AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_dna_polymerase_hpyl_reg_300.orf -o193_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e 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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP00255 91 AE000511 #2 RHP00256 76 AE000511 #3 RHP00851 67 AE000511 #4 RHP00852 65 AE000511 #5 RHP00853 30 AE000511 #6 RHP00864 26 AE000511 #7 RHP00871 104 AE000511 #8 RHP00872 138 AE000511 Motif number 1 CAATAATTTAGATTTTTTAGCTAGCATGTT 1 21 1 GATTTTTTAG 0.888911 -71 TCCTTAGCTTACTTTTTAACAATATCCATG 1 66 0 ACTTTTTAAC 0.749945 -26 CAATATTATAGTTATTTAAAGCTTAAATAA 2 47 1 GTTATTTAAA 0.688161 -30 AAGGGGTTTTAAGCGCGCTAGCT 3 4 1 GGGTTTTAAG 0.948209 -64 TCAATCAAGCGAATTTTAAGTTTATTGTAA 3 38 0 GAATTTTAAG 0.96769 -30 TTATAATTTTATTTTTTAAAAGGATACCC 5 12 1 ATTTTTTAAA 0.805019 -19 GGTTTTTGAAGGCTTGATTTT 7 2 1 GTTTTTGAAG 0.861517 -103 TTGAAGGCTTGATTTTTAAAAGTTAGGCTT 7 16 1 GATTTTTAAA 0.975329 -89 TAAAATCTCAGAATTTTAACATAAAAGATT 7 46 0 GAATTTTAAC 0.913765 -59 ATTTTAAAGAGAGTTTTAAAAA 8 3 0 GAGTTTTAAA 0.944441 -136 TCTTAAAGTAAAATTTTAAAGAGAGTTTTA 8 15 0 AAATTTTAAA 0.758164 -124 ATCAAACAACGCTTTTTAAGAGTGGCTCAA 8 67 1 GCTTTTTAAG 0.977053 -72 ATTAGAACAAGGTTTTTATGACGAT 8 124 1 GGTTTTTATG 0.819206 -15 ********** Masking position 5 Map Score: 13.6518 Number of sites scoring better than the average of aligned sites = 2196 Number in coding regions = 1886 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 2 ATCTAAATTATTGTAACAAAAGC 1 4 0 TTGTAACAAA 0.963858 -88 TTAGCTTACTTTTTAACAATATCCATGCCT 1 63 0 TTTTAACAAT 0.871991 -29 ATCGCTTCAATTTAATCAAAATTAGATTAC 2 18 1 TTTAATCAAA 0.923573 -59 TTTAAGTTTATTGTAACACAAGCTAGCGCG 3 24 0 TTGTAACACA 0.865 -44 TCAACCCTCTTCAATCAAGCGAATTTTAA 3 49 0 TTCAATCAAG 0.74335 -19 TTCAAACAAATCCCCCAATC 4 56 0 TTCAAACAAA 0.959259 -10 GGGTATCCTTTTAAAAAATAAAATTATA 5 13 0 TTTTAAAAAA 0.749496 -18 AATCTCAGAATTTTAACATAAAAGATTAAG 7 43 0 TTTTAACATA 0.9308 -62 AACTTTAAACCTAAAACCTAACG 7 92 0 TTTAAACCTA 0.752893 -13 AATGAGCCATTTTTATCAAACAACGCTTTT 8 53 1 TTTTATCAAA 0.888962 -86 AGTGGTCTTATTCTATCCAATTAGCCCTTG 8 94 0 TTCTATCCAA 0.898796 -45 ********** Masking position 5 Map Score: 11.5502 Number of sites scoring better than the average of aligned sites = 874 Number in coding regions = 699 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 AAAAGTAAGCTAAGGAGTGTTT 1 80 1 TAAGGAGTGT 0.882208 -12 AAGGGGTTTTAAGCGCGCTAGCTTGTGT 3 9 1 TTAAGCGCGC 0.948882 -59 TTCGCTTGATTGAAGAGGGTTGA 3 55 1 TGAAGAGGGT 0.978767 -13 GAGTTGGCTATTAAGGGGGC 4 1 0 TTAAGGGGGC 0.9803 -65 CTCAACGCTATTAAGTGGGGCGAGTTCAGA 4 28 1 TTAAGTGGGG 0.971076 -38 AGTAAAATTTTAAAGAGAGTTTTAAAAA 8 9 0 TAAAGAGAGT 0.932449 -130 ACAACGCTTTTTAAGAGTGGCTCAAGGGCT 8 72 1 TTAAGAGTGG 0.98001 -67 ********** Masking position 3 Map Score: 2.84651 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 324 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 AACAATATCCATGCCTTAATGAATTGCTAA 1 49 0 ATGCCTTAAT 0.846519 -43 GATTAAATTGAAGCGATAAAAAAG 2 5 0 AAGCGATAAA 0.869348 -72 ACCCTTATTTAAGCTTTAAATAACTATAAT 2 51 0 AAGCTTTAAA 0.889968 -26 CCCCACTTAATAGCGTTGAGTTGGCTATTA 4 18 0 TAGCGTTGAG 0.852156 -48 AGACAAGCCATGAAAAAAGAAAAG 6 5 1 AAGCCATGAA 0.917085 -22 GGTTTTTGAAGGCTTGATTTTTAAAAGT 7 9 1 AAGGCTTGAT 0.971385 -96 TTTTAAAAGTTAGGCTTAATCTTTTATGTT 7 29 1 TAGGCTTAAT 0.909714 -76 CGTTAGGTTTTAGGTTTAAAGTT 7 92 1 TAGGTTTAAA 0.652469 -13 CACTCTTAAAAAGCGTTGTTTGATAAAAAT 8 61 0 AAGCGTTGTT 0.921066 -78 AGAGTGGCTCAAGGGCTAATTGGATAGAAT 8 85 1 AAGGGCTAAT 0.826735 -54 ATCGTCATAAAAACCTTGTTCTAATAGTGG 8 119 0 AAACCTTGTT 0.53246 -20 ********** Masking position 7 Map Score: 3.91774 Number of sites scoring better than the average of aligned sites = 2831 Number in coding regions = 2576 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 5 AATATTGTAATCTAATTTTGATTAAATTGA 2 24 0 TCTAATTTTG 0.973652 -53 TTTAAATAACTATAATATTGTAATCTAATT 2 37 0 TATAATATTG 0.960571 -40 GTTATAATTTTATTTTTTAAAA 5 3 1 TATAATTTTA 0.685885 -28 TCTTTTATGTTAAAATTCTGAGATTTTATA 7 48 1 TAAAATTCTG 0.872989 -57 TATCTTAAAGTAAAATTTTAAAGAGAGTTT 8 17 0 TAAAATTTTA 0.494521 -122 AAAACCTTGTTCTAATAGTGGTCTTATTCT 8 110 0 TCTAATAGTG 0.904327 -29 ********** Masking position 5 Map Score: 2.54572 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 93 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ********** No masking Map Score: -5.44113e-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 7 ********** No masking Map Score: -5.44113e-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: -5.44113e-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