AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -intrC_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 HP0512 290 glutamine synthetase (glnA) #2 HP0698 187 H. pylori predicted coding region HP0698 #3 HP0699 39 H. pylori predicted coding region HP0699 #4 HP1169 212 glutamine ABC transporter, permease protein (glnP) Motif number 1 CTTATCATTCCCACCAATTTTTATAATA 1 7 1 ATTCCACAAT 0.987988 -284 AAAAAGGAATAATGCGAACAATTATGGGATGA 1 39 0 AATGCACAAT 0.906538 -252 TCAATTTGTCATTCCTATCTATCAGAGGTTGT 1 79 0 ATTCCACTAT 0.941158 -212 TTTTGAAGAAAATCAAAACAATCAATTTGTCA 1 100 0 AATCAACAAT 0.989591 -191 CATGCGGTAAAATCCGCTAAATCAAGGAGTGT 1 168 0 AATCCCAAAT 0.933659 -123 TAAATGCTATAATCACCCCTATCAATCAAACT 1 243 1 AATCACCTAT 0.934488 -48 ATCAAACTCAATTCATAACAATTAAAGGTGGT 1 267 1 ATTCAACAAT 0.982039 -24 GCTTGAGTTAAATCAACCCAAGCTTTTAGCAC 2 53 0 AATCACCAAG 0.92934 -135 AATTTTCTTCAATCCTAACAAATTTGGCTGCA 2 86 1 AATCCACAAA 0.955973 -102 CCTAGTATTAAATCAAAAAAAAAGAAAAAAGC 2 133 0 AATCAAAAAA 0.809254 -55 ACTGGCTGAAATTAACAACAATGATTAAACAA 4 29 0 ATTAAACAAT 0.854707 -184 TTTTGCCACTATTCAAAGAAATTTTGGATTAT 4 70 0 ATTCAAAAAT 0.941517 -143 AACAGCTCTTATTCACCCCAATTGTTAGAAGT 4 143 0 ATTCACCAAT 0.983484 -70 ***** * **** Masking position 11 Map Score: 19.3647 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 341 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 TATGGGATGATATTATAAAAATTGGTGGGA 1 19 0 TATTATAAAA 0.592298 -272 TTTTGAAGAAAATCAAAACAATCAATTTGT 1 102 0 AATCAAAACA 0.949311 -189 TTTTGATTTTCTTCAAAAAATCCTAATAGT 1 114 1 CTTCAAAAAA 0.926257 -177 CGTCTGCTTCCATAATAACACTCCTTGATT 1 151 1 CATAATAACA 0.74785 -140 CCGCATGCATCTTAATAAAACTTGATACAG 1 193 1 CTTAATAAAA 0.756847 -98 ATCAAACTCAATTCATAACAATTAAAGGTG 1 267 1 ATTCATAACA 0.935425 -24 ATAAAGCCTCTTTCATAAAAAGGATTGAGC 2 15 0 TTTCATAAAA 0.873807 -173 AATTTTCTTCAATCCTAACAAATTTGGCTG 2 86 1 AATCCTAACA 0.690907 -102 TTTGGCTGCAAATTAAAAAATTTAAGCTTT 2 108 1 AATTAAAAAA 0.7784 -80 CCTAGTATTAAATCAAAAAAAAAGAAAAAA 2 135 0 AATCAAAAAA 0.957987 -53 ATCACTATACTTTCAATAAAATAAGGGGTT 3 16 1 TTTCAATAAA 0.642712 -24 ATGATTAAACAATCATTAAATGGAGAGGAC 4 11 0 AATCATTAAA 0.776818 -202 TTTGGATTATAATAAAAAAACTGGCTGAAA 4 50 0 AATAAAAAAA 0.867625 -163 TTTTGCCACTATTCAAAGAAATTTTGGATT 4 72 0 ATTCAAAGAA 0.731293 -141 AAGCACCATGTTTAAAAACAGCTCTTATTC 4 161 0 TTTAAAAACA 0.710496 -52 ********** Masking position 10 Map Score: 12.5924 Number of sites scoring better than the average of aligned sites = 1260 Number in coding regions = 1060 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 3 ATTAGGATTTTTTGAAGAAAATCAAAACAATCAATT 1 105 0 TTGAAATAAA 0.691115 -186 AGAAAATTTGCTTGAGTTAAATCAACCCAAGCTTTT 2 58 0 CTGAAATAAC 0.946835 -130 CCTAACAAATTTGGCTGCAAATTAAAAAATTTAAGC 2 99 1 TTGAAATAAA 0.988973 -89 AAAATTATACCTAGTATTAAATCAAAAAAAAAGAAA 2 138 0 CTGAAATAAA 0.985516 -50 CTTTTCCTTGTTAGGTGGAATTAAAATTATACCTAG 2 160 0 TTGAATTAAA 0.982431 -28 AATAAAAAAACTGGCTGAAATTAACAACAATGATTA 4 34 0 CTGAATTACA 0.935742 -179 CAAAGAAATTTTGGATTATAATAAAAAAACTGGCTG 4 53 0 TTGTAATAAA 0.944374 -160 TATGAGCCGTTTTGCCACTATTCAAAGAAATTTTGG 4 75 0 TTGTATTAAA 0.953097 -138 ** * **** *** Masking position 10 Map Score: 7.75936 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 98 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AAAATTGGTGGGAATGATAAG 1 2 0 GGAATGATAA 0.968962 -289 GAACAATTATGGGATGATATTATAAAAATT 1 26 0 GGGATGATAT 0.980205 -265 CTGATAGATAGGAATGACAAATTGATTGTT 1 86 1 GGAATGACAA 0.919451 -205 GCTAAATCAAGGAGTGTTATTATGGAAGCA 1 155 0 GGAGTGTTAT 0.886706 -136 TTGATTGATAGGGGTGATTATAGCATTTAT 1 242 0 GGGGTGATTA 0.98732 -49 CTAAAAGCTTGGGTTGATTTAACTCAAGCA 2 56 1 GGGTTGATTT 0.937696 -132 TCTAACAATTGGGGTGAATAAGAGCTGTTT 4 146 1 GGGGTGAATA 0.950517 -67 ********** Masking position 5 Map Score: 5.92756 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 152 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 CGCATTATTCCTTTTTCCAACTATACAACCT 1 55 1 CTTTTTCCAC 0.970927 -236 AGATTCTACTTTTTTTGCCCCATAAATGCTA 1 221 1 TTTTTTGCCC 0.980684 -70 ATGAAAGAGGCTTTATGCCTCTTGGTGCTAA 2 29 1 CTTTATGCCC 0.987734 -159 TCAACCCAAGCTTTTAGCACCAAGAGGCATA 2 42 0 CTTTTAGCAC 0.972781 -146 GTTTATGAGCCGTTTTGCCACTATTCAAAGA 4 83 0 CGTTTTGCCC 0.991691 -130 ********* * Masking position 4 Map Score: 2.6209 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 121 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 CAAGTTTTATTAAGATGCATGCGGTAAAAT 1 187 0 TAAGATGCAT 0.9064 -104 TTATAGCATTTATGGGGCAAAAAAAGTAGA 1 225 0 TATGGGGCAA 0.779922 -66 CATAACAATTAAAGGTGGTTA 1 280 1 AAAGGTGGTT 0.825666 -11 CCTTTTTATGAAAGAGGCTTTATGCCTCTT 2 22 1 AAAGAGGCTT 0.969771 -166 CTTTTAGCACCAAGAGGCATAAAGCCTCTT 2 33 0 CAAGAGGCAT 0.955734 -155 TTCAATAAAATAAGGGGTTTTTT 3 27 1 TAAGGGGTTT 0.868436 -13 TGTTTTTAAACATGGTGCTTTAAAGCGTCA 4 171 1 CATGGTGCTT 0.943121 -42 CTTAAAAATTAATGACGCTTTAAAGCACCA 4 183 0 AATGACGCTT 0.850287 -30 ********** Masking position 2 Map Score: 1.54236 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 818 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 TAGTTGGAAAAAGGAATAATGCGAACAATT 1 48 0 AAGGAATAAT 0.945056 -243 TGGGGCAAAAAAAGTAGAATCTGTATCAAG 1 213 0 AAAGTAGAAT 0.830077 -78 GATTTAATACTAGGTATAATTTTAATTCCA 2 151 1 TAGGTATAAT 0.887858 -37 TCCACCTAACAAGGAAAAGCT 2 177 1 AAGGAAAAGC 0.872043 -11 TATTTTATTGAAAGTATAGTGATAGAAC 3 9 0 AAAGTATAGT 0.944602 -31 ATTAATTTTTAAGGTATAGCGTT 4 200 1 AAGGTATAGC 0.976655 -13 ********** Masking position 6 Map Score: 0.703739 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 65 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 ********** No masking Map Score: 1.43773e-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: 1.43773e-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: 1.43773e-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