AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_hpyl_reg_100.orf -o00620_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 HP0121 186 phosphoenolpyruvate synthase (ppsA) #2 HP0282 50 H. pylori predicted coding region HP0282 #3 HP0289 66 toxin-like outer membrane protein #4 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #5 HP0371 123 biotin carboxyl carrier protein (fabE) #6 HP0557 22 acetyl-coenzyme A carboxylase (accA) #7 HP0558 300 beta ketoacyl-acyl carrier protein synthase II (fabF) #8 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #9 HP0950 77 acetyl-CoA carboxylase beta subunit (accD) #10 HP1045 197 acetyl-CoA synthetase (acoE) #11 HP1222 65 D-lactate dehydrogenase (dld) #12 HP1483 26 gerC2 protein (gerC2) #13 HP1490 103 hemolysin Motif number 1 GGTGTATTCTTTTTGGTTTATGATTTTATTG 1 56 0 TTTTGGTTTT 0.894291 -131 CATTGTTATATTTTTGTTTTAAGAAACTTAA 1 145 1 TTTTTGTTTA 0.776789 -42 ATATCCAAGATTAAGGCTTAAACG 2 4 0 TTAAGGCTTA 0.767775 -47 ATGAGAGAGTTTTTGGCTACTATCTAGGAAA 3 29 1 TTTTGGCTAT 0.915207 -38 CTTTTTTGCTATAATGCTTCGTT 4 3 1 TTTTTGCTAA 0.816172 -45 AAATTTTATGGTTAGGTTTTTCT 4 35 1 GTTAGGTTTT 0.912074 -13 TAACAATAATTTTTTGCTAAAAACGCTTATG 5 46 1 TTTTTGCTAA 0.815753 -78 CTAAAAACGCTTATGGCTAGTAAGATTATGT 5 62 1 TTATGGCTAT 0.539176 -62 TTTTACAAAGTTAGGATTTTGA 6 10 1 GTTAGGATTT 0.843263 -13 TTAGTCAAAAATTTGGCTTTAGCTAAAATCT 7 36 1 ATTTGGCTTA 0.759048 -265 GTGCATAGCTGTTAGGCTATATTCAAGCTAA 7 118 1 GTTAGGCTAA 0.95792 -183 TTTTAACCTCTTTTAGCTTGAATATAGCCTA 7 130 0 TTTTAGCTTA 0.6135 -171 AGATATGCACTTTAGGCTCATGTTTCTCTAA 8 70 0 TTTAGGCTCT 0.732794 -212 TTAGGTTTTGTTTTGGATTGAGGGCGATCCG 8 184 0 TTTTGGATTA 0.883121 -98 TGGATTTTATTTTAGGTTTTGTTTTGGATTG 8 195 0 TTTAGGTTTG 0.682682 -87 TTGTATCCAAGTTTTGCTTATAATAAACAAA 9 26 0 GTTTTGCTTT 0.833385 -52 TTGCAGTTTTGTTAGGATTGTATCCAAGTTT 9 43 0 GTTAGGATTT 0.843263 -35 TAATATCCCCTTTAGGTTTCATCGTGCTATT 10 60 1 TTTAGGTTTA 0.940665 -138 AAGAGTGTGAGTTTGGATATAATAATAAAAA 10 146 1 GTTTGGATAA 0.831736 -52 TTAAAATAAGGTTATGTTACAATGATTTGAT 11 26 1 GTTATGTTAA 0.712472 -40 GATTTTTAAAGTTAGGCTTAATCTTTTATGT 13 26 1 GTTAGGCTTA 0.974773 -78 GGCTTAATCTTTTATGTTAAAATTCTGAGAT 13 40 1 TTTATGTTAA 0.686133 -64 TATATTTATCGTTAGGTTTTAGGTTTAAAGT 13 82 1 GTTAGGTTTA 0.946986 -22 ********* * Masking position 8 Map Score: 23.6437 Number of sites scoring better than the average of aligned sites = 1572 Number in coding regions = 1400 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 AATACACCCTCTTATTAAAAAGCTTAGTAATA 1 79 1 CTATTAAAAG 0.792886 -108 AAAACTCCCTTAAAATGATCATTAAG 1 171 0 CTCCTTAAAT 0.665382 -16 ACTTCCTAAAAAATGATTACGCC 2 38 0 CTCCTAAAAA 0.939224 -13 AGAAAAACCTAACCATAAAATTTGAACGAA 4 28 0 CTACCAAAAA 0.828735 -20 TAATTATTAACAAACTTTAAAGGCTTT 5 6 0 CAACTTAAAG 0.840812 -118 GTGTTTGTGGCATATTTTAAAATAATATAAGG 5 91 1 CAATTTAAAA 0.747028 -33 TGGATATTTCCTACCCCAAAAAGACTATTTTA 7 156 0 CTCCCCAAAA 0.778818 -145 AATATCCATGCAGACTTTAAAGAACAAAGCCT 7 180 1 CAACTTAAAG 0.840812 -121 CCATTGAATGCTAACACGAAAGGCTTTGTTCT 7 200 0 CTACACAAAG 0.75379 -101 CAATAGCTCCTCATTTCAAAACTTTAATTCA 7 280 0 CTATTTAAAA 0.895494 -21 AATTCTATTAAAACCCTGAAACT 8 2 1 ATCTATAAAA 0.615368 -280 TAGGCAAAGACTGCTTAGAAAGAAATTTTTTA 8 33 1 CTCTTAAAAG 0.817179 -249 ACGGATCGCCCTCAATCCAAAACAAAACCTAA 8 183 1 CTAATCAAAA 0.320413 -99 TAGGGTGTCAATCACCTAAAAGTGATACTATG 8 232 1 ATACCTAAAG 0.636851 -50 CTTGGATACAATCCTAACAAAACTGCAAAATT 9 46 1 ATCTAAAAAA 0.49972 -32 GTAGAACATTATGACTACAAAAAGGGTGAT 10 9 0 ATACTAAAAA 0.80715 -189 TGGATTGAGACTGATAAAAAAGGAAATAGCAC 10 83 0 CTATAAAAAG 0.662792 -115 AAAAGTATCCCTCCCTTTAAAAGAGTGTGAGT 10 126 1 CTCCTTAAAA 0.961176 -72 GAGTTTGGATATAATAATAAAAAATGCGCTTA 10 154 1 ATATAAAAAA 0.462292 -44 AATGCGCTTAAAACCATGAAAAAGGAGATGCG 10 176 1 AACCATAAAA 0.578256 -22 GTAACATAACCTTATTTTAAAAACTAAGGATA 11 14 0 CTATTTAAAA 0.895494 -52 AGACAAGCCATGAAAAAAGAAAAGTC 12 5 1 AACCATAAAA 0.578256 -22 TTTAAAAATCAAGCCTTCAAAAACC 13 4 0 AACCTTAAAA 0.728561 -100 AAGATTAAGCCTAACTTTAAAAATCAAGCCTT 13 19 0 CTACTTAAAA 0.955175 -85 ** **** **** Masking position 9 Map Score: 15.7129 Number of sites scoring better than the average of aligned sites = 2012 Number in coding regions = 1726 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 3 AACCACCCTTTCTATTCAAAA 1 2 1 ACCACCCTTT 0.974968 -185 TACCTAACTAACCGCCCATTATACAATAAA 1 33 1 ACCGCCCATT 0.93439 -154 AAAGAATACACCCTCTTATTAAAAAGCTTA 1 75 1 CCCTCTTATT 0.820861 -112 TAGCCAAAAACTCTCTCATTTGATTAAATC 3 18 0 CTCTCTCATT 0.896773 -49 TAAATGCTACCCTCTCATTTCCTAGATAG 3 48 0 CCCTCTCATT 0.963646 -19 ATTCAGTGAAACCACCCCTTGCTTAAAGCA 7 255 0 ACCACCCCTT 0.934391 -46 ATCACCCTTTTTGTAGTCAT 10 1 1 ATCACCCTTT 0.927353 -197 AAAAAAGTATCCCTCCCTTTAAAAGAGTGT 10 124 1 CCCTCCCTTT 0.987101 -74 TATCCAAACTCACACTCTTTTAAAGGGAGG 10 135 0 CACACTCTTT 0.774684 -63 CGCATCTCCTTTTTCATGGTTTT 10 185 0 ATCTCCTTTT 0.731092 -13 ********** Masking position 9 Map Score: 8.57229 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 370 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 CAAACTAGCTAAAACTAAAGCTCTATCATGC 1 111 1 AAAATAAAGC 0.888086 -76 CATTATATCCAAGATTAAGGCTTAAACG 2 8 0 AAGATAAGGC 0.970795 -43 GCAGACTTTAAAGAACAAAGCCTTTCGTGTT 7 189 1 AAGACAAAGC 0.893921 -112 ACCCCTTGCTTAAAGCAAGGAGCTTCCTAAC 7 241 0 TAAACAAGGA 0.80631 -60 GTGGGGATCTAAAATCAAGCAGATATGCACT 8 90 0 AAAACAAGCA 0.931549 -192 ACAAAACTGCAAAATTAAGGAAAAAC 9 62 1 AAAATAAGGA 0.953513 -16 CCTTATTTTAAAAACTAAGGATAAAC 11 6 0 AAAATAAGGA 0.953513 -60 CCTAACTTTAAAAATCAAGCCTTCAAAAACC 13 11 0 AAAACAAGCC 0.963948 -93 TTTAACATAAAAGATTAAGCCTAACTTTAAA 13 30 0 AAGATAAGCC 0.944844 -74 **** ****** Masking position 7 Map Score: 7.93198 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 309 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TAATGGGCGGTTAGTTAGGTATTTTTGAAT 1 24 0 TTAGTTAGGT 0.940281 -163 TTCAAATTTTATGGTTAGGTTTTTCT 4 32 1 ATGGTTAGGT 0.973152 -16 TTTTACAAAGTTAGGATTTTGA 6 7 1 AAAGTTAGGA 0.960572 -16 TCTCTACCTAAAGGATAGGAGTTTTTCGTG 7 83 0 AAGGATAGGA 0.822629 -218 ATGGAATGCTTTAGTTAGGAAGCTCCTTGC 7 228 1 TTAGTTAGGA 0.940281 -73 ATTTTGCAGTTTTGTTAGGATTGTATCCAA 9 47 0 TTTGTTAGGA 0.827158 -31 TTTTTAAAATAAGGTTATGTTACAATGATT 11 23 1 AAGGTTATGT 0.742549 -43 CTTGATTTTTAAAGTTAGGCTTAATCTTTT 13 23 1 AAAGTTAGGC 0.916493 -81 TTTTATATTTATCGTTAGGTTTTAGGTTTA 13 79 1 ATCGTTAGGT 0.931137 -25 ********** Masking position 6 Map Score: 5.32486 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 66 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 GCCCATTATACAATAAAATCATAAACCAAA 1 46 1 CAATAAAATC 0.917476 -141 ATTTGGCTTTAGCTAAAATCTAGTTTTATC 7 46 1 AGCTAAAATC 0.970254 -255 TTGAGTGGGGATCTAAAATCAAGCAGATAT 8 95 0 ATCTAAAATC 0.954724 -187 ACAAAACCTAAAATAAAATCCAACCTGTTA 8 204 1 AAATAAAATC 0.930605 -78 AGCATATTAACGCTAATATCCCCTTTAGGT 10 47 1 CGCTAATATC 0.869643 -151 AATATAAAATATATAAAATCTCAGAATTTT 13 58 0 ATATAAAATC 0.930606 -46 ********** Masking position 5 Map Score: 2.0067 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 312 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ACCCTCTTATTAAAAAGCTTAGTAATACAAAC 1 84 1 TAAAGCTTAG 0.789497 -103 TTAGTAATACAAACTAGCTAAAACTAAAGCTC 1 102 1 AAAAGCTAAA 0.877266 -85 ATTTTTGTTTTAAGAAACTTAATGATCATTTT 1 154 1 TAAAACTTAA 0.735488 -33 AAAACTCCCTTAAAATGATCATT 1 174 0 AAACCCTTAA 0.856859 -13 ATTTTTTGCTAAAAACGCTTATGGCTAGTAAG 5 54 1 AAACGCTTAT 0.919325 -70 TATTCAAGCTAAAAGAGGTTAAAATAGTCTTT 7 137 1 AAAAGGTTAA 0.931358 -164 TATGAATAATAAATCAACTTAAAGGCAAAGAC 8 260 1 AAAAACTTAA 0.909114 -22 ATAATAAACAAAATTAGCTTAAGAGTA 9 6 0 AAAAGCTTAA 0.980694 -72 TAATAATAAAAAATGCGCTTAAAACCATGAAA 10 165 1 AAACGCTTAA 0.973011 -33 TTAGTTTTTAAAATAAGGTTATGTTACAATGA 11 19 1 AAAAGGTTAT 0.81105 -47 *** ******* Masking position 9 Map Score: 6.09882 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 333 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 8 TATCATTGTTATATTTTTGTTTTAAGAAAC 1 142 1 ATATTTTTGT 0.949519 -45 TAATGGCGTAATCATTTTTTAGGAAGT 2 34 1 ATCATTTTTT 0.773499 -17 AAGTTTGTTAATAATTATGTTATTATAACA 5 21 1 ATAATTATGT 0.747777 -103 TATTATAACAATAATTTTTTGCTAAAAACG 5 41 1 ATAATTTTTT 0.935826 -83 TCTATTCCTTATATTATTTTAAAATATGCC 5 99 0 ATATTATTTT 0.696862 -25 GATAAGAATAATATTTTTGTGAAAAAAATA 8 152 1 ATATTTTTGT 0.949519 -130 GGCGATCCGTTTATTTTTTTCACAAAAATA 8 163 0 TTATTTTTTT 0.72371 -119 TACTCTTAAGCTAATTTTGTTTATTATAAG 9 11 1 CTAATTTTGT 0.833278 -67 AAAGGGAGGGATACTTTTTTCTTTCTGTGT 10 114 0 ATACTTTTTT 0.868148 -84 ********** Masking position 5 Map Score: 3.12722 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 98 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 TTAAGCCTTAATCTTGGATATAATGGCGTA 2 14 1 ATCTTGGATA 0.950814 -37 AACTTGGAGCGTTTGTCTCC 7 1 1 AACTTGGAGC 0.936734 -300 TTTTGACTAAAACCTGGAGACAAACGCTCC 7 16 0 AACCTGGAGA 0.936734 -285 AACCTCTTTTAGCTTGAATATAGCCTAACA 7 127 0 AGCTTGAATA 0.890793 -174 TTATAAGCAAAACTTGGATACAATCCTAAC 9 34 1 AACTTGGATA 0.979937 -44 AAAGAGTGTGAGTTTGGATATAATAATAAA 10 145 1 AGTTTGGATA 0.890793 -53 ********** Masking position 5 Map Score: 1.10052 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 69 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** No masking Map Score: -2.96764e-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: -2.96764e-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: -2.96764e-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