AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_dna_polymerase_hpyl_reg_100.orf -o193_hpyl_100.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 Motif number 1 ATGCTAGCTAAAAAATCTAAATTATTGTAACAA 1 15 0 AAAAATAATT 0.834409 -77 ATGGATATTGTTAAAAAGTAAGCTAAGGAGTGT 1 67 1 TTAAAGAAGC 0.948381 -25 TCTAATTTTGATTAAATTGAAGCGATAAAAAAG 2 11 0 ATTAATAAGC 0.904029 -66 TTATAGTTATTTAAAGCTTAAATAAGGGTCTAG 2 52 1 TTAAATAAAT 0.976284 -25 TTGTGTTACAATAAACTTAAAATTCGCTTGATT 3 33 1 ATAAATAAAT 0.971943 -35 GGTATCCTTTTAAAAAATAAAATTATAAC 5 7 0 TAAAATAAAT 0.96043 -24 ACAAGCCATGAAAAAAGAAAAGTC 6 13 1 AAAAAAAAGT 0.820891 -14 AGCCTAACTTTTAAAAATCAAGCCTTCAAAAAC 7 12 0 TTAAATAAGC 0.988776 -93 AATTTTAACATAAAAGATTAAGCCTAACTTTTA 7 32 0 TAAAATAAGC 0.981112 -73 AAACCTAACGATAAATATAAAATATATAAAATC 7 69 0 ATAAATAAAT 0.971943 -36 AACTTTAAACCTAAAACCTAACGATAA 7 88 0 TTAAATAAAC 0.98222 -17 ***** * **** Masking position 5 Map Score: 14.627 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 420 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 GCTTTTGTTACAATAATTTAGATT 1 3 1 TTGTTACAAT 0.992875 -89 GTAATCTAATTTTGATTAAATTGAAGCGATAA 2 16 0 TTATTAAATT 0.880832 -61 TTAATCAAAATTAGATTACAATATTATAGTTA 2 29 1 TTATTACAAT 0.988845 -48 TATTTAAGCTTTAAATAACTATAATATTGTAA 2 44 0 TTATAACTAT 0.843666 -33 GCGCGCTAGCTTGTGTTACAATAAACTTAAAA 3 23 1 TTGTTACAAT 0.992879 -45 GCTTAATCTTTTATGTTAAAATTCTGAGATTT 7 42 1 TTGTTAAAAT 0.979214 -63 ** ******** Masking position 6 Map Score: 5.77533 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 18 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AATTTAGATTTTTTAGCTAGCATGTTAGCAATT 1 25 1 TTTAGCTAGT 0.932521 -67 TAGCAATTCATTAAGGCATGGATATTGTTAAAA 1 50 1 TAAGGCATGT 0.943736 -42 CTTTTTTATCGCTTCAATTTAATCAAAA 2 6 1 TATCGCTTCT 0.95594 -71 TTATAGTTATTTAAAGCTTAAATAAGGGTCTAG 2 52 1 TAAAGCTTAT 0.883128 -25 ATAAACTTAAAATTCGCTTGATTGAAGAGGGTT 3 43 1 ATTCGCTTGT 0.867203 -25 TTTTCTTTTTTCATGGCTTGTCT 6 1 0 TATGGCTTGT 0.992429 -26 GGTTTTTGAAGGCTTGATTTTTAAAAGTT 7 7 1 TAAGGCTTGT 0.990689 -98 GCTTGATTTTTAAAAGTTAGGCTTAATCTTTTA 7 22 1 TAAAGTTAGT 0.874838 -83 TATTTTATATTTATCGTTAGGTTTTAGGTTTAA 7 78 1 TATCGTTAGT 0.931228 -27 * ******** * Masking position 13 Map Score: 5.54481 Number of sites scoring better than the average of aligned sites = 1238 Number in coding regions = 1108 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 CTTTTTTATCGCTTCAATTTAAT 2 3 1 TTTTATCGCT 0.977335 -74 ATATTATAGTTATTTAAAGCTTAAATAAGGG 2 49 1 TATTAAAGCT 0.883375 -28 AAGGGGTTTTAAGCGCGCTAGCTTGTG 3 7 1 TTTTAGCGCG 0.985177 -61 TTGAGTTGGCTATTAAGGGGGC 4 2 0 TATTAGGGGG 0.96557 -64 AACTCAACGCTATTAAGTGGGGCGAGTTCAG 4 26 1 TATTAGTGGG 0.875909 -40 GACTTTTCTTTTTTCATGGCTTGTCT 6 6 0 TTTTATGGCT 0.977335 -21 GGTTTTTGAAGGCTTGATTTTTAA 7 4 1 TTTTAAGGCT 0.967839 -101 ATATATTTTATATTTATCGTTAGGTTTTAGG 7 75 1 TATTATCGTT 0.869639 -30 **** ****** Masking position 6 Map Score: 6.12618 Number of sites scoring better than the average of aligned sites = 1208 Number in coding regions = 1115 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 GCTTTTGTTACAATAATTTAGATTTTTTAG 1 11 1 CAATAATTTA 0.869862 -81 TCAATTTAATCAAAATTAGATTACAATATT 2 24 1 CAAAATTAGA 0.908016 -53 AATTAGATTACAATATTATAGTTATTTAAA 2 37 1 CAATATTATA 0.960497 -40 TTTTAAAAAATAAAATTATAAC 5 3 0 TAAAATTATA 0.666794 -28 AAGATTAAGCCTAACTTTTAAAAATCAAGC 7 22 0 CTAACTTTTA 0.854308 -83 AAGTTAGGCTTAATCTTTTATGTTAAAATT 7 35 1 TAATCTTTTA 0.83686 -70 TATAAAATCTCAGAATTTTAACATAAAAGA 7 48 0 CAGAATTTTA 0.898206 -57 ********** Masking position 10 Map Score: 2.31531 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 419 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 ********** No masking Map Score: -6.44162e-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 7 ********** No masking Map Score: -6.44162e-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 8 ********** No masking Map Score: -6.44162e-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