AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_hpyl_reg_300.orf -o00410_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 HP0005 121 orotidine 5'-phosphate decarboxylase (pyrF) #2 HP0031 108 H. pylori predicted coding region HP0031 #3 HP0032 30 conserved hypothetical protein #4 HP0832 91 spermidine synthase (speE) #5 HP0833 76 H. pylori predicted coding region HP0833 #6 HP0866 40 transcription elongation factor GreA (greA) #7 HP0869 58 hydrogenase expression/formation protein (hypA) #8 HP0870 207 flagellar hook (flgE) #9 HP0871 300 CDP-diglyceride hydrolase (cdh) Motif number 1 AAACAAACGAATTTTAATCAAAATGAGATTTAA 1 21 0 ATTATCAAAA 0.959632 -101 TTAAAATTCGTTTGTTTTTAAAACGCTTATCAT 1 37 1 TTTTTTAAAA 0.593839 -85 TAAAACGCTTATCATAGCTAAAATTCTTGCATT 1 55 1 ATTACTAAAA 0.896609 -67 AAATAACGCCATTATAACAAAAAGAAATGCAAG 1 80 0 ATTACAAAAA 0.943222 -42 TTTATTTGGTATAATACCAAAACTTCATTTAAG 2 76 1 ATTACAAAAC 0.653811 -33 AATCTAAATTATTGTAACAAAAGC 4 2 0 ATTACAAAAG 0.775933 -90 AATTGCTAACATGCTAGCTAAAAAATCTAAATT 4 25 0 ATTACTAAAA 0.896609 -67 TAAGGCATGGATATTGTTAAAAAGTAAGCTAAG 4 61 1 ATTGTAAAAA 0.926987 -31 TTATCGCTTCAATTTAATCAAAATTAGATTACA 5 16 1 AATATCAAAA 0.759271 -61 TTCAGTAGAGATTATAGTAAAAA 6 1 0 ATTATAAAAA 0.966461 -40 TTTTAAAGTTTTGTTAATCAAAAAGATCGACCA 8 97 0 TTTATCAAAA 0.842459 -111 TCCGCAACCAATCATTCTAAAAAGCTATTTAGG 8 130 1 ATTTTAAAAA 0.929236 -78 TAGGGGGTTGATACTTGTCAAAATAAAGCGTTT 9 16 0 ATTTTCAAAA 0.915149 -285 AAGCTAAAAGAATTTTTTAAAAAATTAAATAGC 9 87 0 AATTTAAAAA 0.62357 -214 AATTAAATTGATAACATTAAAAAAGCTAAAAGA 9 109 0 ATCATAAAAA 0.855924 -192 TTTTTTCTAGTTAGTATTCAAAAATCTCTTTTT 9 141 1 TTTATCAAAA 0.843867 -160 TTTTAGTAACCTATTTTTAAAAAGAGATTTTTG 9 159 0 CTTTTAAAAA 0.753667 -142 TAAAATAATCATAATGATTAAAGATTTTAACCA 9 215 1 ATTGTTAAAG 0.577775 -86 TTTTTCTACAATAGTGGTTAAAATCTTTAATCA 9 229 0 ATTGTTAAAA 0.868924 -72 TTTGCAAAAACTCTCATTAAAAACAAGGAGCAA 9 273 1 CTCATAAAAA 0.580617 -28 ** ** ****** Masking position 10 Map Score: 20.4505 Number of sites scoring better than the average of aligned sites = 982 Number in coding regions = 741 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 2 TTTTAATCAAAATGAGATTTAAGGGTTAAAG 1 12 0 AATGAATTTA 0.867413 -110 TTTAAAAACAAACGAATTTTAATCAAAATGA 1 28 0 AACGATTTTA 0.951005 -94 TTAGCTATGATAAGCGTTTTAAAAACAAACG 1 45 0 TAAGCTTTTA 0.852406 -77 AAAAGAAATGCAAGAATTTTAGCTATGATAA 1 63 0 CAAGATTTTA 0.917752 -59 AGTGTAAAATAACGCCATTATAACAAAAAGA 1 88 0 AACGCATTAT 0.512185 -34 GAAAGCCCTTTAAAGTGTAAAA 1 110 0 AAAGCCTTTA 0.926918 -12 ACCACCCCATAACGCTTTTTAAAGGTTATCG 8 36 0 AACGCTTTTA 0.964794 -172 ATCATTCTAAAAAGCTATTTAGGAACAACTT 8 140 1 AAAGCATTTA 0.976314 -68 CCTTTAATTTAAAGAAATTCAATCTATGCAA 8 181 0 AAAGAATTCA 0.821601 -27 TTGTCAAAATAAAGCGTTTTATAA 9 4 0 AAAGCTTTTA 0.981902 -297 CTGCTTAGTGCAAGCTATTTAATTTTTTAAA 9 74 1 CAAGCATTTA 0.922868 -227 AAAAAAGCTAAAAGAATTTTTTAAAAAATTA 9 93 0 AAAGATTTTT 0.909441 -208 CTATTTTTAAAAAGAGATTTTTGAATACTAA 9 151 0 AAAGAATTTT 0.886936 -150 TGATTATTTTAATGAATTTTAACTTATTAGT 9 195 0 AATGATTTTA 0.896 -106 CATAATGATTAAAGATTTTAACCACTATTGT 9 224 1 AAAGATTTAA 0.878282 -77 ***** ***** Masking position 2 Map Score: 20.0045 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 839 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 AAAATGAGATTTAAGGGTTAAAGA 1 5 0 TTAAGGGTTA 0.981576 -117 GAAAGCCCTTTAAAGTGTAAAATAACGCC 1 103 0 TTAAAGTGTA 0.938099 -19 CAGCGGGTCATTAGGGTTTATTTGGTATAA 2 60 1 TTAGGGTTTA 0.935236 -49 TTATAGTTATTTAAAGCTTAAATAAGGGTC 5 52 1 TTAAAGCTTA 0.933176 -25 AATTTAAAGATTAAGGTTTAGT 7 47 1 TTAAGGTTTA 0.971065 -12 ATAACGCTTTTTAAAGGTTATCGCTCAAGC 8 29 0 TTAAAGGTTA 0.98007 -179 GTTGCGGATTTTAAAGTTTTGTTAATCAAA 8 108 0 TTAAAGTTTT 0.933505 -100 TTTCTTTAAATTAAAGGATAACC 8 195 1 TTAAAGGATA 0.898094 -13 CCATGCGATCTTAGGGGGTTGATACTTGTC 9 30 0 TTAGGGGGTT 0.835271 -271 ATCATAATGATTAAAGATTTTAACCACTAT 9 222 1 TTAAAGATTT 0.81014 -79 ********** Masking position 3 Map Score: 11.7089 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 236 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 AAGAACCAACCTTAAATGAAGTTTTGGTA 2 90 0 AATTAAATGA 0.861375 -19 GCTAGCTAAAAAATCTAAATTATTGTAACAAA 4 14 0 AACTAAATTA 0.853858 -78 AGGCATGGATATTGTTAAAAAGTAAGCTAAGG 4 63 1 ATTTAAAAAG 0.752931 -29 CAATTTAATCAAAATTAGATTACAATATTATA 5 25 1 AATTAGATTA 0.760532 -52 TAGTTATTTAAAGCTTAAATAAGGGTCTAGCG 5 55 1 AATTAAATAA 0.952789 -22 CTAAACCTTAATCTTTAAATTAGCCCCTATTA 7 36 0 ATTTAAATTA 0.901205 -23 TAGATTGAATTTCTTTAAATTAAAGGATAACC 8 186 1 TTTTAAATTA 0.471732 -22 AATTTTTTAAAAAATTAAATAGCTTGCACTAA 9 78 0 AATTAAATAG 0.953427 -223 TTAAATTGATAACATTAAAAAAGCTAAAAGAA 9 108 0 AATTAAAAAA 0.866344 -193 TAACTAGAAAAAAATTAAATTGATAACATTAA 9 122 0 AATTAAATTG 0.953161 -179 GAGATTTTTGAATACTAACTAGAAAAAAATTA 9 137 0 AACTAACTAG 0.672545 -164 TTAGTAACCTATTTTTAAAAAGAGATTTTTGA 9 158 0 ATTTAAAAAG 0.75149 -143 TATTTTAATGAATTTTAACTTATTAGTAACTT 9 190 0 AATTAACTTA 0.843418 -111 ** ******** Masking position 7 Map Score: 6.51737 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 274 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 TCGTTTGTTTTTAAAACGCTTATCATAGCT 1 44 1 TTAAAACGCT 0.804663 -78 CTTATCATAGCTAAAATTCTTGCATTTCTT 1 62 1 CTAAAATTCT 0.729569 -60 TAAAGCGCTACAATCTCGCTTAGAAAAAGG 2 18 0 CAATCTCGCT 0.779822 -91 AAGCTCAAAGATAAAGCGCTACAATCTCGC 2 29 0 ATAAAGCGCT 0.840515 -80 ATAAACCCTAATGACCCGCTGAAAGCTCAA 2 51 0 ATGACCCGCT 0.675259 -58 TAATGAATTGCTAACATGCTAGCTAAAAAA 4 33 0 CTAACATGCT 0.892055 -59 GCTTAAGAATCTAACTCGCT 8 1 0 CTAACTCGCT 0.964126 -207 CAACACCACCCCATAACGCTTTTTAAAGGT 8 41 0 CCATAACGCT 0.630161 -167 GTGGTGTTGCAAAACCCCCTATTTTCTTAT 8 62 1 AAAACCCCCT 0.601097 -146 AAAGTTGTTCCTAAATAGCTTTTTAGAATG 8 142 0 CTAAATAGCT 0.639982 -66 TTATAAAACGCTTTATTTTGAC 9 3 1 ATAAAACGCT 0.95202 -298 TTAATTTTTTAAAAAATTCTTTTAGCTTTT 9 92 1 AAAAAATTCT 0.491692 -209 GTTAGTATTCAAAAATCTCTTTTTAAAAAT 9 150 1 AAAAATCTCT 0.758792 -151 AGAGTTTTTGCAAACCCTCTTGTTATTTTT 9 257 0 CAAACCCTCT 0.897197 -44 AGAGGGTTTGCAAAAACTCTCATTAAAAAC 9 267 1 CAAAAACTCT 0.918694 -34 ********** Masking position 10 Map Score: 6.34257 Number of sites scoring better than the average of aligned sites = 3333 Number in coding regions = 3054 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 6 CCAAGTAGCCAAATAGCATGGAT 3 4 1 AGTAGCCAAA 0.934803 -27 TCTAAATTATTGTAACAAAAGC 4 3 0 TGTAACAAAA 0.887211 -89 TATGGGGTGGTGTTGCAAAACCCCCTATTT 8 56 1 TGTTGCAAAA 0.93256 -152 TAAGATCGCATGGTGAAAAATTATCGCCTG 9 47 1 TGGTGAAAAA 0.895807 -254 TTGAATACTAACTAGAAAAAAATTAAATTG 9 132 0 ACTAGAAAAA 0.812664 -169 TAACCACTATTGTAGAAAAATAACAAGAGG 9 242 1 TGTAGAAAAA 0.967036 -59 ATTAAAAACAAGGAGCAAAAAAG 9 288 1 AGGAGCAAAA 0.969096 -13 ********** Masking position 8 Map Score: 3.07041 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 235 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TGAAAGCTCAAAGATAAAGCGCTACAATCT 2 32 0 AAGATAAAGC 0.818566 -77 GCTAACATGCTAGCTAAAAAATCTAAATTA 4 24 0 TAGCTAAAAA 0.724346 -68 GTTAAAAAGTAAGCTAAGGAGTGTTT 4 76 1 AAGCTAAGGA 0.961332 -16 TAGTTATTTAAAGCTTAAATAAGGGTCTAG 5 55 1 AAGCTTAAAT 0.87881 -22 TCTACTGAATAAGCTTAGGAGATTAA 6 25 1 AAGCTTAGGA 0.952783 -16 GGCTAATTTAAAGATTAAGGTTTAGT 7 43 1 AAGATTAAGG 0.870789 -16 GTTATCGCTCAAGCTTAAGAATCTAACTCG 8 13 0 AAGCTTAAGA 0.97635 -195 ATGCAAAATAAAGCAAAAGTTGTTCCTAAA 8 157 0 AAGCAAAAGT 0.811222 -51 AACATTAAAAAAGCTAAAAGAATTTTTTAA 9 100 0 AAGCTAAAAG 0.932521 -201 ********** Masking position 7 Map Score: 5.60955 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 564 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 ********** No masking Map Score: -1.88842e-14 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 9 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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