AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_hpyl_reg_100.orf -o00410_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 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) Motif number 1 CAAAATGAGATTTAAGGGTTAAAGA 1 5 0 TTTAAGGTTA 0.987895 -117 GAAAGCCCTTTAAAGTGTAAAATAACGCC 1 103 0 TTTAAAGGTA 0.952398 -19 TCAGCGGGTCATTAGGGTTTATTTGGTATAA 2 59 1 ATTAGGGTTA 0.885145 -50 CAAAACTTCATTTAAGGTTGGTTCTT 2 93 1 TTTAAGGTGG 0.892696 -16 TTAGCAATTCATTAAGGCATGGATATTGTTA 4 49 1 ATTAAGGATG 0.850926 -43 ATTATAGTTATTTAAAGCTTAAATAAGGGTC 5 51 1 TTTAAAGTTA 0.986899 -26 TAGGGGCTAATTTAAAGATTAAGGTTTAGT 7 39 1 TTTAAAGTTA 0.986899 -20 CATAACGCTTTTTAAAGGTTATCGCTCAAGC 8 29 0 TTTAAAGTTA 0.986899 -179 GGTTGCGGATTTTAAAGTTTTGTTAATCAAA 8 108 0 TTTAAAGTTT 0.931031 -100 ATTTCTTTAAATTAAAGGATAACC 8 194 1 ATTAAAGATA 0.9151 -14 ******* *** Masking position 4 Map Score: 14.2148 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 228 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 TTAAATCTCATTTTGATTAAAATTCGTTTGTTT 1 21 1 TTTTATAAAT 0.974334 -101 ATGATAAGCGTTTTAAAAACAAACGAATTTTAA 1 37 0 TTTTAAAAAA 0.74275 -85 AATGCAAGAATTTTAGCTATGATAAGCGTTTTA 1 55 0 TTTTGTAGAT 0.970794 -67 CTTGCATTTCTTTTTGTTATAATGGCGTTATTT 1 80 1 TTTTGTAAAT 0.986965 -42 CATTAGGGTTTATTTGGTATAATACCAAAACTT 2 68 1 TATTGTAAAT 0.899483 -41 GCTTTTGTTACAATAATTTAGATT 4 2 1 CTTTGTAAAT 0.929894 -90 AATTTAGATTTTTTAGCTAGCATGTTAGCAATT 4 25 1 TTTTGTACAT 0.970794 -67 TGTAATCTAATTTTGATTAAATTGAAGCGATAA 5 16 0 TTTTATAATT 0.927136 -61 TTTTTACTATAATCTCTACTGAA 6 1 1 TTTTATAAAT 0.974334 -40 TGGTCGATCTTTTTGATTAACAAAACTTTAAAA 8 97 1 TTTTATACAA 0.840506 -111 CCTAAATAGCTTTTTAGAATGATTGGTTGCGGA 8 130 0 TTTTAAAGAT 0.84731 -78 TTTTGCTTTATTTTGCATAGATTGAATTTCTTT 8 169 1 TTTTCTAATT 0.798847 -39 **** * ** *** Masking position 9 Map Score: 12.7163 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 321 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 CCCTTAAATCTCATTTTGATTAAAATTCGTT 1 18 1 TATTTTGATT 0.951098 -104 TAGCGCTTTATCTTTGAGCTTTCAGCGGGTC 2 38 1 TTTTGAGCTT 0.856094 -71 TTTGTTACAATAATTTAGATTTTTTAGCTAG 4 14 1 TATTTAGATT 0.958526 -78 TATTGTAATCTAATTTTGATTAAATTGAAGC 5 21 0 TATTTTGATT 0.951098 -56 GCTAGACCCTTATTTAAGCTTTAAATAACTA 5 55 0 TTTTAAGCTT 0.929604 -22 TAATCTCTACTGAATAAGCTTAGGAGATTAA 6 20 1 TAATAAGCTT 0.72913 -21 GCGAGTTAGATTCTTAAGCTTGAGCGATAAC 8 12 1 TCTTAAGCTT 0.954055 -196 ACCCCCTATTTTCTTATGAATTTGGTCGATC 8 75 1 TCTTATGAAT 0.763641 -133 ATTTGGTCGATCTTTTTGATTAACAAAACTT 8 94 1 TTTTTTGATT 0.923802 -114 AACTTTTGCTTTATTTTGCATAGATTGAATT 8 166 1 TATTTTGCAT 0.86624 -42 TAGATTGAATTTCTTTAAATTAAAGGATAAC 8 186 1 TCTTTAAATT 0.640925 -22 * ********* Masking position 5 Map Score: 7.91588 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 705 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 4 TGAAAGCTCAAAGATAAAGCGCTACAATCTC 2 31 0 AAGATAAAGG 0.976548 -78 GTTAAAAAGTAAGCTAAGGAGTGTTT 4 76 1 AAGCTAAGGG 0.990432 -16 TCTACTGAATAAGCTTAGGAGATTAA 6 25 1 AAGCTTAGGG 0.987577 -16 GGCTAATTTAAAGATTAAGGTTTAGT 7 43 1 AAGATTAAGT 0.897157 -16 TTAGATTCTTAAGCTTGAGCGATAACCTTTA 8 17 1 AAGCTTGAGG 0.977995 -191 AATTCATAAGAAAATAGGGGGTTTTGCAACA 8 66 0 AAAATAGGGG 0.814439 -142 ATGCAAAATAAAGCAAAAGTTGTTCCTAAAT 8 156 0 AAGCAAAAGT 0.829624 -52 ********* * Masking position 2 Map Score: 4.56935 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 273 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CAAAATGAGATTTAAGGGTTAAAGA 1 6 0 TTTAAGGGTT 0.920163 -116 TTTTAGCTATGATAAGCGTTTTAAAAACAA 1 48 0 GATAAGCGTT 0.92507 -74 ATTTTACACTTTAAAGGGCTTTC 1 109 1 TTAAAGGGCT 0.791087 -13 AAGCTCAAAGATAAAGCGCTACAATCTCGC 2 29 0 ATAAAGCGCT 0.874735 -80 TCAGCGGGTCATTAGGGTTTATTTGGTATA 2 59 1 ATTAGGGTTT 0.778725 -50 AAATAGCATGGATAAGCGGC 3 21 1 GATAAGCGGC 0.728494 -10 TTAAAGCTTAAATAAGGGTCTAGCG 5 62 1 AATAAGGGTC 0.943292 -15 AATACAATATAATAGGGGCTAATTTAAAGA 7 27 1 AATAGGGGCT 0.957248 -32 TAATTTAAAGATTAAGGTTTAGT 7 46 1 ATTAAGGTTT 0.848919 -13 GATAACCTTTAAAAAGCGTTATGGGGTGGT 8 37 1 AAAAAGCGTT 0.909587 -171 TTCATAAGAAAATAGGGGGTTTTGCAACAC 8 65 0 AATAGGGGGT 0.938919 -143 ********** Masking position 4 Map Score: 7.65636 Number of sites scoring better than the average of aligned sites = 1723 Number in coding regions = 1459 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 6 ATGAGATTTAAGGGTTAAAGA 1 2 0 AGGGTTAAAG 0.796857 -120 AGCTATGATAAGCGTTTTAAAAACAAACGA 1 44 0 AGCGTTTTAA 0.93674 -78 CCTTTTTCTAAGCGAGATTGTAGCGCTTTA 2 18 1 AGCGAGATTG 0.929449 -91 TTTTTTAGCTAGCATGTTAGCAATTCATTA 4 33 1 AGCATGTTAG 0.89167 -59 ATTAAATTGAAGCGATAAAAAAG 5 4 0 AGCGATAAAA 0.844259 -73 AGCGAGTTAGATTCTTAAGC 8 1 1 AGCGAGTTAG 0.984486 -207 ACCTTTAAAAAGCGTTATGGGGTGGTGTTG 8 41 1 AGCGTTATGG 0.9522 -167 CATTCTAAAAAGCTATTTAGGAACAACTTT 8 142 1 AGCTATTTAG 0.893589 -66 ********** Masking position 1 Map Score: 2.96551 Number of sites scoring better than the average of aligned sites = 1192 Number in coding regions = 1123 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 AAGATAAAGCGCTACAATCTCGCTTAGAAAA 2 21 0 GCTACAACTC 0.979761 -88 CTAATGACCCGCTGAAAGCTCAAAGATAAAG 2 43 0 GCTGAAACTC 0.96215 -66 TAACATGCTAGCTAAAAAATCTAAATTATTG 4 21 0 GCTAAAAATC 0.981146 -71 GCTTTAAATAACTATAATATTGTAATCTAAT 5 38 0 ACTATAAATT 0.911688 -39 TTTTTACTATAATCTCTACTGAATAA 6 6 1 ACTATAACTC 0.976549 -35 GCTAAAAGATTACTCTAATAC 7 1 1 GCTAAAAATT 0.953181 -58 TTAAGCTTGAGCGATAACCTTTAAAAAGCGT 8 25 1 GCGATAACTT 0.91772 -183 GATTAACAAAACTTTAAAATCCGCAACCAAT 8 111 1 ACTTTAAATC 0.846093 -97 ******* *** Masking position 6 Map Score: 5.41174 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 334 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 ********** No masking Map Score: -1.39023e-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 9 ********** No masking Map Score: -1.39023e-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: -1.39023e-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