAAAAGT 0.794724 -124 TAAAATGACCGGTTAAAATGGAGTAAAATT 5 69 1 GGTTAAAATG 0.802763 -80 TTATTAGGGTGGGTAAAAATTTTACTCCAT 5 86 0 GGGTAAAAAT 0.712587 -63 AAATCCTAAGTGTTAAATATAGTGGCATTG 5 126 0 TGTTAAATAT 0.62 -23 TTTGTGTTAAAATGACTCTCAAAA 7 5 1 TGTTAAAATG 0.889651 -42 CTCTCAAAAACCTTAAAAATGGAAAAATTT 7 26 1 CCTTAAAAAT 0.954311 -21 GAATAAGGCGTGTTAAAAAACCACTATAAT 8 24 1 TGTTAAAAAA 0.800149 -46 CTATAATACCCCTAAAAAATGCGAGTTTAA 8 47 1 CCTAAAAAAT 0.562281 -23 TTAGCGTCGTTTTTAAAAAGCTTGTGAAAA 9 139 0 TTTTAAAAAG 0.847504 -162 GTGTGATTCCTTAAAAATAATTTTTTGT 10 9 1 CCTTAAAAAT 0.954311 -179 AAACCCCCTTTTTTAAAATTTTGTTTCAAG 10 147 1 TTTTAAAATT 0.846913 -41 TTAAGCCTAACTTTAAAAATCAAGCCTTCA 12 17 0 CTTTAAAAAT 0.928728 -87 TAATCTTTTATGTTAAAATTCTGAGATTTT 12 44 1 TGTTAAAATT 0.935801 -60 TTTTTAAAACTCTCTTTAAAA 13 2 1 TTTTAAAACT 0.594987 -137 TTAAAACTCTCTTTAAAATTTTACTTTAAG 13 14 1 CTTTAAAATT 0.8776 -125 AAGCGTTGTTTGATAAAAATGGCTCATTAT 13 51 0 TGATAAAAAT 0.642929 -88 CTTGAGCCACTCTTAAAAAGCGTTGTTTGA 13 68 0 TCTTAAAAAG 0.899117 -71 ********** Masking position 5 Map Score: 18.7537 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 969 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 AGTAAAATCCTTTTGTGATAGG 1 2 1 GTAAAATCCT 0.766714 -97 AAATCCTAGCCTAAAATCTATTATAATAAAA 1 41 0 CTAAAATCTT 0.702757 -58 AGAAATGATAATAAAACCATTCTTTTTTGAA 2 99 1 ATAAAACCAT 0.974893 -84 CTCTTGCAACATAAAACCATT 2 172 1 ATAAAACCAT 0.974893 -11 ATCCTAGAGCATAAAATCCCTAAGCTGTTGG 4 33 1 ATAAAATCCT 0.95036 -135 TAGGTAATAAATACAACCAGTATGCTAAAAA 4 76 0 ATACAACCAT 0.849946 -92 ATATGCTAACAAAAAAACACTGAAAATTAGG 4 103 0 AAAAAAACAT 0.672769 -65 TTTAGCTAAAATAAAATCTATATTATAACTA 6 23 0 ATAAAATCTT 0.88208 -44 TCCTTGCTAAAACCCATGCCATTTTTA 6 50 0 CTAAAACCCT 0.942735 -17 AAGGCGTGTTAAAAAACCACTATAATACCCC 8 28 1 AAAAAACCAT 0.879322 -42 AAAAACCACTATAATACCCCTAAAAAATGCG 8 39 1 ATAATACCCT 0.847219 -31 ATTAATAAAAATAAAAACTTTTCATGAATTT 10 90 1 ATAAAAACTT 0.85179 -98 ATTGGATAGAATAAGACCACTATTAGAACAA 13 103 1 ATAAGACCAT 0.859637 -36 ATCGTCATAAAAACCTTGTTCTAATAG 13 122 0 ATAAAAACCT 0.936318 -17 ********* * Masking position 6 Map Score: 15.8703 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 523 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 GCCTAAAATCTATTATAATAAAAGGACTTACCC 1 31 0 TATTTATAAA 0.89648 -68 TTGATTTGTTTATTCTATCAAATCCTAGCCTAA 1 58 0 TATTTACAAT 0.907278 -41 TAAATTACCTTATTGAATTTGATTTGTTTATTC 1 76 0 TATTAATTAT 0.355436 -23 TAAAAGGAGCTATTATACTTCAAAAAAGAATGG 2 115 0 TATTTATTAA 0.909428 -68 AAAAAAGAAATATGCTAACAAAAAAACACTGAA 4 110 0 TATGTACAAA 0.906582 -58 TCATTTTAATTATTTTAGTATAATTGAAAGAAA 5 44 0 TATTTATAAA 0.896559 -105 ATAAAATCTATATTATAACTAAAAGGGGGTTTT 6 11 0 TATTTACTAA 0.97483 -56 ATATAGATTTTATTTTAGCTAAAAATGGCATGG 6 31 1 TATTTACTAA 0.974832 -36 TTTTGAGAGTCATTTTAACACAAA 7 2 0 CATTTACAAA 0.840597 -45 TAACACGCCTTATTCAATCTCAAAAAAA 8 6 0 TATTAACTAA 0.879057 -64 ACATACTATTGTAGCTTAAAGCTTGAAAC 10 169 0 TATTTACTAA 0.974832 -19 AAAATCTCAGAATTTTAACATAAAAGATTAAGC 12 41 0 AATTTACAAA 0.780606 -63 TGGCTCATTATATGGTATCTTAAAGTAAAATTT 13 29 0 TATGTACTAA 0.918319 -110 ATAGTGGTCTTATTCTATCCAATTAGCCCTTGA 13 93 0 TATTTACCAT 0.750674 -46 **** ** ** ** Masking position 7 Map Score: 15.4541 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 61 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 TCTATCAAATCCTAGCCTAAAATCTATTAT 1 48 0 CCTAGCCTAA 0.985572 -51 AAAATTTTTACCCACCCTAATAAAGTCATG 5 93 1 CCCACCCTAA 0.954427 -56 TTGCTGTTTGCCTTGCCTAAATACTCCCCC 9 60 1 CCTTGCCTAA 0.989887 -241 TAAATACTCCCCCTGCCTTAACAAACCCCC 9 77 1 CCCTGCCTTA 0.98662 -224 GGTCGCTAAACCTTGGCTTAAATTTTTCGT 9 197 0 CCTTGGCTTA 0.950981 -104 ********** Masking position 8 Map Score: 3.18481 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CATAAAATAATAGCATGTTTATCCTTAATC 2 41 1 TAGCATGTTT 0.80348 -142 TTTTATGCTCTAGGATTTTTGGCTTTTTAC 4 19 0 TAGGATTTTT 0.887089 -149 ACCAACAGCTTAGGGATTTTATGCTCTAGG 4 35 0 TAGGGATTTT 0.882031 -133 GTTTTTTTGTTAGCATATTTCTTTTTTCAA 4 116 1 TAGCATATTT 0.387819 -52 ATTTAACACTTAGGATTTTTA 5 138 1 TAGGATTTTT 0.887089 -11 TTATAACTAAAAGGGGGTTTT 6 2 0 AAGGGGGTTT 0.940731 -65 TTTCCATTTTTAAGGTTTTTGAGAGTCATT 7 21 0 TAAGGTTTTT 0.648485 -26 AGGGGTATTATAGTGGTTTTTTAACACGCC 8 30 0 TAGTGGTTTT 0.929499 -40 TCGCATTTTTTAGGGGTATTATAGTGGTTT 8 41 0 TAGGGGTATT 0.898309 -29 TTTGTAAATTTAGGGGGTTTGTTAAGGCAG 9 89 0 TAGGGGGTTT 0.987296 -212 AAACAATAGCGAGCGGTTTTCACAAGCTTT 9 123 1 GAGCGGTTTT 0.870099 -178 TTTTTCGTTGTAGCGGGCTTTAAACTCTCG 9 175 0 TAGCGGGCTT 0.926238 -126 AATTTTAAAAAAGGGGGTTTTAATTGCTTT 10 137 0 AAGGGGGTTT 0.940731 -51 CTTGTTCTAATAGTGGTCTTATTCTATCCA 13 105 0 TAGTGGTCTT 0.8064 -34 ********** Masking position 2 Map Score: 12.6855 Number of sites scoring better than the average of aligned sites = 1839 Number in coding regions = 1600 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 8 ATGCTCTAGGATTTTTGGCTTTTTACGGGATT 4 13 0 ATTTTTGTTT 0.883189 -155 TTTATTACCTAATTTTCAGTGTTTTTTTGTTA 4 96 1 AATTTTCTGT 0.867136 -72 TTTTGTTAGCATATTTCTTTTTTCAAATTCTT 4 120 1 ATATTTCTTT 0.890887 -48 CAAATTTTTCCATTTTTAAGGTTTT 7 32 0 ATTTTTCTTT 0.975202 -15 GCTTGCTATAATTTTGCTGTTTGCCTTGCCTA 9 47 1 ATTTTGCTTT 0.92367 -254 CTTGGCTTAAATTTTTCGTTGTAGCGGGCTTT 9 184 0 ATTTTTCTGT 0.96359 -117 GACTTTTCTTTTTTCATGGCTTG 11 14 0 ACTTTTCTTT 0.934981 -13 ******* *** Masking position 1 Map Score: 1.6076 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 120 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 TTTATTATCATTTCTTATTCATAAGAGTTA 2 84 0 TTTCTTATTC 0.765748 -99 TAATAAAACCATTCTTTTTTGAAGTATAAT 2 107 1 ATTCTTTTTT 0.789063 -76 TTTAATCCATTTTCTTATTTTAAGGAAACT 2 144 1 TTTCTTATTT 0.945529 -39 TTTTATCCCTTTTTTATTTCTTGTT 3 7 0 TTTTTTATTT 0.901249 -19 TGGTTAAAAATATTTTTTTTAGCATACTGG 4 61 1 TATTTTTTTT 0.662934 -107 ATTTTCAGTGTTTTTTTGTTAGCATATTTC 4 107 1 TTTTTTTGTT 0.744573 -61 TGTTAGCATATTTCTTTTTTCAAATTCTTA 4 123 1 TTTCTTTTTT 0.967149 -45 CATGAAAAGTTTTTATTTTTATTAATGTTT 10 86 0 TTTTATTTTT 0.793416 -102 GGGGTTTTAATTGCTTTTTTATCATCTTAT 10 124 0 TTGCTTTTTT 0.847194 -64 GACTTTTCTTTTTTCATGGCTTGT 11 13 0 TTTCTTTTTT 0.967149 -14 ATTTTATATATTTTATATTTATCGTTAGGT 12 69 1 TTTTATATTT 0.693671 -35 ********** Masking position 6 Map Score: 9.57139 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 633 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 10 AGTAAAATCCTTTTGTGATAGGGT 1 4 1 AAATCCTTTT 0.791322 -95 TGTGATAGGGTAAGTCCTTTTATTATAATAG 1 24 1 TAATCCTTTT 0.960187 -75 ATAGCTCCTTTTAATCCATTTTCTTATTTTA 2 135 1 TTATCCATTT 0.973902 -48 TTTTATCCCTTTTTTATTTCTTG 3 13 0 TTACCCTTTT 0.924307 -13 AATTCTTATATTATACCATTTAAGGATTAAA 4 145 1 TTAACCATTT 0.869921 -23 GGTAAAAATTTTACTCCATTTTAACCGGTCA 5 74 0 TTATCCATTT 0.973903 -75 CAAATTTTTCCATTTTTAAGGTTTT 7 32 0 TTTTCCATTT 0.854712 -15 GTTTCATTATTTAATCGTTTTTAATTATTTT 10 59 0 TTATCGTTTT 0.869795 -129 AAGGGGGTTTTAATTGCTTTTTTATCATCTT 10 126 0 TAATGCTTTT 0.777911 -62 *** ******* Masking position 9 Map Score: 5.77746 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 123 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 11 ********** No masking Map Score: -7.01005e-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 12 ********** No masking Map Score: -7.01005e-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 13 ********** No masking Map Score: -7.01005e-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