AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifis_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 HP0281 50 tRNA-guanine transglycosylase (tgt) #2 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #3 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #4 HP0681 39 H. pylori predicted coding region HP0681 #5 HP0682 153 H. pylori predicted coding region HP0682 #6 HP0683 300 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #7 HP1058 148 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) #8 HP1060 67 H. pylori predicted coding region HP1060 #9 HP1550 62 protein-export membrane protein (secD) #10 HP1551 47 conserved hypothetical secreted protein #11 HP1552 23 Na+/H+ antiporter (nhaA) #12 HP1553 248 helicase Motif number 1 AGAAGCAGTATTTTAGCTTTTTAATCCTTTAAA 2 56 1 TTTAGTTTTA 0.982664 -150 AACTTCAATTTTTCAGTATTTTTAAAGGATTAA 2 76 0 TTTAGTTTTT 0.964124 -130 TACTGAAAAATTGAAGTTTTTTAAAATTTGGAG 2 91 1 TTGAGTTTTA 0.892099 -115 TTTTTTAAAATTTGGAGTTTTTTCTGGCTTTTA 2 107 1 TTTGATTTTT 0.772396 -99 TTTCTGGCTTTTAGGGGGTTTTAAATTCTTTTA 2 127 1 TTAGGTTTTA 0.944933 -79 AGAATAAGTTTTAAAGTTTTTTAATTTTTTTAT 3 42 0 TTAAGTTTTA 0.956726 -130 TTTTCTTTTTCTTAAGTTTTTTATTGATACAAT 3 102 1 CTTAGTTTTA 0.961993 -70 ATGATTAATATTTTAGGATTTTTCATTATTCAA 5 16 0 TTTAGTTTTT 0.964124 -138 TTTTGCGTTTTTTCATTTTTTTAATCCTCATTT 6 193 0 TTTATTTTTA 0.924721 -108 TAAACTCATTTTAGGGAATTTTAACATGCCTTA 6 269 0 TTAGGTTTTA 0.944933 -32 CTAAAATGAGTTTAAGGATTTTA 6 288 1 TTTAGTTTTA 0.982645 -13 AACCGGTCATTTTAATTATTTTAGTATAATTGA 7 50 0 TTTATTTTTA 0.924702 -99 ATATTTAACACTTAGGATTTTTA 7 136 1 CTTGGTTTTA 0.95051 -13 CTTTTACACCCTTTAAAATTTTATCGTTATTGT 8 36 0 CTTAATTTTA 0.808152 -32 TTAACGCTCGTTTAATCGTTTTTATTGGCGCGC 9 17 1 TTTATTTTTT 0.853449 -46 TAATCTCAAATTATAGCATTTTTAG 10 3 0 TTAAGTTTTT 0.914683 -45 AGACAACCTTAAAATTTTTAATT 11 4 0 CTTAATTTTA 0.808151 -20 AATCGTAGGGTTTTGTCGTTTTTCTATCATTTT 12 138 0 TTTGTTTTTT 0.815459 -111 TAGCAAAAGATTAAGGTTTTTTAGCTTAAGTAA 12 172 1 TTAGGTTTTA 0.944918 -77 *** ** ***** Masking position 9 Map Score: 33.4049 Number of sites scoring better than the average of aligned sites = 1209 Number in coding regions = 993 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 2 ATAATGGCGTAATCATTTTTTAGGAAGT 1 4 0 AATTTTAGGA 0.980288 -47 AAAATAAAGAAGCAGTATTTTAGCTTTTTAATCCT 2 49 1 AGTTTTAGCT 0.789858 -157 TCAATTTTTCAGTATTTTTAAAGGATTAAAAAGCT 2 70 0 ATTTAAAGGA 0.691732 -136 AGGGGGTTTTAAATTCTTTTAAGGTATTCTAACAA 2 139 1 ATTTTAAGGT 0.923378 -67 TATATCATTGAGATAGTTTTAAGGAAATTAAGGAA 2 177 1 AATTTAAGGA 0.985943 -29 TATTAATGAGAATAAGTTTTAAAGTTTTTTAATTT 3 48 0 AATTTAAAGT 0.812225 -124 AAACGATTTAATTCAAATTTAAGGAAAAATT 3 151 1 AATTTAAGGA 0.985943 -21 AAAGTAAATGATTAATATTTTAGGATTTTTCATTA 5 21 0 AATTTTAGGA 0.980288 -133 AAGGGTGGTTACAAGCTGTTTAGGATCATTAGGAG 6 92 1 AGGTTTAGGA 0.877972 -209 TAGGATCATTAGGAGCGTTTAAAGAGAGATTGACG 6 112 1 AGTTTAAAGA 0.924168 -189 AAATTCCCTAAAATGAGTTTAAGGATTTTA 6 281 1 AGTTTAAGGA 0.988405 -20 GTATAATTGAAAGAAACTTTTAACAAACAATTCAA 7 25 0 AATTTTAACA 0.506187 -124 TTGAGATTAAAACATCTTTTAAGGAAATTAA 10 27 1 ATTTTAAGGA 0.965443 -21 AATTAAAAATTTTAAGGTTGTCT 11 4 1 TATTTAAGGT 0.708461 -20 AAGAGAACCAAAATAACTTTAAGGAGAATTCTC 12 9 0 AATTTAAGGA 0.985943 -240 GCTTAAGTAAAAAAGGCTTTTAGGTTATAATAAAG 12 195 1 AGTTTTAGGT 0.96306 -54 TAAAGACAAAATTAGAATTTTAGGATAGATCTCA 12 225 1 AGTTTTAGGA 0.983724 -24 * * ******** Masking position 9 Map Score: 25.4959 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 310 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 CACATAAGAAGTAGAAAATAAAGAAGCAGTA 2 35 1 GTAGAAATAA 0.668798 -171 GAGATAGTTTTAAGGAAATTAAGGAACAAA 2 186 1 TAAGAAATTA 0.913693 -20 GGGTATAAAAAAATTAAAAAACTTTAAAACT 3 38 1 AAATAAAAAA 0.676096 -134 ATAAAAAACTTAAGAAAAAGAAAAGTTCAAG 3 95 0 TAAGAAAAGA 0.943875 -77 TGATGGGGTGGAAGGAAATAAT 4 28 1 GAAGAAATAA 0.914972 -12 TTAAATGATTAAAGTAAATGATTAATATTTT 5 35 0 AAAGAAATGA 0.961257 -119 GTTTTTACACAAATTAAATGATTAAAGTAAA 5 48 0 AAATAAATGA 0.854039 -106 TTGTTATAGATCAGCAAAAGATCACAAAAAA 5 94 0 TCAGAAAAGA 0.726216 -60 AGGATTAAAAAAATGAAAAAACGCAAAATTC 6 198 1 AAATAAAAAA 0.676098 -103 TCTTGTTTAGAAAGAAAATTACACTACAATA 8 11 1 AAAGAAATTA 0.913712 -57 AAACATCTTTTAAGGAAATTAA 10 36 1 TAAGAAATTA 0.913693 -12 AGAAAATTAAGAATCAAATGAGCATGGAGGA 12 43 0 GAATAAATGA 0.828518 -206 TAGGTGTTCTTAAGAAAATTAAGAATCAAAT 12 55 0 TAAGAAATTA 0.913693 -194 CCCTACGATTATAGCAAAAGATTAAGGTTTT 12 161 1 ATAGAAAAGA 0.759375 -88 TTTTTTAGCTTAAGTAAAAAAGGCTTTTAGG 12 188 1 TAAGAAAAAA 0.898393 -61 **** ****** Masking position 6 Map Score: 13.9532 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 601 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 CTTAAAAGAATTTAAAACCCCCTAAAAGCCAGA 2 129 0 TTTAAACCCT 0.840717 -77 TTTAACCCAAATGTCATTAAATG 3 1 1 TTTAACCATG 0.768063 -171 TTTTTAATTTTTTTATACCCCCTCCATTTAATG 3 25 0 TTTTATCCCT 0.93746 -147 AAACAAACGATTTAATTCAAATTTAAGGAAAAA 3 147 1 TTTAATCATT 0.871332 -25 AGTGTTTTGTTTTTACACAAATTAAATGATTAA 5 54 0 TTTTACCATT 0.947708 -100 TCATTTGCCCTTTAATATGCCCTTTAATGAGCG 6 166 0 TTTAATTCCT 0.775647 -135 TTTTCATTTTTTTAATCCTCATTTGCCCTTTAA 6 184 0 TTTAATCCTT 0.944573 -117 TTTAGGGAATTTTAACATGCCTTATCTTATAAT 6 260 0 TTTAACTCTT 0.913187 -41 TGGGTAAAAATTTTACTCCATTTTAACCGGTCA 7 74 0 TTTTACCATT 0.947708 -75 GGAGTAAAATTTTTACCCACCCTAATAAAGTCA 7 88 1 TTTTACCCCT 0.978936 -61 AACAATCTACTTTTACACCCTTTAAAATTTTAT 8 45 0 TTTTACCCTT 0.978544 -23 AACTTTTTAACGCTCGTTTAATCGTTTT 9 6 1 TTTAACCCTT 0.981425 -57 TAAAAGCCTTTTTTACTTAAGCTAAAAAACCTT 12 184 0 TTTTACTACT 0.786175 -65 ****** * * ** Masking position 5 Map Score: 15.8599 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 426 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 TTTTCAGTATTTTTAAAGGATTAAAAAGCT 2 70 0 TTTTAAAGGA 0.753693 -136 TTTTTTCTGGCTTTTAGGGGGTTTTAAATT 2 124 1 CTTTTAGGGG 0.979555 -82 GTTTTAAATTCTTTTAAGGTATTCTAACAA 2 144 1 CTTTTAAGGT 0.909657 -62 ACCCAAATGTCATTAAATGGAGGGGGTATA 3 15 1 CATTAAATGG 0.806922 -157 AGGGCGATGACATTAAGGGTGGTTACAAGC 6 78 1 CATTAAGGGT 0.892281 -223 TATCAGCGCTCATTAAAGGGCATATTAAAG 6 160 1 CATTAAAGGG 0.983119 -141 TTAAAGGGCATATTAAAGGGCAAATGAGGA 6 172 1 TATTAAAGGG 0.927839 -129 TCCTTAAACTCATTTTAGGGAATTTTAACA 6 276 0 CATTTTAGGG 0.830507 -25 AACGATAAAATTTTAAAGGGTGTAAAAGTA 8 41 1 TTTTAAAGGG 0.946525 -27 TGGCGCGCTTCTTTTAGGGGTAGGGTTTTC 9 42 1 CTTTTAGGGG 0.979555 -21 ATTAAAACATCTTTTAAGGAAATTAA 10 32 1 CTTTTAAGGA 0.909643 -16 ACCAAAATAACTTTAAGGAGAATTCTC 12 8 0 CTTTAAGGAG 0.825571 -241 ********** Masking position 4 Map Score: 15.7607 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 679 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 CCTAAAAGCCAGAAAAAACTCCAAATTTTA 2 112 0 AGAAAAAACT 0.850852 -94 TAGTCTTGTTAGAATACCTTAAAAGAATTT 2 149 0 AGAATACCTT 0.745304 -57 TTGTGTAAAAACAAAACACTTATTGAGTTT 5 67 1 ACAAAACACT 0.958386 -87 GCAAAAGATCACAAAAAACTCAATAAGTGT 5 82 0 ACAAAAAACT 0.850852 -72 AATATTTATACCACAACCCTATTAAAAGCG 5 125 0 CCACAACCCT 0.937765 -29 AATCGCCAAATCCCTTGAATTGTTT 7 6 1 CCAAATCCCT 0.753504 -143 AGAAAACCCTACCCCTAAAA 9 53 0 AGAAAACCCT 0.984297 -10 AGACAACCTTAAAATTTTTA 11 14 0 AGACAACCTT 0.935168 -10 TAGAAAAACGACAAAACCCTACGATTATAG 12 145 1 ACAAAACCCT 0.984298 -104 TACTTAAGCTAAAAAACCTTAATCTTTTGC 12 174 0 AAAAAACCTT 0.780838 -75 GTTATAATAAAGACAAAATTAGAATTTTAG 12 218 1 AGACAAAATT 0.56761 -31 ********** Masking position 3 Map Score: 7.48654 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 690 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 ATTTTAAAAAACTTCAATTTTTCAGTATTTTT 2 86 0 ACTTAATTTT 0.932143 -120 TCCTTAATTTCCTTAAAACTATCTCAATGATA 2 179 0 CCTTAAACAT 0.816822 -27 AAATTAAAAAACTTTAAAACTTATTCTCATTA 3 48 1 ACTTAAAATT 0.699525 -124 AACAAATCCAACTTGAACTTTTCTTTTTCTTA 3 84 1 ACTTAACTTT 0.840565 -88 CTTAAATTTGAATTAAATCGTTTGTTTTTTAA 3 142 0 AATTAATCTT 0.639092 -30 CACCCCATCACCTTGACTCATTTAAGA 4 6 0 CCTTACTCTT 0.883275 -34 TTAATCATTTACTTTAATCATTTAATTTGTGT 5 41 1 ACTTAATCTT 0.966767 -113 AAAATTCTAGCCTTAAATCTTTGATGAAACGA 6 222 1 CCTTAATCTT 0.983517 -79 TAAAATCCTTAAACTCATTTTAGGGAAT 6 283 0 CCTTAACTAT 0.635792 -18 TCGCCAAATCCCTTGAATTGTTTGTTAAAAGT 7 13 1 CCTTAATTTT 0.965726 -136 TTAACCGGTCATTTTAATTATTTTAGTATAAT 7 53 0 ATTTAATTTT 0.455393 -96 ACTTTTACACCCTTTAAAATTTTATCGTTATT 8 38 0 CCTTAAAATT 0.826849 -30 TTTTAACGCTCGTTTAATCGTTTTTATTGGCG 9 15 1 CGTTAATCTT 0.843344 -48 AGACAACCTTAAAATTTTTAATT 11 6 0 CCTTAAATTT 0.928796 -18 AAGCTAAAAAACCTTAATCTTTTGCTATAATC 12 167 0 ACCTAATCTT 0.786742 -82 TTTATTATAACCTAAAAGCCTTTTTTACTTAA 12 197 0 CCTAAAGCTT 0.515684 -52 **** **** ** Masking position 6 Map Score: 11.3521 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 457 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 TGGCGTAATCATTTTTTAGGAAGT 1 5 0 ATTTTTTAGG 0.802435 -46 TTTTTCAGTATTTTTAAAGGATTAAAAAGC 2 71 0 TTTTTAAAGG 0.746828 -135 ATAACAACGCTTTTAATAGGGTTGTGGTAT 5 118 1 TTTTAATAGG 0.963518 -36 CTCATTTGCCCTTTAATATGCCCTTTAATG 6 170 0 CTTTAATATG 0.664906 -131 TGTAGCATGACTTTATTAGGGTGGGTAAAA 7 98 0 CTTTATTAGG 0.94662 -51 ATTGGCGCGCTTCTTTTAGGGGTAGGGTTT 9 40 1 TTCTTTTAGG 0.835143 -23 ATGCTAATCCTTGTATTAGGTGTTCTTAAG 12 72 0 TTGTATTAGG 0.890433 -177 TTTTCTATCATTTTAATAGGAACAAGGCAA 12 122 0 TTTTAATAGG 0.963518 -127 ********** Masking position 8 Map Score: 2.72816 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 256 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 ********** No masking Map Score: -3.0529e-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 10 ********** No masking Map Score: -3.0529e-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 11 ********** No masking Map Score: -3.0529e-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