AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_hpyl_reg_100.orf -o00030_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 HP0175 300 cell binding factor 2 #2 HP0737 146 conserved hypothetical integral membrane protein #3 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #4 HP0742 64 phosphoribosylpyrophosphate synthetase (prsA) #5 HP1085 66 H. pylori predicted coding region HP1085 #6 HP1088 46 transketolase A (tktA) #7 HP1100_HP1101 65 HP1100: 6-phosphogluconate dehydratase, HP1101: glucose-6-phosphate dehydrogenase (g6pD) #8 HP1166 63 glucose-6-phosphate isomerase (pgi) #9 HP1180 300 pyrimidine nucleoside transport protein (nupC) #10 HP1385_HP1386 70 HP1385: fructose-1,6-bisphosphatase, HP1386: D-ribulose-5-phosphate 3 epimerase (rpe) #11 HP1492 138 conserved hypothetical nifU-like protein Motif number 1 TTGAATCTTCTTTAACATTTTTTTTCTTTCCAAAA 1 70 1 TTTAATTTTT 0.980715 -231 TGTAATAATATTTATTGTCTTTTTTGGTGTTAGTT 1 112 0 TTTATTTTTT 0.757654 -189 AATGAATAACTTTAAGCATTTCTTACTCTTTAATG 1 183 1 TTTAATCTTA 0.72904 -118 TTTCTTACTCTTTAATGTGAGTTTTCTGTGATCAT 1 201 1 TTTAAGTTTT 0.97392 -100 TTAAATTTGCTATAATGTGAATTTAATGATGAAAA 1 252 1 TATAAATTTA 0.770192 -49 CTCTCAAAAATTAAAGGTTAATTTTA 2 2 0 TTAAAATTTT 0.901893 -145 AAGGCTTAATTTTAAGCACGTTTTAGTATGATAAC 2 46 0 TTTAATTTTA 0.967135 -101 TTTATTTGCATTAAAAAGCGATTTTCTTAAACAAT 2 81 0 TTAAAATTTT 0.901893 -66 AATGCCATGATTTAAAAAGAATTTAAGGCAATGA 2 123 1 TTTAAATTTA 0.967242 -24 TTTAAGAAAATTCAAAAGCCTTTTTTTAGGTAAAT 3 12 1 TTCAATTTTT 0.843573 -66 CTACAATTGATTTTAATTCATTTTAGGGAGTGTAA 4 37 1 TTTTATTTTA 0.7884 -28 CCCTTTTAGTTATAATATAGATTTTATTTTAGCTA 5 17 1 TATAAATTTT 0.852595 -50 TTTTAAGGTTTTTGAGAGTCATTTTAACACAAA 6 9 0 TTTGAATTTT 0.908464 -38 CAATAACCCTTTTAGAGTGTTTTTGAGTTATTAT 7 10 1 TTTTATTTTT 0.865159 -56 GAATACCCCTTTAATTAAGATTTAATATATAATA 7 42 0 TTTAAATTTA 0.967242 -24 ATAAGCTAGTTTTAATTACAATTTTCAA 8 4 0 TTTAAATTTT 0.980716 -60 ATAATAAAAGTTTAATGTAATTTTAATGGATTTTT 9 54 1 TTTAATTTTA 0.967135 -247 TTAATGGATTTTTAAGAAAGGTTTTTGTATAATCT 9 76 1 TTTAAGTTTT 0.97392 -225 ATGATTTTGATTTAAACTTCATTTAATATCCGTTT 9 205 1 TTTAAATTTA 0.967242 -96 TTAATATCCGTTTAATCTTTTTTTTAGCAAAACTA 9 227 1 TTTAATTTTT 0.980715 -74 AAGACCACTATTAGAACAAGGTTTTTATGACGAT 11 10 0 TTAGAGTTTT 0.568486 -129 AAAGTAAAATTTTAAAGAGAGTTTTAAAAA 11 119 1 TTTAAGTTTT 0.97392 -20 ***** ***** Masking position 13 Map Score: 34.5106 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 647 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 AGAGTAAGAAATGCTTAAAGTTATTCATTCCATTC 1 177 0 ACTTAAAGTT 0.870682 -124 ACAGAAAACTCACATTAAAGAGTAAGAAATGCTTA 1 195 0 CATTAAAGGA 0.754255 -106 AATTCTCTCAAAAATTAAAGGTTAATTTTA 2 6 0 AATTAAAGTA 0.837291 -141 GCATTTTATTTGCATTAAAAAGCGATTTTCTTAAA 2 85 0 TATTAAAAGA 0.862882 -62 TAAAATGCCATGATTTAAAAAGAATTTAAGGCAAT 2 120 1 TTTTAAAAGT 0.726468 -27 GATCAAACTCCCTAAAAACGATTGCAATAAAGT 3 55 0 TCTAAAAAGT 0.900328 -23 TAGCGCACCCAAACTAAAAGCGTTTGTTT 4 5 0 ACTAAAAGGT 0.959004 -60 ATCTATATTATAACTAAAAGGGGGTTTT 5 4 0 TCTAAAAGGT 0.959004 -63 GATTTTATTTTAGCTAAAAATGGCATGGGTTTTAG 5 36 1 TCTAAAAAGA 0.908333 -31 ACTCTCAAAAACCTTAAAAATGGAAAAATTTG 6 25 1 ATTAAAAAGA 0.761682 -22 ACTCAAAAACACTCTAAAAGGGTTATTG 7 4 0 ACTAAAAGGA 0.962493 -62 ATATTAAATCTTAATTAAAGGGGTATTC 7 48 1 TATTAAAGGA 0.94219 -18 CAATACCCCTTAAATAAAAGATATAATGCTGTATT 8 39 0 TATAAAAGTA 0.849512 -25 AGTAGGATTGATAATAAAAGTTTAATGTAATTTTA 9 44 1 AATAAAAGTA 0.849512 -257 TACAAAAACCTTTCTTAAAAATCCATTAAAATTAC 9 70 0 TCTTAAAATA 0.740382 -231 CTAATGCAAGAAATTAAAAGATGCAAGGCTATTGT 9 266 0 ATTAAAAGTA 0.723247 -35 CTTTTATGATTTGATTAAAGATGCTAATATTTTAC 10 39 0 TATTAAAGTT 0.824282 -32 CTTTAATCAAATCATAAAAGGGTTTTT 10 54 1 AATAAAAGGT 0.94219 -17 CCCTTGAGCCACTCTTAAAAAGCGTTGTTTGATAA 11 60 1 ACTTAAAAGT 0.891685 -79 AAAGCGTTGTTTGATAAAAATGGCTCATTATATGG 11 78 1 TATAAAAAGT 0.86289 -61 CTTAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 11 116 1 ATTTAAAGGT 0.873064 -23 * ******* * * Masking position 5 Map Score: 22.1912 Number of sites scoring better than the average of aligned sites = 1975 Number in coding regions = 1731 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 CTTAAACAATAAGGCTTAATTTTAAGCACG 2 61 0 AAGGCTTAAT 0.676807 -86 GTTTAAGAAAATCGCTTTTTAATGCAAATA 2 84 1 ATCGCTTTTT 0.862601 -63 TTTTTAAATCATGGCATTTTAGCATTTTAT 2 111 0 ATGGCATTTT 0.774377 -36 TACCTAAAAAAAGGCTTTTGAATTTTCTTA 3 14 0 AAGGCTTTTG 0.947167 -64 AAACAAACGCTTTTAGTTTGGGTGC 4 6 1 AACGCTTTTA 0.701443 -59 TATAACTAAAAGGGGGTTTT 5 1 0 AGGGGGTTTT 0.822616 -66 TAAAAATGGCATGGGTTTTAGCAAGGA 5 50 1 ATGGGTTTTA 0.753616 -17 TTCCATTTTTAAGGTTTTTGAGAGTCATTT 6 20 0 AAGGTTTTTG 0.61033 -27 AACACTCTAAAAGGGTTATTG 7 2 0 AAGGGTTATT 0.963079 -64 ATCTTAATTAAAGGGGTATTC 7 55 1 AAGGGGTATT 0.904647 -11 TCTTTTATTTAAGGGGTATTG 8 53 1 AAGGGGTATT 0.904647 -11 TGTAATTTTAATGGATTTTTAAGAAAGGTT 9 69 1 ATGGATTTTT 0.650052 -232 GATTTTTAAGAAAGGTTTTTGTATAATCTC 9 82 1 AAAGGTTTTT 0.713091 -219 AAAAAGATTAAACGGATATTAAATGAAGTT 9 219 0 AACGGATATT 0.554237 -82 TAAAAGATGCAAGGCTATTGTAGTTTAGTT 9 257 0 AAGGCTATTG 0.717441 -44 CAAATCATAAAAGGGTTTTT 10 61 1 AAGGGTTTTT 0.977741 -10 GAGTGGCTCAAGGGCTAATTGGATAGAATA 11 44 0 AGGGCTAATT 0.546134 -95 TTTATCAAACAACGCTTTTTAAGAGTGGCT 11 66 0 AACGCTTTTT 0.935707 -73 TTTGATAAAAATGGCTCATTATATGGTATC 11 87 1 ATGGCTCATT 0.600476 -52 ********** Masking position 1 Map Score: 15.1916 Number of sites scoring better than the average of aligned sites = 2543 Number in coding regions = 2225 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 4 ATGATAGCTGATTTTGTTTTAAATTTGCTATA 1 234 1 ATTTTGTTAA 0.947679 -67 GCATTTTAGCATTTTATTTGCATTAAAAAGCG 2 96 0 ATTTTATTCA 0.898862 -51 GCTACAATTGATTTTAATTCATTTTAGGGAGT 4 36 1 ATTTTATTAT 0.894263 -29 TATAATATAGATTTTATTTTAGCTAAAAATGG 5 27 1 ATTTTATTAG 0.9711 -40 TATATATTAAATCTTAATTAAAGGGGTATTC 7 45 1 ATCTTATTAA 0.898862 -21 TTGAAAATTGTAATTAAAACTAGCTTAT 8 7 1 ATTGTATTAA 0.947679 -57 AGCATTATATCTTTTATTTAAGGGGTATTG 8 44 1 CTTTTATTAG 0.863532 -20 TGACACCATGATTTTGATTTAAACTTCATTTA 9 198 1 ATTTTGTTAA 0.947679 -103 ATGCAAGGCTATTGTAGTTTAGTTTTGCTAAA 9 249 0 ATTGTATTAG 0.928039 -52 AGATGCTAATATTTTACTTGAAAACATTGAAA 10 24 0 ATTTTATTAA 0.97925 -47 TCTCTTTAAAATTTTACTTTAAGATACCATAT 11 107 0 ATTTTATTAA 0.97925 -32 ****** ** ** Masking position 5 Map Score: 14.141 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 41 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 ATCGAGAATTTTTGAATCTTCTTTAACATTTT 1 59 1 TTTAATTTCT 0.96516 -242 TTGGTGTTAGTTTTATTCTTTTTGGAAAGAAA 1 92 0 TTTATTTTTT 0.925392 -209 CTGATTTTGTTTTAAATTTGCTATAATGTGAA 1 241 1 TTTAATTGCT 0.914032 -60 TATGATAACTTTTAAATTCTCTCAAAAATTAA 2 23 0 TTTAATCTCT 0.839151 -124 AAAAAAGGCTTTTGAATTTTCTTAAAA 3 6 0 TTTAATTTCT 0.96516 -72 TACAATTGATTTTAATTCATTTTAGGGAGTGT 4 38 1 TTTATTATTT 0.611801 -27 ATTTTTCCATTTTTAAGGTTTTTGAGAGTCAT 6 22 0 TTTAAGTTTT 0.80413 -25 AATCTCATTCTTTTATTTTTTTGTCAAGGTAG 9 106 1 TTTATTTTTT 0.925392 -195 TTTAATATCCGTTTAATCTTTTTTTTAGCAAA 9 226 1 GTTAATTTTT 0.80413 -75 GCTATTGTAGTTTAGTTTTGCTAAAAAAAAGA 9 242 0 TTTGTTTGCT 0.486301 -59 GCCTTGCATCTTTTAATTTCTTGCATTAGGGA 9 272 1 TTTAATTCTT 0.832982 -29 ACTTCCCTATTTTCAATGTTTTCAAGTAAAAT 10 14 1 TTTAATTTTT 0.959863 -57 *** *** **** Masking position 3 Map Score: 8.92904 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 368 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 AAATTCTCGATGCAATTATGAATATAATAT 1 40 0 TGCAATTATG 0.813563 -261 AAACAAAATCAGCTATCATGATCACAGAAA 1 223 0 AGCTATCATG 0.85662 -78 GTTTTAAATTTGCTATAATGTGAATTTAAT 1 249 1 TGCTATAATG 0.980266 -52 GCAAATAAAATGCTAAAATGCCATGATTTA 2 107 1 TGCTAAAATG 0.980267 -40 TAAAAACGATTGCAATAAAGTCTATCTATA 3 46 0 TGCAATAAAG 0.793329 -32 TGCCATTTTTAGCTAAAATAAAATCTATAT 5 31 0 AGCTAAAATA 0.815815 -36 TTTGTGTTAAAATGACTCTCAAAA 6 5 1 TGTTAAAATG 0.829643 -42 CTTAAATAAAAGATATAATGCTGTATTATA 8 36 0 AGATATAATG 0.688004 -28 AGTTTAGTTTTGCTAAAAAAAAGATTAAAC 9 236 0 TGCTAAAAAA 0.731124 -65 TGATTAAAGATGCTAATATTTTACTTGAAA 10 33 0 TGCTAATATT 0.63676 -38 ********** Masking position 5 Map Score: 3.49797 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 335 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 CATTTTTTTTCTTTCCAAAAAGAATAAAAC 1 85 1 CTTTCCAAAA 0.886012 -216 CTTTTAAATTCTCTCAAAAATTAAAGGTTA 2 17 0 CTCTCAAAAA 0.954169 -130 GATCAAACTCCCTAAAAACGATTGCAA 3 61 0 CTCCCTAAAA 0.880225 -17 CGCTTACACTCCCTAAAATGAATTAAAA 4 47 0 CTCCCTAAAA 0.880225 -18 TCCTTGCTAAAACCCATGCCAT 5 55 0 CTTGCTAAAA 0.864209 -12 GTTAAAATGACTCTCAAAAACCTTAAAAAT 6 16 1 CTCTCAAAAA 0.954169 -31 ATAATAATAACTCAAAAACACTCTAAAAGG 7 18 0 CTCAAAAACA 0.689596 -48 GCTGAGCTACCTTGACAAAAAAATAAAAGA 9 114 0 CTTGACAAAA 0.840297 -187 GAGACCAGCGCTCTAAACCAGCTGAGCTAC 9 134 0 CTCTAAACCA 0.757336 -167 AAGTCCCCCTCTTGACACCATGATTTTGAT 9 186 1 CTTGACACCA 0.600026 -115 TAATATTTTACTTGAAAACATTGAAAATAG 10 20 0 CTTGAAAACA 0.839943 -51 CCTTGAGCCACTCTTAAAAAGCGTTGTTTG 11 61 1 CTCTTAAAAA 0.729756 -78 ********** Masking position 7 Map Score: 5.67951 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 633 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TTCCATTTTTAAGGTTTTTGAGAGTCATTT 6 20 0 AAGGTTTTTG 0.970288 -27 ACACTCTAAAAGGGTTATTG 7 1 0 AGGGTTATTG 0.988742 -65 ACCCTTTTAGAGTGTTTTTGAGTTATTATT 7 16 1 AGTGTTTTTG 0.897419 -50 TCTTAATTAAAGGGGTATTC 7 56 1 AGGGGTATTC 0.93332 -10 CTTTTATTTAAGGGGTATTG 8 54 1 AGGGGTATTG 0.986451 -10 ATTTTTAAGAAAGGTTTTTGTATAATCTCA 9 83 1 AAGGTTTTTG 0.970288 -218 TAAAAGATGCAAGGCTATTGTAGTTTAGTT 9 257 0 AAGGCTATTG 0.950385 -44 ********** Masking position 1 Map Score: 8.68779 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 241 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 ********** No masking Map Score: 3.24961e-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: 3.24961e-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: 3.24961e-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