AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -irpoN_hpyl_opreg_100.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 HP0512 290 glutamine synthetase (glnA) #4 HP0698 187 H. pylori predicted coding region HP0698 #5 HP0699 39 H. pylori predicted coding region HP0699 #6 HP0900 108 hydrogenase expression/formation protein (hypB) #7 HP1169 212 glutamine ABC transporter, permease protein (glnP) Motif number 1 TTCAACGCTTATTGATCGTATTTGTGAAAGCT 2 149 1 ATTGTGTATT 0.886464 -26 TATTATAAAAATTGGTGGGAATGATAAG 3 7 0 ATTGTGGAAT 0.97867 -284 TCATCCCATAATTGTTCGCATTATTCCTTTTT 3 39 1 ATTGTGCATT 0.866966 -252 ACAACCTCTGATAGATAGGAATGACAAATTGA 3 79 1 ATAGTGGAAT 0.887498 -212 TGACAAATTGATTGTTTTGATTTTCTTCAAAA 3 100 1 ATTGTTGATT 0.984278 -191 ACACTCCTTGATTTAGCGGATTTTACCGCATG 3 168 1 ATTTGGGATT 0.929252 -123 AGTTTGATTGATAGGGGTGATTATAGCATTTA 3 243 0 ATAGGTGATT 0.899245 -48 ACCACCTTTAATTGTTATGAATTGAGTTTGAT 3 267 0 ATTGTTGAAT 0.974701 -24 GTGCTAAAAGCTTGGGTTGATTTAACTCAAGC 4 53 1 CTTGGTGATT 0.898252 -135 TGCAGCCAAATTTGTTAGGATTGAAGAAAATT 4 86 0 TTTGTGGATT 0.952102 -102 GCTTTTTTCTTTTTTTTTGATTTAATACTAGG 4 133 1 TTTTTTGATT 0.812235 -55 TTTTTTATCTTTTTGGCTGATTTTTTAGATCA 6 20 0 TTTTGTGATT 0.78036 -89 TTGTTTAATCATTGTTGTTAATTTCAGCCAGT 7 29 1 ATTGTTTAAT 0.831274 -184 ATAATCCAAAATTTCTTTGAATAGTGGCAAAA 7 70 1 ATTTTTGAAT 0.908907 -143 ACTTCTAACAATTGGGGTGAATAAGAGCTGTT 7 143 1 ATTGGTGAAT 0.972041 -70 **** * ***** Masking position 10 Map Score: 19.0651 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 445 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 TCATAGGGCTTTAAAAAAAGGATCTAGCGAAGAGGA 2 26 1 TTAAAAGATA 0.795782 -149 CGAAGAGGAGTTTCAAAAACGCTTGATTAGAAACAT 2 53 1 TTAAAAGCTA 0.90746 -122 TTCAAGCTTTCACAAATACGATCAATAAGCGTTGA 2 150 0 TCAAAAGATA 0.766096 -25 CATGCATCTTAATAAAACTTGATACAGATTCTACTT 3 196 1 AAAAATGATA 0.959175 -95 CACCCCTATCAATCAAACTCAATTCATAACAATTAA 3 256 1 AAAAATAATA 0.607456 -35 CAATCCTTTTTATGAAAGAGGCTTTATGCCTCTTGG 4 18 1 TAAAAAGCTA 0.977662 -170 GTTAGGATTGAAGAAAATTTGCTTGAGTTAAATCAA 4 69 0 AAAAATGCTA 0.983368 -119 CTTCAATCCTAACAAATTTGGCTGCAAATTAAAAAA 4 92 1 AAAATTGCTA 0.92981 -96 AATCAAAAAAAAAGAAAAAAGCTTAAATTTTTTAAT 4 119 0 AAAAAAGCTA 0.98561 -69 CCAAAAAGATAAAAAAAGTCGCTAAATCATAGTCGT 6 36 1 AAAAATGCTA 0.983368 -73 TGGCTGAAATTAACAACAATGATTAAACAATCATTA 7 23 0 TAAACAGATA 0.766096 -190 GGATTATAATAAAAAAACTGGCTGAAATTAACAACA 7 41 0 AAAAATGCTA 0.983368 -172 ATACCTTAAAAATTAATGACGCTTTAAAGCACCATG 7 181 0 AAAATAGCTA 0.938824 -32 ** *** * *** * Masking position 6 Map Score: 14.0308 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 518 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 AAATAACTATAACACAATCTCATTCAAATAGCG 1 14 0 AACCAATCAT 0.96727 -38 AGAATGTTTCTAATCAAGCGTTTTTGAAACTCC 2 59 0 TAACAAGCTT 0.953914 -116 GAAGAAAATCAAAACAATCAATTTGTCATTCCT 3 95 0 AAACAATCTT 0.968362 -196 CTATCAATCAAACTCAATTCATAACAATTAAAG 3 261 1 AACCAATTTA 0.743399 -30 GATTGCTCAATCCTTTTTATGAAAGA 4 4 1 TGCCAATCTT 0.919754 -184 GAGTTAAATCAACCCAAGCTTTTAGCACCAAGA 4 48 0 AACCAAGCTT 0.991747 -140 GGGTTGATTTAACTCAAGCAAATTTTCTTCAAT 4 66 1 AACCAAGCAT 0.974392 -122 CAACAATGATTAAACAATCATTAAATGGAGAGG 7 13 0 TAACAATCTA 0.835487 -200 AAGTTTGGAAAACCCAAGCCCTTATTATGGGAA 7 114 0 AACCAAGCTT 0.991762 -99 *** ***** ** Masking position 7 Map Score: 7.25746 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 358 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 GTTATTTAAAAGGATATTTTGA 1 40 1 AGGATTTTGA 0.974092 -12 CTTTAAAAAAAGGATCTAGCGAAGAGGAGTTT 2 34 1 AGGATTACGA 0.973802 -141 TTTGAAACCGATGATTTTTCAACGCTTATTGA 2 132 1 ATGATTTCAA 0.959485 -43 CAATTATGGGATGATATTATAAAAATTGGTGG 3 21 0 ATGATTTTAA 0.937281 -270 CCACACTATTAGGATTTTTTGAAGAAAATCAA 3 116 0 AGGATTTTGA 0.974092 -175 TTTCATAAAAAGGATTGAGCAATC 4 3 0 AGGATGACAA 0.929928 -185 TTAAACGACTATGATTTAGCGACTTTTTTTAT 6 44 0 ATGATTACGA 0.959076 -65 TCTCCATTTAATGATTGTTTAATCATTGTTGT 7 15 1 ATGATGTTAA 0.894319 -198 ***** ** *** Masking position 4 Map Score: 6.63656 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 117 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 AAGCCCTATGACAAGTAGGGCAAAGT 2 7 0 ACAAGTAGGG 0.971664 -168 TGATATTATAAAAATTGGTGGGAATGATAA 3 12 0 AAAATTGGTG 0.831785 -279 AATAATGCGAACAATTATGGGATGATATTA 3 34 0 ACAATTATGG 0.915631 -257 TCAATTCATAACAATTAAAGGTGGTTA 3 274 1 ACAATTAAAG 0.780551 -17 TACTTTCAATAAAATAAGGGGTTTTTT 5 23 1 AAAATAAGGG 0.958678 -17 CGAAAATTTTAAAAGAAAGGAACAAC 6 93 1 AAAAGAAAGG 0.815935 -16 TAAACTTCCCATAATAAGGGCTTGGGTTTT 7 109 1 ATAATAAGGG 0.875802 -104 CAAACTTCTAACAATTGGGGTGAATAAGAG 7 140 1 ACAATTGGGG 0.971664 -73 CTATACCTTAAAAATTAATGACGCTTTAAA 7 189 0 AAAATTAATG 0.798153 -24 ********** Masking position 4 Map Score: 4.63037 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 377 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AAATATCCTTTTAAATAACTATAACACAATCT 1 27 0 TTATAACTAT 0.76697 -25 GATCCTTTTTTTAAAGCCCTATGACAAGTAGG 2 18 0 TTAGCCCTAT 0.954149 -157 CATTATTCCTTTTTCCAACTATACAACCTCTG 3 57 1 TTTCAACTAT 0.901345 -234 GATTCTACTTTTTTTGCCCCATAAATGCTATA 3 222 1 TTTGCCCCAT 0.954845 -69 CAACCCAAGCTTTTAGCACCAAGAGGCATAAA 4 40 0 TTTGCACCAA 0.87214 -148 GTTCTATCACTATACTTTCAATA 5 2 1 TTTTCACTAT 0.946605 -38 GCGCACTTAATTAAACGACTATGATTTAGCGA 6 54 0 TTACGACTAT 0.861743 -55 TTATGAGCCGTTTTGCCACTATTCAAAGAAAT 7 80 0 TTTCCACTAT 0.975575 -133 TAATGACGCTTTAAAGCACCATGTTTAAAAAC 7 172 0 TTAGCACCAT 0.972306 -41 ** * ******* Masking position 2 Map Score: 3.63472 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 214 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 TTTTCAACGCTTATTGATCGTATTTGTGAA 2 147 1 TTATTGATCG 0.960992 -28 ATACAACCTCTGATAGATAGGAATGACAAA 3 77 1 TGATAGATAG 0.932627 -214 GAATTGAGTTTGATTGATAGGGGTGATTAT 3 251 0 TGATTGATAG 0.978422 -40 ACCCCTTATTTTATTGAAAGTATAGTGATA 5 15 0 TTATTGAAAG 0.927785 -25 TCCTCTCCATTTAATGATTGTTTAATCATT 7 12 1 TTAATGATTG 0.835677 -201 ********** Masking position 7 Map Score: 0.201872 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 74 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 AAACGCTATTTGAATGAGAT 1 1 1 AAACGCTATT 0.972359 -51 AAACATTCTCAATCGCAATAAAGACAATTT 2 83 1 AATCGCAATA 0.910276 -92 ATCGGTTTCAAAACGCAATTGCGCAAACTC 2 114 0 AAACGCAATT 0.965505 -61 TTTGCCCCATAAATGCTATAATCACCCCTA 3 234 1 AAATGCTATA 0.846513 -57 CCTATCAATCAAACTCAATTCATAACAATT 3 260 1 AAACTCAATT 0.919579 -31 ********** Masking position 8 Map Score: 2.07059 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 160 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 ********** No masking Map Score: -1.59629e-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: -1.59629e-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: -1.59629e-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