AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifhlA_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 HP0049 51 H. pylori predicted coding region HP0049 #2 HP0051 174 cytosine specific DNA methyltransferase (DDEM) #3 HP0052 194 H. pylori predicted coding region HP0052 #4 HP0054 37 adenine/cytosine DNA methyltransferase #5 HP0055 26 proline permease (putP) #6 HP0056 300 delta-1-pyrroline-5-carboxylate dehydrogenase {Synechocystis sp.) #7 HP0900 108 hydrogenase expression/formation protein (hypB) #8 HP0902 300 H. pylori predicted coding region HP0902 Motif number 1 AGATTGTGTTATAGTTATTTAAAAGGATATTTTGA 1 27 1 ATGTATAAAA 0.85848 -25 TTGAAAAATCATCGGTTTCAAAACGCAATTGCGCAAA 2 117 0 ATGTTTAAAA 0.985103 -58 ATGATTTTTCAACGCTTATTGATCGTATTTGTGAAAG 2 142 1 AAGTTAGATA 0.805854 -33 TGAACAAAGCATGGCTTAAGAAAAGGATAAGATAAGT 3 47 0 ATGTTAAAAA 0.971533 -148 TTTTTGTTTAAAGGTTTTAGAATGCTATGAACAAAGC 3 74 0 AAGTTTAATA 0.967702 -121 CTATCTTATAATCCTTTTAAAAAATAAAAGGTTATTG 3 121 1 ATCTTTAAAA 0.855289 -74 AAAAGGGTCAATAGCGTTAAAAAGCAAGAAACAAGCA 3 159 0 ATGGTTAAAA 0.899907 -36 CATTGAACGAAACGATTTTAAATTAAACGGATTTACA 6 18 0 AAGTTTAATA 0.96757 -283 CGTTTCGTTCAATGGTTTTAAATTACACGATGCGAAT 6 41 1 AAGTTTAATA 0.967764 -260 GAATGTTATAATTTATTATTAAACGAAAAGTAAATGA 6 74 1 ATTTTAAAAA 0.67028 -227 ATTTATTGGTAATGTTTTTTAATTTTAAATTTTGTTC 6 207 0 AAGTTTAATA 0.967593 -94 AGCGTGTGTGAAGGCTTAGAAAATTTAGGGATCGCTT 8 31 1 AAGTTAAAAA 0.967755 -270 AGAATTAGAAATCGCTTTGCAAACCAAAAAGGTTTTG 8 162 1 ATGTTTAAAA 0.985109 -139 TGCAAACCAAAAAGGTTTTGGAAAAAACAGAATAAAG 8 179 1 AAGTTTGAAA 0.939935 -122 AGAATAAAGAATTGTTTAAGAAATCTATAAGAAATTT 8 207 1 ATGTTAAAAA 0.971523 -94 ** * *** *** * Masking position 12 Map Score: 20.6189 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 463 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 TTGTCATAGGGCTTTAAAAAAAGGATCTAGC 2 23 1 GCTTAAAAAA 0.967466 -152 TTCAAGCTTTCACAAATACGATCAAT 2 159 0 GCTTCACAAA 0.840055 -16 ATTGAAACTGGCTATAAAAACCCGCTTGACT 3 19 1 GCTAAAAAAC 0.8049 -176 ACAAAGCATGGCTTAAGAAAAGGATAAGATA 3 50 0 GCTTAGAAAA 0.80138 -145 GTTTTAGAATGCTATGAACAAAGCATGGCTT 3 67 0 GCTAGAACAA 0.937915 -128 CATTCTAAAACCTTTAAACAAAAACTAATGA 3 87 1 CCTTAAACAA 0.820101 -108 GCGTTAAAAAGCAAGAAACAAGCAACAATAA 3 152 0 GCAAAAACAA 0.814039 -43 GGGGATTAAGGATTAAACCAAATTCATTTGA 4 15 0 GATTAACCAA 0.632287 -23 AGTAAATGAAGCTAAAAACAATACAAATTAT 6 102 1 GCTAAAACAA 0.979516 -199 ATTAATTACCGCTAGAACAAAATTTAAAATT 6 193 1 GCTAAACAAA 0.935996 -108 AAAGCCACCCGCTTAAAACATGCTACAATCA 6 251 1 GCTTAAACAT 0.91072 -50 CTTAAAACATGCTACAATCAAGTCAAATTCT 6 262 1 GCTAAATCAA 0.944447 -39 GTGTGTGAAGGCTTAGAAAATTTAGGGATCG 8 34 1 GCTTGAAAAT 0.63807 -267 TCGTTGGTGGGCTTACATAAAGCGATCCCTA 8 56 0 GCTTCATAAA 0.769594 -245 CCAACCTGACGCTAAAATCCAAATTTTACGC 8 117 1 GCTAAATCCA 0.697581 -184 **** ****** Masking position 3 Map Score: 12.0379 Number of sites scoring better than the average of aligned sites = 1325 Number in coding regions = 1168 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 3 AACTATAACACAATCTCATTCAAATAGCGTT 1 12 0 CATCTCATTC 0.936738 -40 TGATTAGAAACATTCTCAATCGCAATAAAGA 2 76 1 CATCTCAATC 0.8727 -99 CAATTGCGCAAACTCTAAATTGTCTTTATTG 2 98 0 AATCTAAATT 0.867619 -77 ATTAAGGATTAAACCAAATTCATTTGAAGCA 4 11 0 AACCAAATTC 0.931409 -27 AATTTGGTTTAATCCTTAATCCCCTT 4 22 1 AACCTTAATC 0.681609 -16 TACAAATTATCACTCAAATTCTTATCATTGT 6 123 1 CATCAAATTC 0.892858 -178 AGCGGTAATTAATTCTCATTCCAACCTTTTT 6 175 0 AATCTCATTC 0.966987 -126 GGGTGGCTTTAAGTCTCATTTATTGGTAATG 6 230 0 AATCTCATTT 0.920883 -71 TGCTACAATCAAGTCAAATTCTTAAATAAAA 6 271 1 AATCAAATTC 0.942875 -30 ACATAAAGCGATCCCTAAATTTTCTAAGCCT 8 42 0 ATCCTAAATT 0.524306 -259 CTGACGCTAAAATCCAAATTTTACGCATCCC 8 122 1 AACCAAATTT 0.843594 -179 TTGCAAAGCGATTTCTAATTCTTCATCAGTA 8 153 0 ATTCTAATTC 0.879269 -148 TTAATTTAAGAAAGCTAATTTTTTACCCAAA 8 243 0 AAGCTAATTT 0.767954 -58 ** ******** Masking position 8 Map Score: 9.27059 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 430 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 TTATAGTTATTTAAAAGGATATTTTGA 1 35 1 TTAAAAGGAT 0.974153 -17 TAGGGCTTTAAAAAAAGGATCTAGCGAAGA 2 29 1 AAAAAAGGAT 0.932669 -146 GCATGGCTTAAGAAAAGGATAAGATAAGTC 3 46 0 AGAAAAGGAT 0.890414 -149 TTAGTTTTTGTTTAAAGGTTTTAGAATGCT 3 85 0 TTTAAAGGTT 0.827253 -110 CTTTTATTTTTTAAAAGGATTATAAGATAG 3 121 0 TTAAAAGGAT 0.974153 -74 CTTTTAAAAAATAAAAGGTTATTGTTGCTT 3 134 1 ATAAAAGGTT 0.968346 -61 CCCTAAATTAAAAGGGTCAATAGCGTT 3 178 0 TTAAAAGGGT 0.932345 -17 CGATTTTAAATTAAACGGATTTACAAAAAA 6 13 0 TTAAACGGAT 0.876507 -288 GTGATAAACTCAAAAAGGTTGGAATGAGAA 6 164 1 CAAAAAGGTT 0.919896 -137 AAATTCTTAAATAAAAGGTAAGCTC 6 286 1 ATAAAAGGTA 0.795374 -15 CTTTGCAAACCAAAAAGGTTTTGGAAAAAA 8 176 1 CAAAAAGGTT 0.919896 -125 ********** Masking position 5 Map Score: 15.0241 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 213 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 TGTGTTATAGTTATTTAAAAGGATATTTTG 1 31 1 TTATTTAAAA 0.942449 -21 CCCTAAATTAAAAGGGTCAATAG 3 182 0 TAAATTAAAA 0.881193 -13 TTTGATCTCCTTATTTAATACAATAT 5 7 0 TTATTTAATA 0.832726 -20 TAAATCCGTTTAATTTAAAATCGTTTCGTT 6 20 1 TAATTTAAAA 0.942459 -281 TCGCATCGTGTAATTTAAAACCATTGAACG 6 46 0 TAATTTAAAA 0.942459 -255 AGCTTACCTTTTATTTAAGAATTTGACTTG 6 280 0 TTATTTAAGA 0.969863 -21 TCATAGTCGTTTAATTAAGTGCGCTACGAT 7 62 1 TTAATTAAGT 0.672179 -47 GAATAAAGAATTGTTTAAGAAATCTATAAG 8 208 1 TTGTTTAAGA 0.870323 -93 ATTTAGAACTTAATTTAAGAAAGCTAATTT 8 253 0 TAATTTAAGA 0.969863 -48 AATTAAGTTCTAAATTAAGAAAATATCACA 8 268 1 TAAATTAAGA 0.935783 -33 ********** Masking position 5 Map Score: 13.6317 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 107 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 ATAAGCGTTGAAAAATCATCGGTTTCAAAA 2 131 0 AAAAATCATC 0.878541 -44 AACTGGCTATAAAAACCCGCTTGACTTATC 3 24 1 AAAAACCCGC 0.982403 -171 TTAAAAAGCAAGAAACAAGCAACAATAACC 3 150 0 AGAAACAAGC 0.85635 -45 TTTTTAGATCAGAAATCCGC 7 1 0 AGAAATCCGC 0.978409 -108 TTCTGATCTAAAAAATCAGCCAAAAAGATA 7 17 1 AAAAATCAGC 0.982384 -92 AAAAAGATAAAAAAAGTCGCTAAATCATAG 7 38 1 AAAAAGTCGC 0.911116 -71 TTTTTGGGTAAAAAATTAGCTTTCTTAAAT 8 241 1 AAAAATTAGC 0.949604 -60 ********** Masking position 5 Map Score: 5.00032 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 249 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TTTAAATAACTATAACACAATCTCATTCAA 1 20 0 TATAACACAA 0.910666 -32 TTTCTTGCTTTTTAACGCTATTGACCCTTT 3 165 1 TTTAACGCTA 0.854395 -30 CAATACAAATTATCACTCAAATTCTTATCA 6 120 1 TATCACTCAA 0.900891 -181 TATCACGCATTTTTACACAATGATAAGAAT 6 140 0 TTTTACACAA 0.935917 -161 TTTTTGAGTTTATCACGCATTTTTACACAA 6 150 0 TATCACGCAT 0.929685 -151 AAAATCCAAATTTTACGCATCCCTACTGAT 8 130 1 TTTTACGCAT 0.893713 -171 AAAGCTAATTTTTTACCCAAAAATTTCTTA 8 234 0 TTTTACCCAA 0.895487 -67 ATTAAGAAAATATCACACTAGGAGTTTTTG 8 281 1 TATCACACTA 0.893708 -20 ********** Masking position 5 Map Score: 2.78677 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 205 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 TTAAAAAAAGGATCTAGCGAAGAGGAGTTTC 2 36 1 GTCTAGCGAA 0.869914 -139 TTCTAATCAAGCGTTTTTGAAACTCCTCTTC 2 54 0 GGTTTTTGAA 0.923863 -121 AGACAATTTAGAGTTTGCGCAATTGCGTTTT 2 104 1 GGTTTGCGCA 0.932485 -71 CTTATTGATCGTATTTGTGAAAGCTTGAA 2 156 1 GATTTGTGAA 0.910442 -19 TAAGTTTTATTGAAACTGGCTATA 3 4 1 GTTTATTGAA 0.854548 -191 AAACGACTATGATTTAGCGACTTTTTTTATC 7 43 0 GTTTAGCGAC 0.869914 -66 TTAAGAGAGAGCGTGTGTGAAGGCTTAGAAA 8 22 1 GGTGTGTGAA 0.933734 -279 TCCGGGCAGTGGGTTAGTGAATTTAAGCCAA 8 90 1 GGTTAGTGAA 0.981499 -211 * ********* Masking position 9 Map Score: 1.32838 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 255 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CGCTTGACTTATCTTATCCTTTTCTTAAGC 3 41 1 ATCTTATCCT 0.883647 -154 TTAATTTAAAATCGTTTCGTTCAATGGTTT 6 29 1 ATCGTTTCGT 0.957512 -272 AATTATAACATTCGCATCGTGTAATTTAAA 6 57 0 TTCGCATCGT 0.966314 -244 TAGCTTCATTTACTTTTCGTTTAATAATAA 6 86 0 TACTTTTCGT 0.86837 -215 ATCACTCAAATTCTTATCATTGTGTAAAAA 6 131 1 TTCTTATCAT 0.905308 -170 TTTTAAAATTTTCGTATCGTAGCGCACTTA 7 77 0 TTCGTATCGT 0.987414 -32 ********** Masking position 7 Map Score: 0.804171 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 52 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ATAGGGCTTTAAAAAAAGGATCTAGCGAAGAGGA 2 28 1 AAAAAAACTA 0.912087 -147 TCAAGCTTTCACAAATACGATCAATAAGCGTTGA 2 150 0 ACAAAAACAA 0.938938 -25 CGTTAAAAAGCAAGAAACAAGCAACAATAACCTT 3 148 0 CAAGAAACAA 0.896986 -47 AAATGAAGCTAAAAACAATACAAATTATCACTCA 6 105 1 AAAAAAAAAA 0.957681 -196 TTTAAAATTAAAAAACATTACCAATAAATGAGAC 6 215 1 AAAAAAACAA 0.98302 -86 AAAATCAGCCAAAAAGATAAAAAAAGTCGCTAAA 7 28 1 AAAAAAAAAA 0.957681 -81 GAAAATTTTAAAAGAAAGGAACAAC 7 94 1 AAAGAAACAA 0.9704 -15 AGGTTTTGGAAAAAACAGAATAAAGAATTGTTTA 8 191 1 AAAAAAAAAA 0.957681 -110 ***** * * *** Masking position 7 Map Score: 6.19117 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 122 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 ********** No masking Map Score: 3.38462e-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: 3.38462e-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: 3.38462e-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