AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_hpyl_reg_100.orf -o00740_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 HP0004 121 carbonic anhydrase (icfA) #2 HP0802 88 GTP cyclohydrolase II (ribA) #3 HP0803 88 H. pylori predicted coding region HP0803 #4 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #5 HP1574 74 riboflavin synthase alpha subunit (ribC) Motif number 1 TGCATTTCTTTTTGTTATAATGGCGTTATTT 1 30 0 TTTGTTAAAT 0.969174 -92 TTAAAATTCGTTTGTTTTTAAAACGCTTATC 1 75 0 TTTGTTTTAA 0.755358 -47 TAAATCTCATTTTGATTAAAATTCGTTTGTT 1 90 0 TTTGATTAAA 0.785907 -32 CTCTTTATAATTTTCTTAAATTTTAAGCTC 2 10 0 TTTTCTTAAT 0.836018 -79 TATAAAGAGTTTTGATAGAATACCTTTTTTT 2 32 1 TTTGATAAAT 0.971404 -57 ATAGAATACCTTTTTTTAAAAGATGCGTTTT 2 46 1 TTTTTTTAAA 0.778093 -43 ACTCCTAAAATTAGTTTTAAAACGCATCTTT 2 64 0 TTAGTTTAAA 0.854947 -25 GCTCGTTAAGTTTTATTGAATGTGTTGTAAT 3 14 1 TTTTATTAAT 0.948186 -75 ATAGGGGGAGTTTCATTCAATTAATTTAGAG 4 38 1 TTTCATTAAT 0.860903 -133 ATTGCTTTATTTAGATACAAATCGCTAAAGC 4 69 0 TTAGATAAAA 0.790158 -102 TAATATTGAGTTTTATAGAAAAAAGAAATAT 4 127 0 TTTTATAAAA 0.8415 -44 AACTCCCTAGTTTTATTCAATAATATTGAGT 4 147 0 TTTTATTAAT 0.934728 -24 TTTTATTTAGTATGTTACAATAATCAAACAT 5 26 1 TATGTTAAAT 0.855915 -49 TTATTCTCCTTATGTTAGAATGTTTGATTAT 5 45 0 TATGTTAAAT 0.856094 -30 ******* *** Masking position 10 Map Score: 19.1808 Number of sites scoring better than the average of aligned sites = 1018 Number in coding regions = 772 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 TTGTTATAATGGCGTTATTTTACACTTTAAA 1 19 0 GGCGTTATTT 0.822949 -103 CTTAAATCTCATTTTGATTAAAATTCGTTTG 1 92 0 ATTTTGATTA 0.922289 -30 ATTATAAAGAGTTTTGATAGAATACCTTTTT 2 30 1 GTTTTGATAA 0.654381 -59 AGGCTCGTTAAGTTTTATTGAATGTGTTGTA 3 12 1 AGTTTTATTA 0.983264 -77 TGATAGGGGGAGTTTCATTCAATTAATTTAG 4 36 1 AGTTTCATTA 0.932073 -135 ATTACTTTATTGCTTTATTTAGATACAAATC 4 77 0 TGCTTTATTA 0.91212 -94 TAAAGTAATAATCGTTATTAAACATGCTATA 4 99 1 ATCGTTATTA 0.855542 -72 AATAATATTGAGTTTTATAGAAAAAAGAAAT 4 129 0 AGTTTTATAA 0.929395 -42 CTAACTCCCTAGTTTTATTCAATAATATTGA 4 149 0 AGTTTTATTA 0.983262 -22 TTTATCCTATGGTTTTATTTAGTATGTTACA 5 14 1 GGTTTTATTA 0.976652 -61 TATGTTAGAATGTTTGATTATTGTAACATAC 5 35 0 TGTTTGATTT 0.805204 -40 AATTGATTGTTATTCTCCTTATGTTA 5 59 0 ATTGTTATTT 0.790195 -16 ********* * Masking position 7 Map Score: 12.1049 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 519 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 GTTTTAAAAACAAACGAATTTTAATCAAAA 1 82 1 CAAACGAATT 0.836837 -40 TTTAACCCTTAAATCTCATTTTGATTAAAA 1 100 0 AAATCTCATT 0.926808 -22 GTATTCTATCAAAACTCTTTATAATTTTCT 2 25 0 AAAACTCTTT 0.971958 -64 AATTAGTTTTAAAACGCATCTTTTAAAAAA 2 57 0 AAAACGCATC 0.943073 -32 GATGCGTTTTAAAACTAATTTTAGGAGTAT 2 67 1 AAAACTAATT 0.960336 -22 CACATTCAATAAAACTTAACGAGCCTC 3 8 0 AAAACTTAAC 0.872738 -81 TAAGGTATAATAAACTCTTTTTAAGTCAAG 3 50 1 TAAACTCTTT 0.879557 -39 CAGGTTGCAAACTTTATTGCTTGACTT 3 72 0 CAAACTTTAT 0.779147 -17 GAAATGCTCAAAGACTTATT 4 1 0 AAGACTTATT 0.879831 -170 TTTTTTCTATAAAACTCAATATTATTGAAT 4 134 1 AAAACTCAAT 0.976075 -37 ********** Masking position 2 Map Score: 8.16535 Number of sites scoring better than the average of aligned sites = 1031 Number in coding regions = 853 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 CTTATCATAGCTAAAATTCTTGCATTTCTTT 1 50 0 CTAAAATCTT 0.954441 -72 TCTTTAACCCTTAAATCTCATT 1 110 0 CTTTAACCTT 0.944189 -12 TATCAAAACTCTTTATAATTTTCTTAAATTT 2 18 0 CTTTATATTT 0.786397 -71 ACAACACATTCAATAAAACTTAACGAGCCTC 3 11 0 CAATAAACTT 0.84087 -78 TTTATTATACCTTAAAAACATTACAACACAT 3 33 0 CTTAAAACAT 0.70525 -56 AGGTTGCAAACTTTATTGCTTGACTTAAAAA 3 67 0 CTTTATTCTT 0.978844 -22 GCTAAAGCCTCTAAATTAATTGAATGAAACT 4 46 0 CTAAATTATT 0.672505 -125 ACGATTATTACTTTATTGCTTTATTTAGATA 4 83 0 CTTTATTCTT 0.978844 -88 ATTAAACATGCTATATTTCTTTTTTCTATAA 4 115 1 CTATATTCTT 0.978842 -56 TTTCTTTTTTCTATAAAACTCAATATTATTG 4 130 1 CTATAAACTC 0.886773 -41 ******* *** Masking position 5 Map Score: 7.93485 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 520 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 GCCATTATAACAAAAAGAAATGCAAGAATTT 1 37 1 CAAAAAGAAT 0.937085 -85 TCATTTTGATTAAAATTCGTTTGTTTTTAAA 1 84 0 TAAAATTCGT 0.813807 -38 GAATTTTAATCAAAATGAGATTTAAGGGTTA 1 97 1 CAAAATGAGT 0.975957 -25 TTAAGAAAATTATAAAGAGTTTTGATAGAAT 2 22 1 TATAAAGAGT 0.945481 -67 ACGCATCTTTTAAAAAAAGGTATTCTATCAA 2 43 0 TAAAAAAAGT 0.937386 -46 GGATACTCCTAAAATTAGTTTTAAAACGCA 2 69 0 TAAAATTAGT 0.942712 -20 TTGCTTGACTTAAAAAGAGTTTATTATACCT 3 52 0 TAAAAAGAGT 0.989772 -37 AGTTTTATAGAAAAAAGAAATATAGCATGTT 4 119 0 AAAAAAGAAT 0.845216 -52 ********* * Masking position 5 Map Score: 6.85362 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 481 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 6 ********** No masking Map Score: 4.99812e-13 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 7 ********** No masking Map Score: 4.99812e-13 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 8 ********** No masking Map Score: 4.99812e-13 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