AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_hpyl_reg_300.orf -o00740_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 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 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) #6 HP1574 74 riboflavin synthase alpha subunit (ribC) Motif number 1 AAAATAACGCCATTATAACAAAAAGAAATGCA 1 29 1 CATTTACAAA 0.967286 -93 TGATAAGCGTTTTAAAAACAAACGAATTTTAA 1 74 1 TTTAAACAAA 0.77589 -48 AAACAAACGAATTTTAATCAAAATGAGATTTA 1 89 1 ATTTAACAAA 0.936268 -33 GAGCTTAAAATTTAAGAAAATTATAAAGAG 2 9 1 AATTAAAAAA 0.893184 -80 TAAAAAAAGGTATTCTATCAAAACTCTTTATA 2 32 0 TATTTACAAA 0.935042 -57 TAAAACGCATCTTTTAAAAAAAGGTATTCTAT 2 46 0 CTTTAAAAAA 0.856252 -43 AAAAGATGCGTTTTAAAACTAATTTTAGGAGT 2 63 1 TTTTAACTAA 0.841772 -26 CATTACAACACATTCAATAAAACTTAACGAGC 3 14 0 CATTAAAAAA 0.914878 -75 AAAAAGAGTTTATTATACCTTAAAAACATTAC 3 40 0 TATTTACTTA 0.732809 -49 CCTCTAAATTAATTGAATGAAACTCCCCCTAT 4 38 0 AATTAAGAAA 0.754716 -133 GGCTTTAGCGATTTGTATCTAAATAAAGCAAT 4 68 1 ATTTTACTAA 0.752142 -103 TATATTTCTTTTTTCTATAAAACTCAATATTA 4 126 1 TTTTTAAAAA 0.491248 -45 AACTCAATATTATTGAATAAAACTAGGGAGTT 4 146 1 TATTAAAAAA 0.896665 -25 GATGCGTATTTTACTAAAATTTGCGCTA 5 7 1 TATTTATAAA 0.607545 -75 TAACATACTAAATAAAACCATAGGATAAAAGC 6 11 0 AATAAACATA 0.562812 -64 AATGTTTGATTATTGTAACATACTAAATAAAA 6 26 0 TATTTACATA 0.861323 -49 AATAATCAAACATTCTAACATAAGGAGAATAA 6 44 1 CATTTACATA 0.9062 -31 **** ** **** Masking position 7 Map Score: 17.2972 Number of sites scoring better than the average of aligned sites = 1548 Number in coding regions = 1164 Number in noncoding regions = 384 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 2 TTTTTGTTATAATGGCGTTATTTTACACTTT 1 22 0 AATGGCTTAT 0.754392 -100 TTTAGCTATGATAAGCGTTTTAAAAACAAAC 1 66 1 ATAAGCTTTT 0.842757 -56 TTTTAAAAACAAACGAATTTTAATCAAAATG 1 83 1 AAACGATTTT 0.909727 -39 TTAACCCTTAAATCTCATTTTGATTAAAATT 1 98 0 AATCTCTTTT 0.946871 -24 TATTCTATCAAAACTCTTTATAATTTTCTTA 2 23 0 AAACTCTTAT 0.984641 -66 ATTAGTTTTAAAACGCATCTTTTAAAAAAAG 2 55 0 AAACGCTCTT 0.899373 -34 ATGCGTTTTAAAACTAATTTTAGGAGTATCC 2 68 1 AAACTATTTT 0.908326 -21 AAGGTATAATAAACTCTTTTTAAGTCAAGCA 3 51 1 AAACTCTTTT 0.982018 -38 CAATAAAGTAATAATCGTTATTAAACATGCT 4 96 1 ATAATCTTAT 0.865973 -75 TTTTATAGAAAAAAGAAATATAGCATGTTTA 4 117 0 AAAAGAATAT 0.571448 -54 TTTTTCTATAAAACTCAATATTATTGAATAA 4 135 1 AAACTCATAT 0.953791 -36 TAATGCAAATAAAATCAATATCAAACAGACT 5 46 0 AAAATCATAT 0.863354 -36 ATTGATTGTTATTCTCCTTATGTTAGAATGT 6 53 0 ATTCTCTTAT 0.869373 -22 ****** **** Masking position 1 Map Score: 14.3434 Number of sites scoring better than the average of aligned sites = 2248 Number in coding regions = 1875 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 3 AAAGAAATGCAAGAATTTTAGCTATGATAAG 1 50 1 AAGATTTTAG 0.940618 -72 AATGAGATTTAAGGGTTAAAGA 1 110 1 AAGGTTAAAG 0.97519 -12 TTTTTAAGTCAAGCAATAAAGTTTGCAACCT 3 67 1 AAGAATAAAG 0.989057 -22 AGTTTCATTCAATTAATTTAGAGGCTTTAGC 4 46 1 AATAATTTAG 0.825099 -125 TTTAGATACAAATCGCTAAAGCCTCTAAATT 4 60 0 AATGCTAAAG 0.840601 -111 TATCTAAATAAAGCAATAAAGTAATAATCGT 4 83 1 AAGAATAAAG 0.989057 -88 TTATAGAAAAAAGAAATATAGCATGTTTAAT 4 115 0 AAGAATATAG 0.98256 -56 TATTTGCATTAAGAATTAAGGCTAAC 5 66 1 AAGATTAAGG 0.94855 -16 *** ******* Masking position 2 Map Score: 7.80953 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 172 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 ATTTTACACTTTAAAGGGCTTTC 1 2 0 TAAAGGCTTT 0.89251 -120 TTCTTTTTGTTATAATGGCGTTATTTTACACT 1 24 0 TTAATGCGTT 0.7738 -98 TCGTTTGTTTTTAAAACGCTTATCATAGCTAA 1 67 0 TAAAAGCTTA 0.925659 -55 CTCATTTTGATTAAAATTCGTTTGTTTTTAAA 1 84 0 TAAAATCGTT 0.838571 -38 CGAATTTTAATCAAAATGAGATTTAAGGGTTA 1 96 1 TAAAAGAGAT 0.889847 -26 TTTAAGAAAATTATAAAGAGTTTTGATAGAAT 2 21 1 TATAAGAGTT 0.974016 -68 TTATTATACCTTAAAAACATTACAACACATTC 3 31 0 TAAAACATTA 0.632877 -58 ATTGCTTGACTTAAAAAGAGTTTATTATACCT 3 52 0 TAAAAGAGTT 0.984515 -37 ATAGCATGTTTAATAACGATTATTACTTTATT 4 97 0 TATAAGATTA 0.882628 -74 TTTTATTCAATAATATTGAGTTTTATAGAAAA 4 136 0 TATATGAGTT 0.944349 -35 TAAGTCTGTTTGATATTGATTTTATTTGCATT 5 44 1 TATATGATTT 0.899223 -38 * **** ***** Masking position 5 Map Score: 6.1235 Number of sites scoring better than the average of aligned sites = 1876 Number in coding regions = 1590 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 5 AGAAATGCAAGAATTTTAGCTATGATAAGC 1 52 1 GAATTTTAGC 0.893841 -70 TTTAAGTCAAGCAATAAAGTTTGCAACCTG 3 69 1 GCAATAAAGT 0.948397 -20 AGCATTTCTTGCATGATAGGGGGAGTTTCA 4 23 1 GCATGATAGG 0.891824 -148 TAAATTAATTGAATGAAACTCCCCCTATCA 4 36 0 GAATGAAACT 0.832193 -135 TCTAAATAAAGCAATAAAGTAATAATCGTT 4 85 1 GCAATAAAGT 0.948397 -86 ATAGAAAAAAGAAATATAGCATGTTTAATA 4 114 0 GAAATATAGC 0.934281 -57 ATTTGCGCTAGAATGTAAGTCTGTTTGATA 5 29 1 GAATGTAAGT 0.916453 -53 TTTGCATTAAGAATTAAGGCTAAC 5 68 1 GAATTAAGGC 0.906083 -14 ********** Masking position 3 Map Score: 2.09635 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 525 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 CTAAAATTCTTGCATTTCTTTTTGTTATAA 1 41 0 TGCATTTCTT 0.956672 -81 AGTTTTAAAACGCATCTTTTAAAAAAAGGT 2 53 0 CGCATCTTTT 0.960263 -36 CAGGTTGCAAACTTTATTGCTTGAC 3 74 0 TGCAAACTTT 0.882061 -15 TAAGTCTTTGAGCATTTCTTGCATGATAGG 4 13 1 AGCATTTCTT 0.897293 -158 GATGCGTATTTTACTAAAATTT 5 3 1 TGCGTATTTT 0.933129 -79 TACATTCTAGCGCAAATTTTAGTAAAATAC 5 16 0 CGCAAATTTT 0.956671 -66 ********** Masking position 9 Map Score: 0.652586 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 292 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 AAAGAAATATAGCATGTTTAATAACGATTATT 4 105 0 AGTGTTTAAT 0.985795 -66 CTAGAATGTAAGTCTGTTTGATATTGATTTTA 5 36 1 AGTGTTTGAT 0.994762 -46 TCCTTATGTTAGAATGTTTGATTATTGTAACA 6 38 0 AGTGTTTGAT 0.99476 -37 ** ******** Masking position 11 Map Score: 0.211718 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 23 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: 1.77879e-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: 1.77879e-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: 1.77879e-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