AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -idnaA_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 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #2 HP0497 228 sodium- and chloride-dependent transporter #3 HP0500 57 DNA polymerase III beta-subunit (dnaN) #4 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #5 HP1079 110 H. pylori predicted coding region HP1079 #6 HP1529 152 chromosomal replication initiator protein (dnaA) Motif number 1 TAAGAAGTAGAAAATAAAGAAGCAGTATTTTAG 1 39 1 AATAAAGAAC 0.881067 -167 GTATTTTTAAAGGATTAAAAAGCTAAAATACTG 1 61 0 AATTAAAAAC 0.947096 -145 AAAAACTCCAAATTTTAAAAAACTTCAATTTTT 1 96 0 ATTTAAAAAC 0.975335 -110 TTGTTAGAATACCTTAAAAGAATTTAAAACCCC 1 141 0 ATTAAAAGAT 0.699678 -65 TCATTGAGATAGTTTTAAGGAAATTAAGGAACA 1 181 1 ATTTAAGGAA 0.974632 -25 CATATTGTATAATTTTAAGAAAATTTCATTATT 2 27 0 ATTTAAGAAA 0.959752 -202 AGAAAAAACCCACTTTAAAAATACCTAAAAAAT 2 98 0 CTTTAAAAAA 0.834408 -131 AAAGATCTTAAGATTTAAGAAAAAACCCACTTT 2 115 0 ATTTAAGAAA 0.959771 -114 AGTTTTTAAAATCTTTAAAGATCTTAAGATTTA 2 131 0 ATTTAAAGAC 0.985257 -98 CAATAGTTGGACGATTAAGGACATCGCTCTTTA 2 171 1 AATTAAGGAA 0.943099 -58 GTCAATGATTAAAATTAAAGAGCGATGTCCTTA 2 186 0 AATTAAAGAC 0.96648 -43 TCTTAATTATAGCTAAAAGAACGCTTTT 3 7 0 ATAAAAGAC 0.920018 -51 GGGGTATAAAAAAATTAAAAAACTTTAAAACTT 4 37 1 AATTAAAAAC 0.947096 -135 TATCAATAAAAAACTTAAGAAAAAGAAAAGTTC 4 98 0 ACTTAAGAAA 0.790045 -74 ATACAATTCCAAATTTAAAAAACAAACGATTTA 4 128 1 ATTTAAAAAC 0.976453 -44 GATTTAATTCAAATTTAAGGAAAAATT 4 155 1 ATTTAAGGAA 0.974635 -17 TTACGACAAAATTTTAAAAGAACTTGAGAACAA 5 30 0 ATTAAAAGAC 0.963852 -81 TATAGACAAACCCTTAAAAGAAACACCTTAATT 6 56 1 CTTAAAAGAA 0.764026 -97 * ******** * Masking position 5 Map Score: 31.153 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 474 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 TTCTGGCTTTTAGGGGGTTTTAAATTCTTT 1 128 1 TAGGGGGTTT 0.891675 -78 GAGATAGTTTTAAGGAAATTAAGGAACAAA 1 186 1 TAAGGAAATT 0.946421 -20 ATTATTTAAGTAAGGGGAATTA 2 3 0 TAAGGGGAAT 0.96425 -226 CTTACTTAAATAATGAAATTTTCTTAAAAT 2 19 1 TAATGAAATT 0.795891 -210 TAGTATAATCTAAGGGCGTTGCTCTGTATT 2 71 1 TAAGGGCGTT 0.925809 -158 GTTGGACGATTAAGGACATCGCTCTTTAAT 2 176 1 TAAGGACATC 0.872323 -53 TAATCATTGACAAGGAGTTTGGTAGTTAAG 2 208 1 CAAGGAGTTT 0.925279 -21 ACCAAAAATTCAAGGGGATTATTTTAACT 3 39 1 CAAGGGGATT 0.976592 -19 CCCCTCCATTTAATGACATTTGGGTTAAA 4 10 0 TAATGACATT 0.89781 -162 TTTGTTCTATTAATGAGAATAAGTTTTAAA 4 60 0 TAATGAGAAT 0.816068 -112 TCTGCTTGGATAAGGGGATTTA 5 99 1 TAAGGGGATT 0.991761 -12 GCCTTAAAATTAAGGTGTTTCTTTTAAGGG 6 66 0 TAAGGTGTTT 0.881205 -87 ********** Masking position 2 Map Score: 12.9289 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 602 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 AAGAAGCAGTATTTTAGCTTTTTAATCCTTTAA 1 55 1 ATTAGTTTTT 0.956309 -151 AAACTTCAATTTTTCAGTATTTTTAAAGGATTA 1 77 0 TTTAGATTTT 0.918091 -129 ATACTGAAAAATTGAAGTTTTTTAAAATTTGGA 1 90 1 ATTAGTTTTT 0.956309 -116 TTTTTTAAAATTTGGAGTTTTTTCTGGCTTTTA 1 107 1 TTTAGTTTTT 0.988791 -99 TTTTAGGGGGTTTTAAATTCTTTTAAGGTATTC 1 135 1 TTTAATCTTT 0.936403 -71 TGCTCTGTATTTTTTAGGTATTTTTAAAGTGGG 2 90 1 TTTAGTATTT 0.948224 -139 TTTTCTTAAATCTTAAGATCTTTAAAGATTTTA 2 125 1 TCTAGTCTTT 0.983569 -104 CTGTATTAGTTTTTAAAATCTTTAAAGATCTTA 2 138 0 TTTAATCTTT 0.936403 -91 GAGAATAAGTTTTAAAGTTTTTTAATTTTTTTA 4 43 0 TTTAGTTTTT 0.988791 -129 CTTTTCTTTTTCTTAAGTTTTTTATTGATACAA 4 101 1 TCTAGTTTTT 0.982223 -71 GATCGTTTGTTCTCAAGTTCTTTTAAAATTTTG 5 24 1 TCTAGTCTTT 0.983569 -87 *** ** ***** Masking position 6 Map Score: 20.5273 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 239 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 TTAAGGAAATTAAGGAACAAA 1 195 1 TAAGGAACAA 0.800084 -11 TCTTAAGATTTAAGAAAAAACCCACTTTAA 2 113 0 TAAGAAAAAA 0.972255 -116 AYGCTATAATTAAGACCAAAAATTCAAGGG 3 25 1 TAAGACCAAA 0.906538 -33 GTTCTATTAATGAGAATAAGTTTTAAAGTT 4 57 0 TGAGAATAAG 0.745756 -115 ATAAAAAACTTAAGAAAAAGAAAAGTTCAA 4 96 0 TAAGAAAAAG 0.94484 -76 AATTCAAATTTAAGGAAAAATT 4 160 1 TAAGGAAAAA 0.94484 -12 TAAAAGAACTTGAGAACAAACGATCTGATG 5 19 0 TGAGAACAAA 0.942422 -92 CGCATGCAATTACGACAAAATTTTAAAAGA 5 42 0 TACGACAAAA 0.893308 -69 AGCTAATGGATGCGAAAAAAGGATTTTC 6 9 0 TGCGAAAAAA 0.933901 -144 ********** Masking position 9 Map Score: 7.3288 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 221 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 TATTTAAGTAAGGGGAATTA 2 1 0 AGGGGAATTA 0.957104 -228 ACCAAACTCCTTGTCAATGATTAAAATTAA 2 201 0 TTGTCAATGA 0.825867 -28 TTTTCCTTAAATTTGAATTAAATCGTTTGT 4 149 0 ATTTGAATTA 0.780774 -23 TGCTTGGATAAGGGGATTTA 5 101 1 AGGGGATTTA 0.822448 -10 TGTGAATGAAATGTGAATGAAGCCTTAAAA 6 87 0 ATGTGAATGA 0.982672 -66 AAGGAATAACATGTGAATGAAATGTGAATG 6 98 0 ATGTGAATGA 0.982672 -55 CGTGAATAAGTGGTGAATGAAAAAGGAATA 6 120 0 TGGTGAATGA 0.967523 -33 ********** Masking position 6 Map Score: 4.53002 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 153 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TAAAGAAGCAGTATTTTAGCTTTTTAATCC 1 53 1 GTATTTTAGC 0.965428 -153 TTCTTTTAAGGTATTCTAACAAGACTATAT 1 152 1 GTATTCTAAC 0.901719 -54 TTTTTGGTCTTAATTATAGCTAAAAGAAC 3 17 0 TAATTATAGC 0.908962 -41 TTCAAGGGGATTATTTTAACT 3 47 1 TTATTTTAAC 0.87313 -11 CTAAATTTTGGCATTATAGCGCATGCAATT 5 61 0 GCATTATAGC 0.977292 -50 ATCCATTAGCTTATTATAAAGCAAGCATTA 6 28 1 TTATTATAAA 0.78347 -125 TATAAAGCAAGCATTATAGACAAACCCTTA 6 42 1 GCATTATAGA 0.908042 -111 GGCGTTATTATAGCGTGAATAAGT 6 139 0 TTATTATAGC 0.97588 -14 ********** Masking position 3 Map Score: 6.19394 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 137 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 TTCCGCACACCGCACGCAATCGCGCACATA 1 11 1 CGCACGCAAT 0.979873 -195 TTTTTTATACCCCCTCCATTTAATGACATT 4 20 0 CCCCTCCATT 0.912634 -152 GGCATTATAGCGCATGCAATTACGACAAAA 5 52 0 CGCATGCAAT 0.988095 -59 ATCCTTTTTTCGCATCCATTAGCTTATTAT 6 15 1 CGCATCCATT 0.9879 -138 CTTATTATAAAGCAAGCATTATAGACAAAC 6 37 1 AGCAAGCATT 0.900195 -116 ********** Masking position 8 Map Score: 0.735609 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 94 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 AGCAGTATTTTAGCTTTTTAATCCTTTAAA 1 59 1 TAGCTTTTTA 0.832528 -147 TTTGTTCCTTAATTTCCTTAA 1 195 0 TTGTTCCTTA 0.836987 -11 TCTAAGGGCGTTGCTCTGTATTTTTTAGGT 2 79 1 TTGCTCTGTA 0.957042 -150 CGTCCAACTATTGCTGTATTAGTTTTTAAA 2 154 0 TTGCTGTATT 0.797934 -75 ATTAAGGACATCGCTCTTTAATTTTAATCA 2 184 1 TCGCTCTTTA 0.938337 -45 CAAGTTGGATTTGTTCTATTAATGAGAATA 4 69 0 TTGTTCTATT 0.844598 -103 ATTAAATCGTTTGTTTTTTAAATTTGGAAT 4 133 0 TTGTTTTTTA 0.903473 -39 TCTATAATGCTTGCTTTATAATAAGCTAAT 6 32 0 TTGCTTTATA 0.948425 -121 ********** Masking position 5 Map Score: 1.99113 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 389 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 ********** No masking Map Score: -6.51267e-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 10 ********** No masking Map Score: -6.51267e-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 11 ********** No masking Map Score: -6.51267e-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