AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_hpyl_reg_300.orf -o00550_hpyl_300.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 HP0778 127 H. pylori predicted coding region HP0778 #9 HP1154 130 H. pylori predicted coding region HP1154 #10 HP1492 138 conserved hypothetical nifU-like protein Motif number 1 GTAGCGCAAATTGATTTACTTAAAAATAGCATGAAT 1 52 0 TATTTTAAAA 0.976421 -73 TCGCCATGCTTGAAATTTAGAAAAAAGAAAATTGTA 1 85 0 TAATTAAAAA 0.927415 -40 ATTGATTGTTTTGATTTTCTTCAAAAAATCCTAATA 2 106 1 TATTTTAAAA 0.976421 -185 TTTTACCGCATGCATCTTAATAAAACTTGATACAGA 2 188 1 TATCTTAAAC 0.828115 -103 AATGGAATAGTTAATCTTACCTAAAATTTAAGCGTT 3 75 0 TATCTCAAAA 0.920198 -45 ATGATAACTTTTAAATTCTCTCAAAAATTAAAGGTT 4 18 0 TAATTTAAAA 0.980908 -129 GTTATCATACTAAAACGTGCTTAAAATTAAGCCTTA 4 46 1 TAACGTAAAA 0.856679 -101 ATTTTAGCATTTTATTTGCATTAAAAAGCGATTTTC 4 90 0 TATTTTAAAA 0.975603 -57 TCATTGCCTTAAATTCTTTTTAAATCATGGCATT 4 123 0 TAATTTTAAA 0.879166 -24 AAAAAGGCTTTTGAATTTTCTTAAAA 5 1 0 TAATTTAAAA 0.980906 -77 AAAGTCTATCTATATTTACCTAAAAAAAGGCTTTTG 5 24 0 TATTTTAAAA 0.97642 -54 GATCAAACTCCCTAAAAACGATTGCAAT 5 60 0 TAACTTAAAA 0.981581 -18 TGATTGTAACCTAATCTTGCTTAAAAACACCCTTTC 7 42 0 CATCTTAAAA 0.83642 -66 CATTAATTAATAAAATTTTAATAAAACTTGTGATTG 7 72 0 TAATTAAAAA 0.927407 -36 TAAAGTTTCTTACAACTTAACTAAAAGTAAAAAGAG 8 72 0 TAACTCAAAA 0.934667 -56 TGCTTTGTTGTATAATTTTGAAAAAATACGCAACAA 9 82 0 TAATTAAAAA 0.927408 -49 TATACAACAAAGCATTTAAATTAAAAAGGATAGTCC 9 104 1 AATTTTAAAA 0.768845 -27 TTTTTAAAACTCTCTTTAAAATTTTACTTT 10 119 0 TAACTTTAAA 0.883008 -20 * **** * **** Masking position 4 Map Score: 27.2524 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 239 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 AAAAGATTCCTAAAAATTAAAATAAG 1 5 1 GACCTAAAAA 0.704965 -120 CGCAAATTGATTTACTTAAAAATAGCATGAAT 1 52 0 TTCTTAAAAA 0.981436 -73 AAAATCCCCTAAAATCGCCATGCTT 1 110 0 ATCCTAAAAT 0.677487 -15 ATTGTTTTGATTTTCTTCAAAAAATCCTAATA 2 110 1 TTCTTCAAAA 0.848623 -181 AATAGTTAATCTTACCTAAAATTTAAGCGTTA 3 74 0 CTCCTAAAAT 0.931407 -46 AGGGCTACTTTAATCTTAAAATGGAATAGTTA 3 98 0 TACTTAAAAT 0.909479 -22 AACTTTTAAATTCTCTCAAAAATTAAAGGTTA 4 17 0 TTCTCAAAAA 0.841667 -130 CATACTAAAACGTGCTTAAAATTAAGCCTTAT 4 51 1 CGCTTAAAAT 0.756893 -96 TAAAAAGCGATTTTCTTAAACAATAAGGCTTA 4 73 0 TTCTTAAACA 0.848625 -74 AGCATTTTATTTGCATTAAAAAGCGATTTTCT 4 89 0 TTATTAAAAA 0.861867 -58 TCATTGCCTTAAATTCTTTTTAAAT 4 132 0 TTCTTAAATT 0.718582 -15 TCTATCTATATTTACCTAAAAAAAGGCTTTTG 5 24 0 TTCCTAAAAA 0.966933 -54 GCTGAGAATGTAGGCTTAAAATTCAGAAAGGG 7 17 1 TACTTAAAAT 0.909479 -91 GTAACCTAATCTTGCTTAAAAACACCCTTTCT 7 41 0 CTCTTAAAAA 0.973239 -67 CAATCACAAGTTTTATTAAAATTTTATTAATT 7 72 1 TTATTAAAAT 0.808133 -36 TATTATCCTAAAATAGAGCGTTCC 9 3 1 TTCCTAAAAT 0.951783 -128 AAAATAGAGCGTTCCTTAAAAAATGGTTGGAT 9 20 1 GTCTTAAAAA 0.938823 -111 AACAAAGCATTTAAATTAAAAAGGATAGTCCA 9 109 1 TTATTAAAAA 0.861867 -22 GCCCTTGAGCCACTCTTAAAAAGCGTTGTTTG 10 59 1 CACTTAAAAA 0.911017 -80 TTTTTAAAACTCTCTTTAAAATTTTACTTTA 10 118 0 CTCTTTAAAA 0.722372 -21 ** ******** Masking position 9 Map Score: 24.3723 Number of sites scoring better than the average of aligned sites = 884 Number in coding regions = 671 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 3 TGTTCGCATTATTCCTTTTTCCAACTATAC 2 51 1 ATTCCTTTTT 0.848648 -240 CCTAAAATTTAAGCGTTATGGTATGAAACC 3 62 0 AAGCGTTATG 0.735668 -58 AAGATTAACTATTCCATTTTAAGATTAAAG 3 93 1 ATTCCATTTT 0.601226 -27 GCTTAAAATTAAGCCTTATTGTTTAAGAAA 4 64 1 AAGCCTTATT 0.928181 -83 TTGCATTAAAAAGCGATTTTCTTAAACAAT 4 81 0 AAGCGATTTT 0.896543 -66 CATTGCCTTAAATTCTTTTTAAATCATGGC 4 126 0 AATTCTTTTT 0.645249 -21 GAAAATTCAAAAGCCTTTTTTTAGGTAAAT 5 17 1 AAGCCTTTTT 0.984442 -61 ACTTTATTGCAATCGTTTTTAGGGAGTTTG 5 55 1 AATCGTTTTT 0.938342 -23 TAAAAGTAAAAAGAGTTTTGTTATCATGGG 8 57 0 AAGAGTTTTG 0.453394 -71 TTAAAATCCTTTTTTGTATCGCAT 8 114 0 AATCCTTTTT 0.967616 -14 TGGATTTGGAACGCCTTTTGCTTTTACGCT 9 47 1 ACGCCTTTTG 0.80842 -84 TGGACTATCCTTTTTAATTTAAATG 9 116 0 TATCCTTTTT 0.746251 -15 ATCGTCATAAAAACCTTGTTCTAATAGTGG 10 11 1 AAACCTTGTT 0.662142 -128 CACTCTTAAAAAGCGTTGTTTGATAAAAAT 10 69 1 AAGCGTTGTT 0.91057 -70 ACCATATAATGAGCCATTTTTATCAAACAA 10 84 0 GAGCCATTTT 0.712806 -55 ********** Masking position 7 Map Score: 13.1529 Number of sites scoring better than the average of aligned sites = 1802 Number in coding regions = 1547 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 4 AGAAAATTGTAGCGCAAATTGATTTACTTA 1 66 0 AGCGCAAATT 0.935599 -59 AGGGCTACTTTAATCTTAAA 3 110 0 AGGGCTACTT 0.965316 -10 TCAAAAATTAAAGGTTAATTTTA 4 4 0 AAGGTTAATT 0.763938 -143 TTAAACAATAAGGCTTAATTTTAAGCACGT 4 60 0 AGGCTTAATT 0.937252 -87 TAAGCCCTAATTAAGGAATGAA 6 3 1 AGCCCTAATT 0.959501 -21 CTGAATTTTAAGCCTACATTCTCAGCGAAT 7 13 0 AGCCTACATT 0.758638 -95 CCTAAAATAGAGCGTTCCTTAAAAAATGGT 9 17 1 AGCGTTCCTT 0.904085 -114 GAGTGGCTCAAGGGCTAATTGGATAGAATA 10 44 0 AGGGCTAATT 0.982742 -95 TTTGATAAAAATGGCTCATTATATGGTATC 10 87 1 ATGGCTCATT 0.839873 -52 ********** Masking position 9 Map Score: 5.64706 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 5 GTAAATCAATTTGCGCTACAATTTTCTTTTT 1 69 1 TTGCGTACAA 0.967331 -56 ATTTCAAGCATGGCGATTTTAGGGGATTTT 1 105 1 TGGCGTTTTA 0.747488 -20 ATTAAGATGCATGCGGTAAAATCCGCTAAAT 2 178 0 ATGCGTAAAA 0.944948 -113 TTAAATTCTTATGCGCTATTATACTCTTTCT 3 27 1 ATGCGTATTA 0.949666 -93 TTAGTCAATAATGCGATTTAAAAAGGAGAA 8 10 0 ATGCGTTTAA 0.958754 -118 TTTAGCTACCATGCGATACAAAAAAGGATTT 8 104 1 ATGCGTACAA 0.985546 -24 TAAAAGCAAAAGGCGTTCCAAATCCAACCAT 9 42 0 AGGCGTCCAA 0.953859 -89 ***** ***** Masking position 11 Map Score: 2.75604 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 141 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 AAGCTTATTTTAATTTTTAGGAATCTTTT 1 9 0 TAATTTTTGG 0.837291 -116 TATCATCCCATAATTGTTCGCATTATTCCTT 2 37 1 TAATTGTTGC 0.963144 -254 ATACAACCTCTGATAGATAGGAATGACAAAT 2 77 1 TGATAGATGG 0.859455 -214 AATGACAAATTGATTGTTTTGATTTTCTTCA 2 98 1 TGATTGTTTG 0.932178 -193 CAAAAAATCCTAATAGTGTGGTTGCGTCTGC 2 127 1 TAATAGTGGG 0.929997 -164 GAATTGAGTTTGATTGATAGGGGTGATTATA 2 250 0 TGATTGATGG 0.920996 -41 TAACCACCTTTAATTGTTATGAATTGAGTTT 2 270 0 TAATTGTTTG 0.950748 -21 ACTAATGCCCTAATCGTTTGCCCCATGATAA 8 36 1 TAATCGTTGC 0.889391 -92 TTTACGCTTTTAATTGTTGCGTATTTTTTCA 9 69 1 TAATTGTTCG 0.918853 -62 AACCTTGTTCTAATAGTGGTCTTATTCTATC 10 22 1 TAATAGTGTC 0.65891 -117 ******** ** Masking position 4 Map Score: 4.52501 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 195 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TTACTTAAAAATAGCATGAATAGGGTAGGATA 1 41 0 ATGCATGATA 0.901609 -84 AGGGGTGATTATAGCATTTATGGGGCAAAAAA 2 231 0 ATGCATTATG 0.976561 -60 TAGCATTTTATTTGCATTAAAAAGCGATTTTC 4 90 0 TTGCATTAAA 0.822858 -57 TTTTTAAATCATGGCATTTTAGCATTTTATTT 4 109 0 ATGCATTTAG 0.976563 -38 CCTAAAAACGATTGCAATAAAGTCTATCTATA 5 46 0 ATGCAATAAG 0.922957 -32 TCCTTTTTAAATCGCATTATTGACTAATGCCC 8 14 1 ATGCATTTTG 0.962929 -114 CCTTTTTTGTATCGCATGGTAGCTAAAGTTTC 8 99 0 ATGCATGTAG 0.959268 -29 ATTATACAACAAAGCATTTAAATTAAAAAGGA 9 102 1 AAGCATTAAA 0.823988 -29 ** ***** *** Masking position 6 Map Score: 3.15894 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 215 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AAAGAAAATTGTAGCGCAAATTGATTTACT 1 68 0 GTAGCGCAAA 0.80019 -57 CATGGCGATTTTAGGGGATTTT 1 113 1 TTAGGGGATT 0.824515 -12 ACTCCTTGATTTAGCGGATTTTACCGCATG 2 170 1 TTAGCGGATT 0.772227 -121 TATAGCATTTATGGGGCAAAAAAAGTAGAA 2 224 0 ATGGGGCAAA 0.911908 -67 AAAGAGTATAATAGCGCATAAGAATTTAAC 3 26 0 ATAGCGCATA 0.960371 -94 GTTTCATACCATAACGCTTAAATTTTAGGT 3 63 1 ATAACGCTTA 0.668635 -57 TTCTTAAACAATAAGGCTTAATTTTAAGCA 4 63 0 ATAAGGCTTA 0.737304 -84 TAAAAAGAATTTAAGGCAATGA 4 135 1 TTAAGGCAAT 0.7145 -12 CATTCCTTAATTAGGGCTTA 6 1 0 TTAGGGCTTA 0.912971 -23 GGGCAAACGATTAGGGCATTAGTCAATAAT 8 29 0 TTAGGGCATT 0.956195 -99 TTTTGTTATCATGGGGCAAACGATTAGGGC 8 42 0 ATGGGGCAAA 0.911908 -86 TTTGATAAAAATGGCTCATTATATGGTATC 10 87 1 ATGGCTCATT 0.429293 -52 ********** Masking position 2 Map Score: 5.3115 Number of sites scoring better than the average of aligned sites = 1436 Number in coding regions = 1330 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 9 GGATGATATTATAAAAATTGGTGGGAATGA 2 15 0 ATAAAAATTG 0.96107 -276 ATGCATCTTAATAAAACTTGATACAGATTC 2 197 1 ATAAAACTTG 0.98234 -94 TAAAATTTTAATAAAACTTGTGATTGTAAC 7 68 0 ATAAAACTTG 0.98234 -40 ATCGTCATAAAAACCTTGTTCTAATAGT 10 9 1 AAAAACCTTG 0.883938 -130 GCGTTGTTTGATAAAAATGGCTCATTATAT 10 81 1 ATAAAAATGG 0.9175 -58 ********** Masking position 5 Map Score: 3.0037 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 14 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 AATAAGCTTCTATCCTACCCTATTCATGCT 1 31 1 TATCCTACCC 0.938763 -94 CTTATCATTCCCACCAATTTTT 2 3 1 TATCATTCCC 0.938054 -288 ATTTTTATAATATCATCCCATAATTGTTCG 2 27 1 TATCATCCCA 0.971591 -264 TCTTATGCGCTATTATACTCTTTCTTGGTG 3 33 1 TATTATACTC 0.867858 -87 TTCTTGGTGGTTTCATACCATAACGCTTAA 3 54 1 TTTCATACCA 0.895453 -66 ATTTAAAAGTTATCATACTAAAACGTGCTT 4 38 1 TATCATACTA 0.951908 -109 TATTATCCTAAAATAGAGCG 9 1 1 TATTATCCTA 0.818094 -130 ********** Masking position 6 Map Score: 2.6891 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 55 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 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