AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -imodE_hpyl_opreg_300.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #2 HP0474 21 molybdenum ABC transporter, permease protein (modB) #3 HP0768 87 molybdenum cofactor biosynthesis protein A (moaA) #4 HP0801 72 molybdopterin converting factor, subunit 1 (moaD) #5 HP0802 88 GTP cyclohydrolase II (ribA) #6 HP0803 88 H. pylori predicted coding region HP0803 #7 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #8 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) Motif number 1 AGGGTGTAACTTTAATTCAACAAGAAGGATTTAT 1 12 0 TTTATCAAAG 0.875289 -214 AAATTAAAACTTTTAGAAAAATAACCGATCTTAG 1 44 0 TTTAAAAAAA 0.937692 -182 AATCTTCATCTTTGATAAAAAATTAAAACTTTTA 1 63 0 TTTAAAAATT 0.891695 -163 TAACCAACATTTTCACTCTAAAATCTTCATCTTT 1 84 0 TTTATCTAAT 0.92324 -142 CGCCTCAAACTTTTAAAATACAAATTTTTAAGAT 1 153 1 TTTAAATAAA 0.899301 -73 AAATACAAATTTTTAAGATACAAATAGGTATAAT 1 168 1 TTTAGATAAA 0.772521 -58 AGAACTCCCTTTGATTAAATGATTGGAATTGGT 1 203 0 TTTATAAAAT 0.949164 -23 TTATTTAAGCTTTTAGTGTAACATAATAAACAAC 3 42 0 TTTATGTAAT 0.909785 -46 TTAAAGAGGTTTTAAAAATATTTAAAATCATGCT 4 25 1 TTTAAATATA 0.797597 -48 ATATTAAATCTTTTAAAGCATGATTTTAAATATT 4 41 0 TTTAAGCAAT 0.728153 -32 GAGCTTAAAATTTAAGAAAATTATAAAGAGTTTT 5 11 1 TTTAAAAAAT 0.949165 -78 AAACGCATCTTTTAAAAAAAGGTATTCTATCAAA 5 42 0 TTTAAAAATA 0.869042 -47 AAAGATGCGTTTTAAAACTAATTTTAGGAGTATC 5 64 1 TTTAACTATT 0.841362 -25 GCTCGTTAAGTTTTATTGAATGTGTTGTAATGTT 6 14 1 TTTATGAATG 0.721858 -75 GTTGTAATGTTTTTAAGGTATAATAAACTCTTTT 6 37 1 TTTAGGTAAT 0.79468 -52 ATAAACTCTTTTTAAGTCAAGCAATAAAGTTTGC 6 59 1 TTTATCAAAA 0.942279 -30 ATAGGGGGAGTTTCATTCAATTAATTTAGAGGCT 7 38 1 TTTATCAAAA 0.942262 -133 TAATATTGAGTTTTATAGAAAAAAGAAATATAGC 7 124 0 TTTAAGAAAA 0.931914 -47 AACTCCCTAGTTTTATTCAATAATATTGAGTTTT 7 144 0 TTTATCAAAT 0.952932 -27 GATGCGTATTTTACTAAAATTTGCGCTAGAAT 8 9 1 TTTATAAATT 0.891695 -73 *** * **** ** Masking position 3 Map Score: 24.5451 Number of sites scoring better than the average of aligned sites = 1105 Number in coding regions = 824 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 TTCATCTTTGATAAAAAATTAAAACTTTTAGAAA 1 59 0 AAAAATAAAA 0.94522 -167 CTTTTAAAATACAAATTTTTAAGATACAAATAGG 1 162 1 AAAATTAAGA 0.85235 -64 TTTTTAAGATACAAATAGGTATAATCACCAATTC 1 177 1 AAAATTATAA 0.926112 -49 AAAAGCTTAAATAAAAGGGCATAAGGGATAAAGG 3 62 1 AAAAACATAA 0.770615 -26 AAGAGGTTTTAAAAATATTTAAAATCATGCTTTA 4 28 1 AAAATTAAAA 0.965133 -45 TTAAAATTTAAGAAAATTATAAAGAGTTTTGATA 5 15 1 AAAAATAAAG 0.964932 -74 CTATCATGCAAGAAATGCTCAAAGACTTATT 7 8 0 AAAATCAAAG 0.949951 -163 TTATTTAGATACAAATCGCTAAAGCCTCTAAATT 7 60 0 AAAATTAAAG 0.977848 -111 TTGTATCTAAATAAAGCAATAAAGTAATAATCGT 7 80 1 AAAAGTAAAG 0.96743 -91 GTTTTATAGAAAAAAGAAATATAGCATGTTTAAT 7 115 0 AAAAGTATAG 0.930796 -56 * **** ***** Masking position 5 Map Score: 9.77373 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 633 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 AATAAATCCTTCTTGTTGAAT 1 2 1 ATAAATCCTT 0.889238 -224 TTGATAAAAAATTAAAACTTTTAGAAAAAT 1 56 0 ATTAAAACTT 0.943026 -170 CATTTTCACTCTAAAATCTTCATCTTTGAT 1 81 0 CTAAAATCTT 0.859398 -145 GGAATTGGTGATTATACCTATTTGTATCTT 1 182 0 ATTATACCTA 0.719182 -44 TTATGTTACACTAAAAGCTTAAATAAAAGG 3 50 1 CTAAAAGCTT 0.781914 -38 TTACCCTTATATTAAATCTTTTAAAGCATG 4 53 0 ATTAAATCTT 0.943016 -20 GAGTTTTGATAGAATACCTTTTTTTAAAAG 5 38 1 AGAATACCTT 0.712509 -51 CAACACATTCAATAAAACTTAACGAGCCTC 6 11 0 AATAAAACTT 0.699602 -78 AAAAGAGTTTATTATACCTTAAAAACATTA 6 41 0 ATTATACCTT 0.952731 -48 TTTAATAACGATTATTACTTTATTGCTTTA 7 91 0 ATTATTACTT 0.795382 -80 GTTAGCCTTAATTCTTAATGCAAATA 8 66 0 CTTAATTCTT 0.80504 -16 ********** Masking position 4 Map Score: 5.65755 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 402 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TCCCACTTATTAGTATTTAACCAACATTTT 1 105 0 TAGTATTTAA 0.889785 -121 TCTTAAAAATTTGTATTTTAAAAGTTTGAG 1 156 0 TTGTATTTTA 0.967612 -70 TTATACCTATTTGTATCTTAAAAATTTGTA 1 171 0 TTGTATCTTA 0.961218 -55 TGTTAAGTCGTTGTTTATTATGTTACACTA 3 33 1 TTGTTTATTA 0.798559 -55 CCTTATGCCCTTTTATTTAAGCTTTTAGTG 3 58 0 TTTTATTTAA 0.834631 -30 ATGTGTTGTAATGTTTTTAAGGTATAATAA 6 33 1 ATGTTTTTAA 0.779159 -56 CTTTAGCGATTTGTATCTAAATAAAGCAAT 7 70 1 TTGTATCTAA 0.969413 -101 ********** Masking position 10 Map Score: 3.56065 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 239 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 AATTTGTATTTTAAAAGTTTGAGGCGGTTT 1 149 0 TTAAAAGTTT 0.827132 -77 ATGAGTGCTTTAAAGAGGTTTTAAAAATAT 4 16 1 TAAAGAGGTT 0.969724 -57 AAGAAAATTATAAAGAGTTTTGATAGAATA 5 24 1 TAAAGAGTTT 0.979406 -65 GCATCTTTTAAAAAAAGGTATTCTATCAAA 5 42 0 AAAAAAGGTA 0.712034 -47 GCTTGACTTAAAAAGAGTTTATTATACCTT 6 51 0 AAAAGAGTTT 0.973285 -38 TAAGTCAAGCAATAAAGTTTGCAACCTG 6 71 1 AATAAAGTTT 0.885052 -18 TATTCAATAATATTGAGTTTTATAGAAAAA 7 135 0 TATTGAGTTT 0.811286 -36 ********** Masking position 6 Map Score: 2.90884 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 422 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 AAATAACCGATCTTAGGGTGTAACTTTAATT 1 29 0 TCTTAGGTGT 0.90207 -197 GGCGGTTTGTTTTGTGGGTGTATCCCACTTA 1 126 0 TTTGTGGTGT 0.940827 -100 ATTTTAAAAGTTTGAGGCGGTTTGTTTTGTG 1 141 0 TTTGAGGGGT 0.988632 -85 TGCTCGCCTTTTTTATGCGTT 2 1 0 TTTTATGGTT 0.830561 -21 TCTATCCATGTTTGATGTTGTTAAGTCGTTG 3 15 1 TTTGATGTGT 0.953036 -73 TTAAAACTAATTTTAGGAGTATCC 5 75 1 TTTTAGGGTA 0.793414 -14 AATAAGTCTTTGAGCATTTCTTGCATGAT 7 9 1 TTTGAGCTTT 0.902513 -162 TTCAATTAATTTAGAGGCTTTAGCGATTTGT 7 53 1 TTAGAGGTTT 0.909289 -118 ******* *** Masking position 1 Map Score: 2.06292 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 627 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 ********** No masking Map Score: 6.77448e-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: 6.77448e-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 9 ********** No masking Map Score: 6.77448e-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