AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -imodE_hpyl_opreg_100.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) Motif number 1 AGGGTGTAACTTTAATTCAACAAGAAGGAT 1 16 0 TTTAATTCAA 0.758193 -210 AAATTAAAACTTTTAGAAAAATAACCGATC 1 48 0 TTTTAGAAAA 0.733283 -178 AATCTTCATCTTTGATAAAAAATTAAAACT 1 67 0 TTTGATAAAA 0.688424 -159 GATGAAGATTTTAGAGTGAAAATGTTGGTT 1 87 1 TTAGAGTGAA 0.826767 -139 AGAACTCCCTTTGATTAAATGATTGGAAT 1 207 0 TTTGATTAAA 0.732945 -19 CACTAAAAGCTTAAATAAAAGGGCATAAGG 3 58 1 TTAAATAAAA 0.582388 -30 TTACCCTTATATTAAATCTTTTAAAG 4 57 0 TTATATTAAA 0.651377 -16 GAGCTTAAAATTTAAGAAAATTATAAAGAG 5 11 1 TTTAAGAAAA 0.707158 -78 TATAAAGAGTTTTGATAGAATACCTTTTTT 5 32 1 TTTGATAGAA 0.941916 -57 AAAACGCATCTTTTAAAAAAAGGTATTCTA 5 47 0 TTTTAAAAAA 0.550576 -42 GCTCGTTAAGTTTTATTGAATGTGTTGTAA 6 14 1 TTTTATTGAA 0.765577 -75 ATAAACTCTTTTTAAGTCAAGCAATAAAGT 6 59 1 TTTAAGTCAA 0.890573 -30 ATAGGGGGAGTTTCATTCAATTAATTTAGA 7 38 1 TTTCATTCAA 0.855227 -133 ATTGCTTTATTTAGATACAAATCGCTAAAG 7 70 0 TTAGATACAA 0.906593 -101 TAATATTGAGTTTTATAGAAAAAAGAAATA 7 128 0 TTTTATAGAA 0.722762 -43 AACTCCCTAGTTTTATTCAATAATATTGAG 7 148 0 TTTTATTCAA 0.773561 -23 ********** Masking position 5 Map Score: 22.723 Number of sites scoring better than the average of aligned sites = 1039 Number in coding regions = 841 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 TGATAAAAAATTAAAACTTTTAGAAAAATA 1 55 0 TTAAAACTTT 0.954325 -171 CATTTTCACTCTAAAATCTTCATCTTTGAT 1 81 0 CTAAAATCTT 0.89093 -145 AATTTGTATTTTAAAAGTTTGAGGCGGTTT 1 149 0 TTAAAAGTTT 0.968187 -77 TATTTGTATCTTAAAAATTTGTATTTTAAA 1 164 0 TTAAAAATTT 0.950872 -62 TTATGTTACACTAAAAGCTTAAATAAAAGG 3 50 1 CTAAAAGCTT 0.907954 -38 TAAAGAGGTTTTAAAAATATTTAAAATCAT 4 26 1 TTAAAAATAT 0.909402 -47 TTAAAAATATTTAAAATCATGCTTTAAAAG 4 36 1 TTAAAATCAT 0.92438 -37 AAATCATGCTTTAAAAGATTTAATATAAGG 4 49 1 TTAAAAGATT 0.845058 -24 GAGCTTAAAATTTAAGAAAATTAT 5 5 1 TTAAAATTTA 0.849509 -84 TCAAAACTCTTTATAATTTTCTTAAATTTT 5 17 0 TTATAATTTT 0.744839 -72 AAGATGCGTTTTAAAACTAATTTTAGGAGT 5 65 1 TTAAAACTAA 0.708247 -24 TTATTATACCTTAAAAACATTACAACACAT 6 33 0 TTAAAAACAT 0.903735 -56 ********** Masking position 5 Map Score: 12.6901 Number of sites scoring better than the average of aligned sites = 1028 Number in coding regions = 815 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 TCCCTTTATCCCTTATGCCCTTTT 3 74 0 CTTTATCCTT 0.98521 -14 TATCAAAACTCTTTATAATTTTCTTAAATTT 5 18 0 CTTTATATTT 0.82394 -71 AGGTTGCAAACTTTATTGCTTGACTTAAAAA 6 67 0 CTTTATTCTT 0.987708 -22 GCTAAAGCCTCTAAATTAATTGAATGAAACT 7 46 0 CTAAATTATT 0.710322 -125 AATTTAGAGGCTTTAGCGATTTGTATCTAAA 7 60 1 CTTTAGCATT 0.873833 -111 ACGATTATTACTTTATTGCTTTATTTAGATA 7 83 0 CTTTATTCTT 0.987708 -88 ATTAAACATGCTATATTTCTTTTTTCTATAA 7 115 1 CTATATTCTT 0.972187 -56 ******* *** Masking position 5 Map Score: 4.89877 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 91 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 ATAAAAAATTAAAACTTTTAGAAAAATAAC 1 53 0 AAAACTTTTA 0.693122 -173 ATTGGTGATTATACCTATTTGTATCTTAAA 1 179 0 ATACCTATTT 0.924619 -47 AATATTTTTAAAACCTCTTTAAAGCACTCA 4 17 0 AAACCTCTTT 0.978122 -56 AAGAGGTTTTAAAAATATTTAAAATCATGC 4 28 1 AAAAATATTT 0.739969 -45 TACCCTTATATTAAATCTTTTAAAGCATGA 4 52 0 TTAAATCTTT 0.706562 -21 GTATTCTATCAAAACTCTTTATAATTTTCT 5 25 0 AAAACTCTTT 0.980427 -64 TTTTGATAGAATACCTTTTTTTAAAAGATG 5 41 1 ATACCTTTTT 0.895046 -48 GATGCGTTTTAAAACTAATTTTAGGAGTAT 5 67 1 AAAACTAATT 0.780103 -22 TAAGGTATAATAAACTCTTTTTAAGTCAAG 6 50 1 TAAACTCTTT 0.946614 -39 AATAAGTCTTTGAGCATTTCT 7 2 1 ATAAGTCTTT 0.879344 -169 ********** Masking position 6 Map Score: 7.6704 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 661 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 5 AATTAAAGTTACACCCTAAGATCGGTTATTT 1 29 1 ACACCTAAGA 0.888611 -197 TAAGTGGGATACACCCACAAAACAAACCGCC 1 126 1 ACACCACAAA 0.932295 -100 CACAAAACAAACCGCCTCAAACTTTTAAAAT 1 141 1 ACCCCTCAAA 0.986311 -85 AACGCATAAAAAAGGCGAGCA 2 1 1 AACCATAAAA 0.81159 -21 CAACGACTTAACAACATCAAACATGGATAGA 3 15 0 ACACATCAAA 0.945056 -73 ATGTTACACTAAAAGCTTAAATAAAAGGGCA 3 52 1 AAAGCTTAAA 0.761736 -36 GGATACTCCTAAAATTAGTTTTAA 5 75 0 TACCCTAAAA 0.775204 -14 ATCATGCAAGAAATGCTCAAAGACTTATT 7 9 0 AAAGCTCAAA 0.953844 -162 ACAAATCGCTAAAGCCTCTAAATTAATTGAA 7 53 0 AAACCTCTAA 0.914498 -118 *** ******* Masking position 11 Map Score: 3.36835 Number of sites scoring better than the average of aligned sites = 1329 Number in coding regions = 1188 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 6 CGATCTTAGGGTGTAACTTTAATTCAACAAG 1 22 0 GTGTACTTTA 0.953416 -204 TCTTAAAAATTTGTATTTTAAAAGTTTGAGG 1 155 0 TTGTATTTAA 0.937737 -71 TTATACCTATTTGTATCTTAAAAATTTGTAT 1 170 0 TTGTACTTAA 0.990023 -56 TAAGCTTTTAGTGTAACATAATAAACAACGA 3 40 0 GTGTACATAA 0.953337 -48 AAAGAGTTTATTATACCTTAAAAACATTACA 6 39 0 TTATACTTAA 0.937987 -50 CTTTAGCGATTTGTATCTAAATAAAGCAATA 7 70 1 TTGTACTAAA 0.961051 -101 ***** ***** Masking position 5 Map Score: 4.33339 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 26 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 ********** No masking Map Score: -4.67335e-15 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: -4.67335e-15 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: -4.67335e-15 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