AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_hpyl_reg_100.orf -o00360_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 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #4 HP0830 58 amidase #5 HP0832 91 spermidine synthase (speE) #6 HP0833 76 H. pylori predicted coding region HP0833 #7 HP0943 21 D-amino acid dehydrogenase (dadA) #8 HP0944 300 translation initiation inhibitor, putative #9 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #10 HP1483 26 gerC2 protein (gerC2) #11 HP1490 103 hemolysin Motif number 1 AAATCAATATAATTCAAACCCTAAACCCAAACCTT 1 21 1 AATCACTAAA 0.814363 -237 ATTATTTTCAAATTTCAAGTCTAAAGAGTGTGAAT 1 128 0 AATTACTAAA 0.835934 -130 TTGAAATTTGAAAATAATAACACAACTTAAAAAAA 1 145 1 AAATACACAA 0.874589 -113 CAACTTAAAAAAAACTACCCTTAAAAAAATCAATC 1 167 1 AAACATTAAA 0.933794 -91 TACCCTTAAAAAAATCAATCTAAAATTCTTAAATT 1 182 1 AAATATAAAA 0.968436 -76 AAAAACTGCTCCTAAAAACTCAAAATT 2 3 1 AAATCTAAAA 0.800568 -212 CTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 2 22 1 AAATATAAAA 0.968436 -193 GTTTATAAGAAAAATTATTTCAAATGTAGTAGAAT 2 73 0 AAATACAAAT 0.827583 -142 ATTTTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 93 1 TAACACTAAA 0.881356 -122 AATTGAGAAAAAATTCAATTCAAAGGGGCTATTGT 2 116 1 AAATACAAAG 0.838227 -99 GCGTTTAAAAAATGTAAATTTTAAACAATAGCCCC 2 140 0 AATTATTAAA 0.815988 -75 TTTTATAGTAAAACTCATTTTTAAGGGGGATAGTT 3 18 0 AAATATTAAG 0.706554 -188 TTAAAAAGATTAAATAATATTAAATTGAATGGGGT 3 60 1 TAATATAAAT 0.656941 -146 ATATTTGACAAAAATAAGATCAAAAAAATTTTTTA 3 101 1 AAATACAAAA 0.972416 -105 CCTTGATCGCTATCCTACACCAAAAGAGTTAATAA 3 133 0 TATCACAAAA 0.790194 -73 ATAAAAGCCTAAAACAATTTTAAAAAAAGGACTTT 3 179 1 AAACATAAAA 0.963526 -27 CTAAGCATGTTAAACTACCATTAAATTTTTTGTAA 4 24 1 TAACATTAAA 0.866047 -35 CTAAAAAATCTAAATTATTGTAACAAAAGC 5 6 0 TAATATAACA 0.647901 -86 CAATTTAATCAAAATTAGATTACAATATTATAGTT 6 25 1 AAATATACAA 0.858547 -52 ATATTATAGTTATTTAAAGCTTAAATAAGGGTCTA 6 49 1 TATTATTAAA 0.670263 -28 TTTTCTATAATAAGCCATAATAAAAGGGCTTGCAA 8 72 1 TAACATAAAA 0.923717 -229 GGTAGCTTTAAAATTGATGACAACAAAGCCTAAAA 8 113 1 AAATACAACA 0.821821 -188 AACAAAGCCTAAAACTCAAACAAAACCCGTTTAAG 8 134 1 AAACCCAAAA 0.79884 -167 AAAGAAATAAAAAATGAGCGCAAAACGCCATGAAT 8 219 0 AAATACAAAA 0.972416 -82 TTTTTTAGAATAACCAACGCTAAAAATAGCGCTTT 9 118 1 TAACATAAAA 0.923717 -54 AATAGCGCTTTAATTGAATCCAAAACAAGGAGTTT 9 142 1 TAATACAAAA 0.941723 -30 CTAACTTTAAAAATCAAGCCTTCAAAAACC 11 6 0 AAACATTCAA 0.736159 -98 CTTGATTTTTAAAGTTAGGCTTAATCTTTTATGTT 11 23 1 AAATATTAAT 0.690446 -81 AAAATCTCAGAATTTTAACATAAAAGATTAAGCCT 11 39 0 AATTATAAAA 0.892536 -65 *** * * ***** Masking position 2 Map Score: 34.6196 Number of sites scoring better than the average of aligned sites = 1537 Number in coding regions = 1188 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 2 AAGTAACGCTAAATCAATATAATT 1 2 1 ATACCTAAAT 0.575136 -256 ATCAATATAATTCAAACCCTAAACCCAAACCTT 1 23 1 TCAACCTAAA 0.802151 -235 AACAAACACCCATTACTCTTAAATCATGCCAAT 1 97 1 CTACCTTAAA 0.702887 -161 TGAAAATAATAACACAACTTAAAAAAAACTACC 1 153 1 ACCACTTAAA 0.787496 -105 ACTTAAAAAAAACTACCCTTAAAAAAATCAATC 1 169 1 ACACCTTAAA 0.944125 -89 CCCTTAAAAAAATCAATCTAAAATTCTTAAATT 1 184 1 ATAACTAAAA 0.934563 -74 AATATAGCTATAATACACTAAAACAATCTCAAG 1 219 1 TAACCTAAAA 0.655223 -39 AAAAACTCAAAATTAACCTAAAATCGCTTGACG 2 24 1 ATAACTAAAA 0.934547 -191 TTTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 95 1 ACAACCTAAA 0.828794 -120 AGGGATAGTTACCACCTATAAAATAAGGATCGT 2 189 1 ACCCATAAAA 0.621947 -26 TTTGGATAACTATCCCCCTTAAAAATGAGTTTT 3 11 1 TTCCCTTAAA 0.816428 -195 TAAAAATGAGTTTTACTATAAAACAAAATTTTA 3 30 1 TTACATAAAA 0.772885 -176 TTGATCGCTATCCTACACCAAAAGAGTTAATAA 3 133 0 TCACCCAAAA 0.909583 -73 TCAAGGTTTTTATGAAAATAAAAGCCTAAAACA 3 162 1 TTAAATAAAA 0.681541 -44 AAGCATGTTAAACTACCATTAAATTTTTTGTAA 4 26 1 ACACATTAAA 0.751443 -33 TTAAATTTTTTGTAAGGCTAAAAAC 4 44 1 TTAGCTAAAA 0.661057 -15 ATTATAGTTATTTAAAGCTTAAATAAGGGTCTA 6 51 1 TTAACTTAAA 0.874123 -26 ACAGACACTCATTGCCACTAAAAGAGGGCAAAG 8 22 0 ATCCCTAAAA 0.890854 -279 AATTGATGACAACAAAGCCTAAAACTCAAACAA 8 124 1 ACAACCTAAA 0.828794 -177 TTTTAGAATAACCAACGCTAAAAATAGCGCTTT 9 120 1 ACACCTAAAA 0.962925 -52 TAGCGCTTTAATTGAATCCAAAACAAGGAGTTT 9 144 1 ATAACCAAAA 0.868507 -28 AATCTCAGAATTTTAACATAAAAGATTAAGCCT 11 39 0 TTAAATAAAA 0.679228 -65 AACTTTAAACCTAAAACCTAACGATA 11 88 0 TTAACTAAAA 0.910335 -16 * * ** ****** Masking position 11 Map Score: 22.5336 Number of sites scoring better than the average of aligned sites = 1880 Number in coding regions = 1623 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 3 GTTTGTTTTAAGACGCTATGACTATCTTTA 1 74 0 AGACGCTATG 0.905922 -184 TTTAAACAATAGCCCCTTTGAATTGAATTT 2 126 0 AGCCCCTTTG 0.887716 -89 TACATTTTTTAAACGCTATTAGATATAATA 2 159 1 AAACGCTATT 0.962419 -56 AAATATTGATAAACCCCATTCAATTTAATA 3 77 0 AAACCCCATT 0.875995 -129 CAAAAGTCCTTTTTTTAAAATTG 3 193 0 AAGTCCTTTT 0.742572 -13 CGCTAGACCCTTATTTAAGCTTTA 6 63 0 AGACCCTTAT 0.670047 -14 TTATTATAGAAAATGCTTTTGAGCATTTTT 8 55 0 AAATGCTTTT 0.829786 -246 ACTCGCTTGCAAGCCCTTTTATTATGGCTT 8 83 0 AAGCCCTTTT 0.94542 -218 AACTCAAACAAAACCCGTTTAAGAATTTCT 8 146 1 AAACCCGTTT 0.769165 -155 AATGAGCGCAAAACGCCATGAATTTTCATC 8 212 0 AAACGCCATG 0.868559 -89 GATTGAAACTCCTATGATGATGTGTT 8 285 0 AACTCCTATG 0.732439 -16 TTTGCATAGAAACCGCTTATGCA 9 4 0 AACCGCTTAT 0.818148 -168 AAGCTTCAAGAAACGCTTTGCATAGAAACC 9 20 0 AAACGCTTTG 0.961307 -152 CTAAAAAAATAACCGCTATTATACCATAAG 9 96 0 AACCGCTATT 0.957902 -76 GATTCAATTAAAGCGCTATTTTTAGCGTTG 9 132 0 AAGCGCTATT 0.945455 -40 ********** Masking position 1 Map Score: 14.649 Number of sites scoring better than the average of aligned sites = 1827 Number in coding regions = 1607 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 TTAGATTGATTTTTTTAAGGGTAGTTTTTTTT 1 173 0 TTTTTAAGGT 0.679651 -85 ATTGTTTTAGTGTATTATAGCTATATTTTAAT 1 214 0 TGTATATGCT 0.889604 -44 AAATTTACATTTTTTAAACGCTATTAGATATA 2 154 1 TTTTTAAGCT 0.966515 -61 GTAACTATCCCTTATTATATCTAATAGCGTTT 2 169 0 CTTATATTCT 0.598231 -46 AAAAAAATTTTTTATTAACTCTTTTGGTGTAG 3 122 1 TTTATAATCT 0.899982 -84 GCTCGTTTTATCTCTAAGCATGTTA 4 4 1 CGTTTATTCT 0.538376 -55 CCATTAAATTTTTTGTAAGGCTAAAAAC 4 41 1 TTTTGAAGCT 0.885699 -18 CTTTTTTATCGCTTCAATTTAAT 6 2 1 TTTTTATGCT 0.953414 -75 AATATTATAGTTATTTAAAGCTTAAATAAGGG 6 48 1 TTATTAAGCT 0.698645 -29 AATGAGTGTCTGTAAAAATGCTCAAAAGCATT 8 42 1 TGTAAAAGCT 0.663584 -259 TGCAAGCCCTTTTATTATGGCTTATTATAGAA 8 74 0 TTTATATGCT 0.935527 -227 TTTACCCATATTTAGAAATTCTTAAACGGGTT 8 157 0 TTTAGAATCT 0.707228 -144 TTTGCGCTCATTTTTTATTTCTTTATTAATTT 8 230 1 TTTTTATTCT 0.899982 -71 GACTTTTCTTTTTTCATGGCTTGTCT 10 6 0 TTTTTATGCT 0.953414 -21 GGTTTTTGAAGGCTTGATTTTTAA 11 3 1 TTTTTAAGCT 0.966515 -101 TAATCTTTTATGTTAAAATTCTGAGATTTTAT 11 44 1 TGTTAAATCT 0.550197 -60 AAATATAAAATATATAAAATCTCAGAATTTTA 11 57 0 TATATAATCT 0.489162 -47 ***** ** *** Masking position 7 Map Score: 17.5062 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1291 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 TCTAAAATTCTTAAATTAAAATATAGCTATAA 1 200 1 TTAATAAAAT 0.865343 -58 TAGGTTTTGTTTATAAGAAAAATTATTTCAAA 2 84 0 TTTAAAAAAA 0.739673 -131 AAAACCTAAATTGAGAAAAAATTCAATTCAAA 2 108 1 TTAGAAAAAT 0.738138 -107 AAATGTAAATTTTAAACAATAGCCCCTTTGAA 2 134 0 TTAAAAATAG 0.618075 -81 TAAAACAAAATTTTAAAAAGATTAAATAATAT 3 48 1 TTTAAAAGAT 0.866461 -158 ACCAAAAGAGTTAATAAAAAATTTTTTTGATC 3 118 0 TTATAAAAAT 0.508197 -88 CGATCAAGGTTTTTATGAAAATAAAAGCCTAA 3 159 1 TTTATAAAAT 0.931913 -47 CCTAAAACAATTTTAAAAAAAGGACTTTTG 3 186 1 TTTAAAAAAG 0.948308 -20 ATCTAAATTATTGTAACAAAAGC 5 2 0 TTTAAAAAAG 0.94837 -90 TTAGCTTACTTTTTAACAATATCCATGCCTTA 5 61 0 TTTAAAATAT 0.80757 -31 ATCGCTTCAATTTAATCAAAATTAGATTACAA 6 18 1 TTAATAAAAT 0.865344 -59 CAAAAGCATTTTCTATAATAAGCCATAATAAA 8 64 1 TTTATATAAG 0.490294 -237 ATACAATACCTTATAATAAGATGAAAATTCAT 8 193 1 TTTAAAAGAT 0.866501 -108 CATAAGCGGTTTCTATGCAAAGCGTTTCTTGA 9 13 1 TTTATCAAAG 0.587747 -159 GCGTTGGTTATTCTAAAAAAATAACCGCTATT 9 106 0 TTTAAAAAAT 0.957182 -66 GCTTAATCTTTTATGTTAAAATTCTGAGATTT 11 41 1 TTTGTAAAAT 0.785977 -63 ** *** ***** Masking position 2 Map Score: 11.1697 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 597 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 6 TGAAAATAATAACACAACTTAAAAAAAACT 1 153 1 AACACAACTT 0.789775 -105 TTGACGCAAAAACACTGCCTTAATTCTACT 2 51 1 AACACTGCCT 0.941727 -164 TTTTCTTATAAACAAAACCTAAATTGAGAA 2 95 1 AACAAAACCT 0.949239 -120 TATAGGTGGTAACTATCCCTTATTATATCT 2 179 0 AACTATCCCT 0.932057 -36 TGAACGATCCTTATTTTATAGG 2 203 0 AACGATCCTT 0.764086 -12 TTTGGATAACTATCCCCCTTAAAAATG 3 8 1 AACTATCCCC 0.855082 -198 AAACACTCCTTAGCTTACTTT 5 81 0 AACACTCCTT 0.897159 -11 AATTGATGACAACAAAGCCTAAAACTCAAA 8 124 1 AACAAAGCCT 0.939406 -177 CTAAAACTCAAACAAAACCCGTTTAAGAAT 8 142 1 AACAAAACCC 0.88939 -159 GTAAAAAATATACAATACCTTATAATAAGA 8 184 1 TACAATACCT 0.793912 -117 ********** Masking position 2 Map Score: 5.60672 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 343 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 GCATAAAGATAGTCATAGCGTCTTAAAACA 1 71 1 AGTCATAGCG 0.964447 -187 AAAAAATTCAATTCAAAGGGGCTATTGTTT 2 123 1 ATTCAAAGGG 0.922701 -92 TAAGATGAAAATTCATGGCGTTTTGCGCTC 8 209 1 ATTCATGGCG 0.972467 -92 AGCGGTTTCTATGCAAAGCGTTTCTTGAAG 9 17 1 ATGCAAAGCG 0.978435 -155 AAAAACACCGATGCATTGCGCCATAAGCTT 9 44 0 ATGCATTGCG 0.962589 -128 ********** Masking position 5 Map Score: 0.514048 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 106 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ********** No masking Map Score: 4.92707e-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: 4.92707e-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: 4.92707e-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