AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iphoB_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 HP0166 235 response regulator (ompR) #2 HP0168 46 H. pylori predicted coding region HP0168 #3 HP0170 74 H. pylori predicted coding region HP0170 #4 HP0171 60 peptide chain release factor RF-2 (prfB) #5 HP0174 300 H. pylori predicted coding region HP0174 #6 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #7 HP0474 21 molybdenum ABC transporter, permease protein (modB) #8 HP1466 134 conserved hypothetical integral membrane protein Motif number 1 TAAAGTCTTATTTTTTAATGTTTTTAAACAATTC 1 24 0 TTTTTAATTT 0.982414 -212 CATTAATAACTATGATAATGTTTTGAATTTTTAT 1 95 1 TATATAATTT 0.894036 -141 TTGAATTTTTATTTTTAAGATATTTTCAAGGTAT 1 117 1 ATTTTAAATT 0.760843 -119 TCAAGGTATCTTTAATAATAAAATGCTAGAATTA 1 142 1 TTTATAAAAT 0.720508 -94 AACGATTAACTTTGTTAATGTTTTAGGGGACTAA 1 173 0 TTTTTAATTT 0.982414 -63 GCGTTTCTCTTAATCATTTTCAATACCTA 2 28 0 TCTTTAATTT 0.898076 -19 GCCAATTGGTTTTAAAAAGCGTTTTATAGTAACC 3 40 0 TTTAAAATTT 0.784292 -35 TTTTTGAATCTTCTTTAACATTTTTTTTCTTTCC 5 91 0 TTCTTAATTT 0.883446 -210 ATCGGTTATTTTTCTAAAAGTTTTAATTTTTTAT 6 49 1 TTTTAAATTT 0.893944 -177 AATCTTCATCTTTGATAAAAAATTAAAACTTTTA 6 63 0 TTTATAAATT 0.944707 -163 TAAAAATTTGTATTTTAAAAGTTTGAGGCGGTTT 6 149 0 TATTTAATTT 0.951361 -77 TACCTATTTGTATCTTAAAAATTTGTATTTTAAA 6 164 0 TATTTAATTT 0.951361 -62 AGAACTCCCTTTGATTAAATGATTGGAATTGGTG 6 202 0 TTGTTAAATT 0.908175 -24 CAATACTCTGTTTAATAAAGGATTAATTATTTTT 8 14 0 TTTATAAATT 0.944708 -121 AAACAGAGTATTGTTTAACCTTTTGTTTTATCAT 8 35 1 TTGTTAATTT 0.933107 -100 TTAAAACGACTATTTTAACACAATGATAAAACAA 8 57 0 TATTTAAAAT 0.676631 -78 CAAACAAAATTTTGTTAATAGATTTTACCTAATC 8 91 1 TTTTTAAATT 0.975375 -44 *** **** *** Masking position 7 Map Score: 21.3182 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 567 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 TGAAAAATAAAGTCTTATTTTTTAATGTTTTTA 1 32 0 ATCTTTTTTT 0.947843 -204 TAATGTTTTGAATTTTTATTTTTAAGATATTTT 1 110 1 ATTTTTTTTT 0.973787 -126 CATTAACAAAGTTAATCGTTTTTAAAGTTGCAG 1 187 1 GTAATTTTTT 0.674722 -49 TTGTAATAATATTTATTGTCTTTTTTGGTGTTA 5 44 1 ATTATTCTTT 0.938694 -257 TTTTGGTGTTAGTTTTATTCTTTTTGGAAAGAA 5 66 1 ATTTTTCTTT 0.977307 -235 CTTCTTTAACATTTTTTTTCTTTCCAAAAAGAA 5 83 0 ATTTTTCTTT 0.977307 -218 GGTTACCAGGGTTATTATTCTTTATATTTGGTT 5 185 1 GTATTTCTTT 0.871109 -116 ATTATTCTTTATATTTGGTTTTTTAGCATTGCA 5 198 1 AATTTTTTTT 0.811542 -103 TTTTTCTAAAAGTTTTAATTTTTTATCAAAGAT 6 57 1 ATTTTTTTTT 0.973807 -169 TTCACTCTAAAATCTTCATCTTTGATAAAAAAT 6 74 0 ATCTTTCTTT 0.95465 -152 TTAATAAAGGATTAATTATTTTTAAA 8 4 0 ATAATTTTTT 0.85643 -131 CTATTAACAAAATTTTGTTTGTTAAAACGACTA 8 79 0 ATTTTTTGTT 0.864542 -56 * **** ***** Masking position 6 Map Score: 13.3414 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 290 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 CTTTGTTTTCATGGAATATTGAAAAATAAAGTCTT 1 49 0 ATATATAAAA 0.970922 -187 GCGTTTAGAGATTAGGTATTGAAAATGATTAAGAG 2 16 1 ATGTATAAAA 0.927615 -31 GCTTTTAACAATGCTATAATGATAAGTTCAAAACC 4 15 1 ATATATATAA 0.965633 -46 AAAAAATGTTAAAGAAGATTCAAAAATTCTCGATG 5 99 1 AAAGATAAAA 0.726569 -202 ATAATTACGAATATTATATTCATAATTGCATCGAG 5 127 0 ATATATATAA 0.965609 -174 ATGGGATAACATGCAATGCTAAAAAACCAAATATA 5 207 0 ATATGTAAAA 0.862789 -94 ATTGCATGTTATCCCATATTAAATAACTTCTATAC 5 225 1 ATATATAATA 0.892297 -76 CTATTAATCAATCTCATATTGATAAGCTTACTATG 5 261 1 ATATATATAA 0.965633 -40 AAAGATGAAGATTTTAGAGTGAAAATGTTGGTTAA 6 84 1 ATAGATAAAA 0.954336 -142 GAAAATGTTGGTTAAATACTAATAAGTGGGATACA 6 104 1 GTATATATAA 0.841044 -122 ACTCTGTTTAATAAAGGATTAATTATTTTTAAA 8 9 0 ATGGATATTA 0.626294 -126 ** *** * **** Masking position 12 Map Score: 7.97693 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 87 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 AATGTTTTTAAACAATTCCTTTGATCGTTTT 1 11 0 AACAATCCTT 0.965829 -225 ATTCCATGAAAACAAAGCCTTAAATTTCCAT 1 67 1 AACAAACCTT 0.971182 -169 GTTTTATAGTAACCATAATTTATCGGCTGTC 3 23 0 AACCATATTT 0.842759 -52 AATGGCTTTTAACAATGCTATAATGATAAGT 4 11 1 AACAATCTAT 0.810156 -50 AAACAGAACCTTTATGAGTGGG 4 49 0 AACAGACCTT 0.928239 -12 GAATGCATACAACAATAATTACGAATATTAT 5 145 0 AACAATATTA 0.679822 -156 AATAAATCCTTCTTGTTGAAT 6 1 1 AATAAACCTT 0.726382 -225 TTAGAAAAATAACCGATCTTAGGGTGTAACT 6 35 0 AACCGACTTA 0.682494 -191 ATTAGTATTTAACCAACATTTTCACTCTAAA 6 96 0 AACCAAATTT 0.864289 -130 CAAAAGGTTAAACAATACTCTGTTTAATAAA 8 29 0 AACAATCTCT 0.86348 -106 CGTTTTAACAAACAAAATTTTGTTAATAGAT 8 83 1 AACAAATTTT 0.800907 -52 ****** **** Masking position 2 Map Score: 3.31044 Number of sites scoring better than the average of aligned sites = 780 Number in coding regions = 642 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 AAAACGATCAAAGGAATTGTTTAAAA 1 7 1 ATCAAAGGAA 0.92702 -229 TCAAAACATTATCATAGTTATTAATGGAAA 1 91 0 ATCATAGTTA 0.908275 -145 GCATTTTATTATTAAAGATACCTTGAAAAT 1 138 0 ATTAAAGATA 0.900798 -98 CTAAAACATTAACAAAGTTAATCGTTTTTA 1 181 1 AACAAAGTTA 0.908275 -55 TTCTTGTTGAATTAAAGTTACACCCTAAGA 6 20 1 ATTAAAGTTA 0.928629 -206 TTAATTTTTTATCAAAGATGAAGATTTTAG 6 71 1 ATCAAAGATG 0.91105 -155 CAATCATTTAATCAAAGGGAGTTCT 6 211 1 ATCAAAGGGA 0.949562 -15 ********** Masking position 6 Map Score: 1.92888 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 177 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TTTGTTAATGTTTTAGGGGACTAATTCTAG 1 167 0 TTTTAGGGGA 0.907415 -69 ACAGAACCTTTATGAGTGGGGTTTTGAACT 4 39 0 TATGAGTGGG 0.837518 -22 TATTACAACATCTGAGGCGAACACTTTTAC 5 22 0 TCTGAGGCGA 0.91462 -279 AAATAACCGATCTTAGGGTGTAACTTTAAT 6 30 0 TCTTAGGGTG 0.961618 -196 AAGATGAAGATTTTAGAGTGAAAATGTTGG 6 85 1 TTTTAGAGTG 0.849843 -141 GGCGGTTTGTTTTGTGGGTGTATCCCACTT 6 127 0 TTTGTGGGTG 0.904868 -99 ATTTTAAAAGTTTGAGGCGGTTTGTTTTGT 6 142 0 TTTGAGGCGG 0.974864 -84 TTTTACCTAATCTGAGAGAGAATTATATTT 8 113 1 TCTGAGAGAG 0.873737 -22 ********** Masking position 3 Map Score: 1.92872 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 505 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 ********** No masking Map Score: 1.66429e-14 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: 1.66429e-14 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: 1.66429e-14 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