AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -itrpR_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 HP0470 97 oligoendopeptidase F (pepF) #2 HP0471 300 glutathione-regulated potassium-efflux system protein (kefB) #3 HP1279 300 anthranilate isomerase (trpC) #4 HP1282 222 anthranilate synthase component I (trpE) #5 HP1283 97 H. pylori predicted coding region HP1283 #6 HP1284 69 conserved hypothetical protein #7 HP1285 169 conserved hypothetical secreted protein Motif number 1 TTGTATTTTAACATAACACTCACAATACAAG 1 38 0 AATAACACTC 0.857126 -60 AAAATAAAAATTAAAACGCTAGGATTATACT 2 96 0 TAAAACGCTA 0.992201 -205 AAACGCAAACACCAAACGCTCTATTTTAGTA 2 126 0 ACAAACGCTC 0.947807 -175 TAAACCCATATTCAAACGCAAACACCAAACG 2 139 0 TCAAACGCAA 0.940035 -162 TTGATCCATTAAATAACACTATTGAACAAAA 2 216 0 AATAACACTA 0.838158 -85 AATTACAGATTGAAAACGCACAAGAAAGCAC 3 89 1 TAAAACGCAC 0.981273 -212 TTGCAAAAAATCATAAGGCTAAGCC 3 286 1 TATAAGGCTA 0.875269 -15 CTCTAAAAACTTATAACGCAA 4 1 0 TATAACGCAA 0.959117 -222 TTGGAATTTTTGAAAACGCTCACTCATTAGC 4 138 1 TAAAACGCTC 0.99326 -85 AAATGGGCAATAAATACGCTAATGAGTGAGC 4 155 0 TAATACGCTA 0.936452 -68 CATTTTGAATTAAAAACGCTAACTATACAGC 7 24 1 TAAAACGCTA 0.992201 -146 CGGTTAATGGTAAAAACACTCCTAATCATCT 7 59 1 TAAAACACTC 0.970179 -111 * ********* Masking position 6 Map Score: 17.0536 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1120 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 ACAAGCATATTTTAACTCCAAATTGATATAAAAAGGGGATTT 1 65 1 TTTCAATAAA 0.946739 -33 ATCCTAGCGTTTTAATTTTTATTTTACTAAAATAGAGCGTTT 2 102 1 TTTTATTAAA 0.764378 -199 ATATAAGTAATTTATTATTTAAATCTTACTAAACCCATATTC 2 157 0 TTTTAATTAA 0.866571 -144 AATAGGATAGTTTCGCTTTTATTTCTTTAAAACAAATTGATT 2 250 1 TTTTATTAAA 0.764378 -51 CTTGTGCGTTTTCAATCTGTAATTCTTTCAAATCATAGGGGG 3 71 0 TTCTAATAAA 0.906001 -230 AATCCTTGCCTTTATTTTCTAAAATATCTAAACACGCTTGAG 3 119 0 TTTTAAAAAA 0.975676 -182 AATCTTTAGCTTTATGGCTTAAATACAACAAACTCGCCACAT 3 185 0 TTTCAATAAA 0.802431 -116 CATAAGGCGCTTTGGTTTTTAAATGCTCTAAAGTCATGCTCA 3 239 0 TTTTAATAAA 0.915001 -62 TAACTTCAGCTTTAGATTGTAAAAGCATAAAAAGGAATTTTC 4 34 1 TTTTAAAAAA 0.971567 -189 GCTCCTATTTTTTAGTGTTCAACAATGTAAAATCCACGCAAA 5 61 0 TTTTAAAAAA 0.822833 -37 ATAAGAACGATTTTTGCTAAAACATGACAAAAAATTTGATCT 6 25 1 TTTTAAAAAA 0.966948 -45 AATCATCTGTTTTAAGGTATAATACAAAAAATCCCCATTAGG 7 82 1 TTTTAAAAAT 0.825112 -88 *** * ** * *** Masking position 11 Map Score: 13.1822 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 198 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 TGGCGCAAAAACCAAATGATAAGTTTGCT 1 8 1 AAAACAATGA 0.87919 -90 CATAACACTCACAATACAAGCAAACTTATCAT 1 26 0 ACAATCAGCA 0.86495 -72 GTGTTATGTTAAAATACAAGCATATTTTAACT 1 50 1 AAAATCAGCA 0.956644 -48 TAGTAAAATAAAAATTAAAACGCTAGGATTAT 2 99 0 AAAATAAACG 0.795807 -202 TTGTTTTAAAGAAATAAAAGCGAAACTATCCT 2 253 0 GAAATAAGCG 0.852923 -48 TTATTTCTTTAAAACAAATTGATTCTACTGGG 2 268 1 AAAACAATGA 0.87919 -33 GTGAATTGAAAAATAACGGAATTTTAGAGT 3 9 1 AAAAAAAGGA 0.739119 -292 GATATTTTAGAAAATAAAGGCAAGGATTCGCA 3 133 1 AAAATAAGCA 0.977633 -168 TGGCTTAAATACAACAAACTCGCCACATTCGC 3 181 0 ACAACAATCG 0.823714 -120 AGAGCATTTAAAAACCAAAGCGCCTTATGCGC 3 252 1 AAAACAAGCG 0.975909 -49 CTTTACGCTAAAAATAAACTCGTATTTTACAA 4 195 0 AAAATAATCG 0.940468 -28 TCAACAATGTAAAATCCACGCAAACATTAAGA 5 53 0 AAAATCAGCA 0.956644 -45 TTTTTAATTCAAAATGAAGTGAGGAAACA 7 8 0 AAAATAATGA 0.877176 -162 CAATCCTAATAAAACTGATGCAAAGGTCTTTT 7 142 0 AAAACGAGCA 0.893476 -28 ***** ** *** Masking position 8 Map Score: 12.162 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 836 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 TGGCGCAAAAACCAAATGATAAG 1 4 1 CGCAAAAACC 0.953669 -94 AAGGTTGGGGTTCAAAAATCTTTTTCATAA 2 45 1 TTCAAAAATC 0.74483 -256 CATATTCAAACGCAAACACCAAACGCTCTA 2 134 0 CGCAAACACC 0.856625 -167 TCAAGTCATACTCTAAAATTCCGTTATTTT 3 20 0 CTCTAAAATT 0.906507 -281 ATGACTTGAGCGCTAAAGATTTTGATTTGC 3 41 1 CGCTAAAGAT 0.919705 -260 TAAGCCATAAAGCTAAAGATTTAAAAGAGG 3 206 1 AGCTAAAGAT 0.738997 -95 TTTTTAAATGCTCTAAAGTCATGCTCACAC 3 236 0 CTCTAAAGTC 0.88654 -65 TATGCGCATTTGCAAAAAATCATAAGGCTA 3 277 1 TGCAAAAAAT 0.810611 -24 TGAAGTTATCCTCTAAAAACTTATAACGCA 4 12 0 CTCTAAAAAC 0.908395 -211 TGCTTTTACAATCTAAAGCTGAAGTTATCC 4 31 0 ATCTAAAGCT 0.56702 -192 AGTGAGCGTTTTCAAAAATTCCAAGACATT 4 132 0 TTCAAAAATT 0.706035 -91 AATTTCTTTACGCTAAAAATAAACTCGTAT 4 202 0 CGCTAAAAAT 0.945293 -21 GTAAAATCCACGCAAACATTAAGAATAAAC 5 47 0 CGCAAACATT 0.856323 -51 GTCATGTTTTAGCAAAAATCGTTCTTATGC 6 23 0 AGCAAAAATC 0.860753 -47 ********** Masking position 5 Map Score: 9.69288 Number of sites scoring better than the average of aligned sites = 2393 Number in coding regions = 2167 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 AATTGATATAAAAAGGGGATTTC 1 85 1 AAAAGGGTTT 0.97795 -13 CTTTTTCATAAATAGAAAGTTTGCCTTAACGC 2 64 1 AATAGAATTT 0.85757 -237 ATTTTACTAAAATAGAGCGTTTGGTGTTTGCG 2 122 1 AATAGGCTTT 0.880499 -179 ATTCGCATACAATGGTGGTTGTGGCGAATGTG 3 158 1 AATGGGGTGT 0.93914 -143 CTAAAGATTTAAAAGAGGGTGTGAGCATGACT 3 218 1 AAAAGGGTGT 0.977101 -83 TAAAAGCATAAAAAGGAATTTTCTAACCACCA 4 53 1 AAAAGAATTT 0.873953 -170 TGGTTGTGCGAAAAGAAGCTTTCAATTTGGTG 4 83 0 AAAAGAGTTT 0.942122 -140 GCTCTCTTAAAAATGTGGTTGTGCGAAAAGAA 4 98 0 AAATGGGTGT 0.869169 -125 ATTTGATAAGAGACTTTCTACTATAAT 5 6 1 ATAAGGATTT 0.712138 -92 AACACTAAAAAATAGGAGCTGTTT 5 84 1 AATAGAGTGT 0.929551 -14 ACACCTACCTAATGGGGATTTTTTGTATTATA 7 99 0 AATGGGATTT 0.875633 -71 ***** ** *** Masking position 1 Map Score: 9.56254 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 716 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 TTGCTTGTATTGTGAGTGTTATGTTAAAAT 1 35 1 TGTGAGTGTT 0.887843 -63 TTCAAGAGTCGGTTAGGGTTTAATTGGATG 2 16 0 GGTTAGGGTT 0.942611 -285 ACTCTTGAAAGGTTGGGGTTCAAAAATCTT 2 37 1 GGTTGGGGTT 0.986266 -264 AAAATAGAGCGTTTGGTGTTTGCGTTTGAA 2 130 1 GTTTGGTGTT 0.891083 -171 CGCATACAATGGTGGTTGTGGCGAATGTGG 3 161 1 GGTGGTTGTG 0.971009 -140 CTTTCAATTTGGTGGTGGTTAGAAAATTCC 4 67 0 GGTGGTGGTT 0.983044 -156 CTCTTAAAAATGTGGTTGTGCGAAAAGAAG 4 97 0 TGTGGTTGTG 0.884537 -126 ATCCCCATTAGGTAGGTGTTGTTATGATAA 7 112 1 GGTAGGTGTT 0.966662 -58 ********** Masking position 3 Map Score: 7.11233 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 243 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 TTCTTCATCCAATTAAACCCTAACCGA 2 7 1 ATCCAATAAA 0.960928 -294 TTTAATTTTTATTTTACTAAAATAGAGCGTT 2 112 1 ATTTTATAAA 0.66671 -189 TATTATTTAAATCTTACTAAACCCATATTCA 2 156 0 ATCTTATAAA 0.939106 -145 AAGCGAAACTATCCTATTAAATTGATCCATT 2 237 0 ATCCTATAAA 0.982619 -64 AGCTGAAGTTATCCTCTAAAAACTTATAACG 4 14 0 ATCCTCAAAA 0.903708 -209 ACAATGTAAAATCCACGCAAACATTAAGAAT 5 51 0 ATCCACCAAA 0.85818 -47 CAAACTCAATCCTAATAAAACTGATGCAA 7 151 0 ATCCTATAAA 0.982619 -19 ****** **** Masking position 9 Map Score: 3.40274 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 105 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 TTTAGCGCTCAAGTCATACTCTAAAATTCCG 3 27 0 AAGTCATCTC 0.993509 -274 AAATGCTCTAAAGTCATGCTCACACCCTCTT 3 230 0 AAGTCATCTC 0.993697 -71 TCTAAAGCTGAAGTTATCCTCTAAAAACTTA 4 19 0 AAGTTATCTC 0.975475 -204 CAAAAATTCCAAGACATTCTGCTCTCTTAAA 4 119 0 AAGACATCTG 0.958852 -104 ******* *** Masking position 6 Map Score: 1.50528 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 16 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 TTTAGAGTATGACTTGAGCGCTAAAGATTT 3 33 1 GACTTGAGCG 0.946739 -268 CTTGAGTGCTTTCTTGTGCGTTTTCAATCT 3 95 0 TTCTTGTGCG 0.960032 -206 CACAAGAAAGCACTCAAGCGTGTTTAGATA 3 107 1 CACTCAAGCG 0.831527 -194 AAACCAAAGCGCCTTATGCGCATTTGCAAA 3 263 1 GCCTTATGCG 0.963268 -38 GCAAAAATCGTTCTTATGCGATGGATAAAT 6 12 0 TTCTTATGCG 0.966546 -58 AAAATTTGATCTCTTAGGCGGAGTT 6 55 1 CTCTTAGGCG 0.959176 -15 ********** Masking position 4 Map Score: 0.880894 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 99 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 GAAATCCCCTTTTTATATCAA 1 87 0 AAATCCCCTT 0.964071 -11 TGGGGTTCAAAAATCTTTTTCATAAATAGA 2 50 1 AAATCTTTTT 0.758663 -251 TCTACTGGGGAAAGGTTTTT 2 291 1 AAAGGTTTTT 0.659673 -10 TCATACTCTAAAATTCCGTTATTTTTCAAT 3 15 0 AAATTCCGTT 0.718132 -286 TTTAAAAACCAAAGCGCCTTATGCGCATTT 3 258 1 AAAGCGCCTT 0.803397 -43 GGTGGTTAGAAAATTCCTTTTTATGCTTTT 4 54 0 AAATTCCTTT 0.840808 -169 CACCAAATTGAAAGCTTCTTTTCGCACAAC 4 83 1 AAAGCTTCTT 0.90771 -140 ATTATAGTAGAAAGTCTCTTATCAAAT 5 8 0 AAAGTCTCTT 0.882979 -90 ATAATACAAAAAATCCCCATTAGGTAGGTG 7 100 1 AAATCCCCAT 0.800133 -70 AAACTGATGCAAAGGTCTTTTTTATCATAA 7 133 0 AAAGGTCTTT 0.586318 -37 ********** Masking position 3 Map Score: 2.88356 Number of sites scoring better than the average of aligned sites = 1438 Number in coding regions = 1280 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 11 ********** No masking Map Score: -1.93735e-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: -1.93735e-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: -1.93735e-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