AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_hpyl_reg_100.orf -o00550_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 HP0493 124 phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) #2 HP0512 290 glutamine synthetase (glnA) #3 HP0624 119 solute-binding signature and mitochondrial signature protein (aspB) #4 HP0737 146 conserved hypothetical integral membrane protein #5 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #6 HP0774 23 tyrosyl-tRNA synthetase (tyrS) #7 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #8 HP1154 130 H. pylori predicted coding region HP1154 #9 HP1492 138 conserved hypothetical nifU-like protein Motif number 1 GCGCAAATTGATTTACTTAAAAATAGCATGAA 1 53 0 ATTTATAAAA 0.924393 -72 ATTCCCACCAATTTTTATAATATCATCCCATA 2 17 1 ATTTTTAATA 0.809958 -274 GATTGTTTTGATTTTCTTCAAAAAATCCTAAT 2 109 1 ATTTTTCAAA 0.948006 -182 TACCGCATGCATCTTAATAAAACTTGATACAG 2 191 1 ATCTTTAAAA 0.972025 -100 GGAATAGTTAATCTTACCTAAAATTTAAGCGT 3 76 0 ATCTTCTAAA 0.842655 -44 TAACTTTTAAATTCTCTCAAAAATTAAAGGTT 4 18 0 ATTCTCAAAA 0.81511 -129 TTTAAAAGTTATCATACTAAAACGTGCTTAAA 4 39 1 ATCATTAAAA 0.839815 -108 TTAAAAAGCGATTTTCTTAAACAATAAGGCTT 4 74 0 ATTTTTAAAC 0.86328 -73 TTAGCATTTTATTTGCATTAAAAAGCGATTTT 4 91 0 ATTTGTTAAA 0.792999 -56 ATTGCCTTAAATTCTTTTTAAATCATGGCATT 4 123 0 ATTCTTTAAA 0.882571 -24 AGGCTTTTGAATTTTCTTAAAA 5 1 0 ATTTTTAAAA 0.984277 -77 GTCTATCTATATTTACCTAAAAAAAGGCTTTT 5 25 0 ATTTATAAAA 0.924393 -53 TTGTAACCTAATCTTGCTTAAAAACACCCTTT 7 43 0 ATCTTTTAAA 0.94684 -65 AATTAATAAAATTTTAATAAAACTTGTGATTG 7 72 0 ATTTTTAAAA 0.984277 -36 TATTATCCTAAAATAGAGCGTTC 8 2 1 ATTATTAAAA 0.904545 -129 ATTGTTGCGTATTTTTTCAAAATTATACAACA 8 81 1 ATTTTCAAAA 0.949692 -50 ACAACAAAGCATTTAAATTAAAAAGGATAGTC 8 107 1 ATTTATTAAA 0.866884 -24 ATCGTCATAAAAACCTTGTTCT 9 1 1 ATCGTTAAAA 0.815041 -138 ATAATGAGCCATTTTTATCAAACAACGCTTTT 9 77 0 ATTTTTCAAA 0.948006 -62 TCTCTTTAAAATTTTACTTTAAGATACCATAT 9 107 0 ATTTTTTTAA 0.685995 -32 ***** ***** Masking position 2 Map Score: 27.7112 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 561 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 CTTATTTTAATTTTTAGGAATCTTTT 1 6 0 TTTTTAGGAT 0.939835 -119 ATTCATGCTATTTTTAAGTAAATCAATTTGC 1 52 1 TTTTTAAGAA 0.983753 -73 AAGCATGGCGATTTTAGGGGATTTT 1 110 1 ATTTTAGGGA 0.957532 -15 TATTAGGATTTTTTGAAGAAAATCAAAACAA 2 111 0 TTTTGAAGAA 0.884792 -180 TAACGCTTAAATTTTAGGTAAGATTAACTAT 3 74 1 ATTTTAGGAA 0.975962 -46 TAACTATTCCATTTTAAGATTAAAGTAGCCC 3 98 1 ATTTTAAGTT 0.646226 -22 TAACCTTTAATTTTTGAGAGAATTTAAAAGT 4 17 1 TTTTTGAGGA 0.790461 -130 ATAAGGCTTAATTTTAAGCACGTTTTAGTAT 4 52 0 ATTTTAAGAC 0.850968 -95 TAAGCCTTATTGTTTAAGAAAATCGCTTTTT 4 73 1 TGTTTAAGAA 0.871674 -74 TTTAAAAAGAATTTAAGGCAATGA 4 133 1 ATTTAAGGAA 0.859666 -14 CAAAAGCCTTTTTTTAGGTAAATATAGATAG 5 24 1 TTTTTAGGAA 0.98433 -54 ATTGCAATCGTTTTTAGGGAGTTTGATC 5 60 1 TTTTTAGGAG 0.901607 -18 AGAAAGGGTGTTTTTAAGCAAGATTAGGTTA 7 41 1 TTTTTAAGAA 0.983753 -67 AATTAATAAAATTTTAATAAAACTTGTGATT 7 73 0 ATTTTAATAA 0.646396 -35 GGAACGCTCTATTTTAGGATAATA 8 4 0 ATTTTAGGTA 0.883974 -127 ATCCAACCATTTTTTAAGGAACGCTCTATTT 8 21 0 TTTTTAAGAA 0.983753 -110 CAAACAACGCTTTTTAAGAGTGGCTCAAGGG 9 60 0 TTTTTAAGGT 0.893206 -79 TAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 9 118 1 TTTTAAAGGA 0.83538 -21 ******** ** Masking position 4 Map Score: 25.5941 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 677 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 TAAGTAAATCAATTTGCGCTACAATTTTCT 1 66 1 AATTTGCGCT 0.93971 -59 TTTAAGATTAAAGTAGCCCT 3 110 1 AAGTAGCCCT 0.967595 -10 TAAAATTAACCTTTAATTTTTGA 4 4 1 AATTAACCTT 0.776385 -143 ACGTGCTTAAAATTAAGCCTTATTGTTTAA 4 60 1 AATTAAGCCT 0.941264 -87 TTCATTCCTTAATTAGGGCTTA 6 3 0 AATTAGGGCT 0.962148 -21 ATTCGCTGAGAATGTAGGCTTAAAATTCAG 7 13 1 AATGTAGGCT 0.771283 -95 ACCATTTTTTAAGGAACGCTCTATTTTAGG 8 17 0 AAGGAACGCT 0.910004 -114 TATTCTATCCAATTAGCCCTTGAGCCACTC 9 44 1 AATTAGCCCT 0.983896 -95 GATACCATATAATGAGCCATTTTTATCAAA 9 87 0 AATGAGCCAT 0.849108 -52 ********** Masking position 2 Map Score: 6.59361 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 332 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 TAAATGCTATAATCACCCCTATCAATCAAAC 2 243 1 AACACCCCTA 0.811561 -48 TAACCACCTTTAATTGTTATGA 2 279 0 AACACCTTTA 0.85352 -12 GGTTTCATACCATAACGCTTAAATTTTAGGT 3 62 1 CAAACGCTTA 0.899596 -58 GCTTAATTTTAAGCACGTTTTAGTATGATAA 4 47 0 AACACGTTTT 0.950434 -100 TTTCTTAAACAATAAGGCTTAATTTTAAGCA 4 63 0 AAAAGGCTTA 0.950152 -84 ATTGTTTAAGAAAATCGCTTTTTAATGCAAA 4 81 1 AAATCGCTTT 0.898176 -66 ATTTACCTAAAAAAAGGCTTTTGAATTTTCT 5 16 0 AAAAGGCTTT 0.964666 -62 TCTTGCTTAAAAACACCCTTTCTGAATTTTA 7 33 0 AACACCCTTT 0.967953 -75 CCACTATTAGAACAAGGTTTTTATGACGAT 9 10 0 AAAAGGTTTT 0.886851 -129 ATTTTTATCAAACAACGCTTTTTAAGAGTGG 9 68 0 AAAACGCTTT 0.984339 -71 ** ******** Masking position 2 Map Score: 8.01741 Number of sites scoring better than the average of aligned sites = 1554 Number in coding regions = 1378 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 5 TCTATCCTACCCTATTCATGCTATTTTTAA 1 39 1 CCTATTCATG 0.705795 -86 ATAATATCATCCCATAATTGTTCGCATTAT 2 33 1 CCCATAATTG 0.889116 -258 CTTTTTTTGCCCCATAAATGCTATAATCAC 2 229 1 CCCATAAATG 0.916914 -62 TAACCACCTTTAATTGTTATGAATTG 2 275 0 CCTTTAATTG 0.929628 -16 CGCTATTATACTCTTTCTTGGTGGTTTCAT 3 40 1 CTCTTTCTTG 0.743609 -80 CATACCATAACGCTTAAATTTTAGGTAAGA 3 67 1 CGCTTAAATT 0.688359 -53 TAAAATTAACCTTTAATTTTTGAGAGAAT 4 10 1 CCTTTAATTT 0.857967 -137 AGTATGATAACTTTTAAATTCTCTCAAAAA 4 27 0 CTTTTAAATT 0.860829 -120 AAGAAAATCGCTTTTTAATGCAAATAAAAT 4 88 1 CTTTTTAATG 0.908248 -59 GATCCCTTCTCATTAATTAATAAAATTT 7 90 0 CTCATTAATT 0.730066 -18 TGCTTTTACGCTTTTAATTGTTGCGTATTT 8 65 1 CTTTTAATTG 0.907984 -66 TGGACTATCCTTTTTAATTTAAATGCTTT 8 112 0 CTTTTTAATT 0.81823 -19 ********** Masking position 5 Map Score: 7.98589 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 595 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 CTGCTTCCATAATAACACTCCTTGATTTAG 2 154 1 AATAACACTC 0.95299 -137 CATGCATCTTAATAAAACTTGATACAGATT 2 196 1 AATAAAACTT 0.97242 -95 CACCCCTATCAATCAAACTCAATTCATAAC 2 256 1 AATCAAACTC 0.978707 -35 GATCAAACTCCCTAAAAACG 5 68 0 GATCAAACTC 0.94384 -10 ATAAAATTTTAATAAAACTTGTGATTGTAA 7 69 0 AATAAAACTT 0.97242 -39 CTCATTAATTAATAAAATTTTAATAAAACT 7 80 0 AATAAAATTT 0.845071 -28 ********** Masking position 5 Map Score: 4.15064 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 73 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CTTATTTTAATTTTTAGGAATCTTTT 1 6 0 TTTTTAGAAT 0.874853 -119 ACAATTTTCTTTTTTCTAAATTTCAAGCATG 1 86 1 TTTTTCAAAT 0.971797 -39 GCATTATTCCTTTTTCCAACTATACAACCTC 2 56 1 TTTTTCAACT 0.974171 -235 TGTTGCGTATTTTTTCAAAATTATACAACAA 8 83 1 TTTTTCAAAT 0.965396 -48 TTTTTAAAACTCTCTTTAAAA 9 128 0 TTTTTAAACT 0.943287 -11 ****** **** Masking position 5 Map Score: 1.72968 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 151 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 GCATGAATAGGGTAGGATAGAAGCTTATTTT 1 29 0 GGTAGGAAGA 0.980405 -96 TATAAAAATTGGTGGGAATGATAAG 2 5 0 GGTGGGATGA 0.986694 -286 ACCTCTGATAGATAGGAATGACAAATTGATT 2 82 1 GATAGGATGA 0.986497 -209 GAGTTTGATTGATAGGGGTGATTATAGCATT 2 245 0 GATAGGGTGA 0.970512 -46 TTAAATTTTAGGTAAGATTAACTATTCCATT 3 80 1 GGTAAGATAA 0.858046 -40 ******* *** Masking position 3 Map Score: 0.418573 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 47 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ********** No masking Map Score: 6.49026e-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: 6.49026e-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 11 ********** No masking Map Score: 6.49026e-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