AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_tpal_reg_100.orf -o00620_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0037 96 D-specific D-2-hydroxyacid dehydrogenase #2 TP0038 48 regulatory protein (pfoS/R) #3 TP0055 206 T. pallidum predicted coding region TP0055 #4 TP0094 137 phosphate acetyltransferase (pta) #5 TP0476 66 acetate kinase (ack) #6 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #7 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #8 TP0479 111 T. pallidum predicted coding region TP0479 Motif number 1 ATACGTGCAGAACGTGGGTAAGGAATGTTGTTT 1 53 1 AACGTGGAGG 0.942678 -44 TTTGCCTTACCAAGGAGGTGCGAA 1 83 1 CAAGGGGGGA 0.968615 -14 AGGGAAAGTAGACGGGTGTGAGGTATGGAACCT 3 15 1 GACGGTGGGG 0.979754 -192 AATTCAGGCGAACGGGGTCGAGGGTAAAAAAAA 3 163 0 AACGGGTGGG 0.985161 -44 CTGAATTCATCACGTAGGAGTTGCCCGC 3 189 1 CACGTGGGTG 0.979238 -18 GAACAGGAAACACGTCCGCGCGGGCGCATTATT 4 32 0 CACGTCGGGG 0.972549 -106 AAATTACCAAAACGGTGGAGGTGTATT 5 50 1 AACGGGGGTG 0.995127 -17 ACTAGAACGTAGCGGGAGAGAGGAGGATGTTCG 6 35 1 AGCGGAGGGG 0.969019 -26 CGCACCGTTGAAAGAAGGGGCGGTTT 7 57 1 AAAGAGGGGG 0.976224 -16 GCCTTTAGAAAAAGGAGGAGCTC 8 1 0 AAAGGGGGTC 0.915234 -111 TCCTTTTTCTAAAGGCTGCGAGGCAATTATTAG 8 18 1 AAAGGTGGGG 0.98802 -94 CTCCTCTTCGCAAGGAAGGGGGGAGGGC 8 94 1 CAAGGAGGGG 0.9872 -18 ***** ** * ** Masking position 4 Map Score: 18.3627 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 365 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 ACTGGCTGCAGTCCGCGCCATTTTAAGTCT 2 9 1 CAGCGCGCCA 0.982061 -40 CACTGCAAAACCAATTGCGCTGTAGGTTCCAT 3 39 0 CCATGCGCTG 0.978093 -168 GGACGCACGTCAACACGCACTGCAAAACCAAT 3 56 0 CAACGCACTG 0.632744 -151 TGACGTGCGTCCGCGTGTGCCTCTGAGAACGC 3 76 1 CCGTGTGCCT 0.872773 -131 TCTGAGAACGCAGCCTGCTCTGTTGTCGCGTA 3 97 1 CAGTGCTCTG 0.883995 -110 TAAAAATAATGCGCCCGCGCGGACGTGTTTCC 4 28 1 GCGCGCGCGG 0.890975 -110 CTGTTCTTTTCAAACCGTTCTGATCGTTGGGT 4 59 1 CAACGTTCTG 0.801704 -79 AGCATACACGCAAAATGCGCCACTTTC 5 6 0 CAATGCGCCA 0.951124 -61 GCGACCTACACCGGATGTGCCGCAGGCAGACT 7 28 0 CCGTGTGCCG 0.985594 -45 ACATCCGGTGTAGGTCGCACCGTTGAAAGAAG 7 42 1 TAGCGCACCG 0.950971 -31 ATTAGGCGTTTAGCGCGCGCCGTCAAGTTTTT 8 46 1 TAGCGCGCCG 0.603105 -66 *** ******* Masking position 10 Map Score: 11.2841 Number of sites scoring better than the average of aligned sites = 1688 Number in coding regions = 1567 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 CCCAGGTCCTGCGTGAGATACGTGCAGAACGTG 1 36 1 GGTGGATAGT 0.892142 -61 TGCAGAACGTGGGTAAGGAATGTTGTTTGCCTT 1 58 1 GGTAGGAAGT 0.99002 -39 TTAAGTCTCTCCGTAAGGAGCGTCTC 2 33 1 CGTAGGAGGT 0.939562 -16 GAGTAGGGAAAGTAGACGGGTGT 3 1 1 GGTAGGAAGT 0.99002 -206 AAGTAGACGGGTGTGAGGTATGGAACCTACAGC 3 20 1 GGTGGGTAGG 0.963383 -187 GTGTGCCTCTGAGAACGCAGCCTGCTCTGTTGT 3 90 1 GGAAGCAGCT 0.913843 -117 CTCTGTTGTCGCGTAGGAAAACTTGTAAAGAGC 3 114 1 GGTAGAAACT 0.896548 -93 ATGAATTCAGGCGAACGGGGTCGAGGGTAAAAA 3 166 0 GGAAGGGGCG 0.852789 -41 CGCATTTTGCGTGTATGCTACGGTGTCCGAGAA 5 19 1 GGTAGCTAGG 0.895429 -48 AACGTAGCGGGAGAGAGGAGGATGTTCGCCC 6 40 1 GGAGGGAGAT 0.891266 -21 TGCCTTAGGGAGCGGAGAGTCTGCCTGCGG 7 8 1 GGAGGGAGGT 0.98656 -65 * *** **** ** Masking position 7 Map Score: 8.87455 Number of sites scoring better than the average of aligned sites = 793 Number in coding regions = 691 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 TCACGCAGGACCTGGGCGGAAACACATAAC 1 22 0 CCTGGGCGGA 0.912342 -75 CTTAAAATGGCGCGGACTGCAGCCAGT 2 8 0 CGCGGACTGC 0.991714 -41 CAGAGGCACACGCGGACGCACGTCAACACG 3 71 0 CGCGGACGCA 0.989226 -136 CCTCTGAGAACGCAGCCTGCTCTGTTGTCG 3 95 1 CGCAGCCTGC 0.950546 -112 AACACGTCCGCGCGGGCGCATTATTTTTAC 4 27 0 CGCGGGCGCA 0.991327 -111 TTGGTAATTTCTCGGACACCGTAGCATACA 5 30 0 CTCGGACACC 0.933991 -37 CCGGATGTGCCGCAGGCAGACTCTCCGCTC 7 20 0 CGCAGGCAGA 0.977112 -53 ********** Masking position 5 Map Score: 6.44545 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 284 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 GGTAAGGAATGTTGTTTGCCTTACCAAGGA 1 69 1 GTTGTTTGCC 0.899047 -28 TCATCACGTAGGAGTTGCCCGC 3 195 1 GGAGTTGCCC 0.979336 -12 GTAGCCATAAGGAGAATGTCT 4 127 1 GGAGAATGTC 0.920599 -11 GAGAGAGGAGGATGTTCGCCC 6 50 1 GATGTTCGCC 0.82484 -11 CGGCACATCCGGTGTAGGTCGCACCGTTGA 7 38 1 GGTGTAGGTC 0.982181 -35 TTTAGAAAAAGGAGGAGCTC 8 1 0 GGAGGAGCTC 0.919768 -111 CTTGCGAAGAGGAGTATGCCAAACGGTGAG 8 78 0 GGAGTATGCC 0.985949 -34 ********** Masking position 4 Map Score: 2.23417 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 210 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 GAGACGCTCCTTACGGAGAGACTTAAAATG 2 29 0 TTACGGAGAG 0.960791 -20 GCAATTGGTTTTGCAGTGCGTGTTGACGTG 3 53 1 TTGCAGTGCG 0.909038 -154 GTAGGAAAACTTGTAAAGAGCTTGCACAAA 3 126 1 TTGTAAAGAG 0.872719 -81 TGTAAAGAGCTTGCACAAAGCGTCTTTTTT 3 137 1 TTGCACAAAG 0.872992 -70 TCAATCAAGTTTGCAGACAGGAACACCCAA 4 85 0 TTGCAGACAG 0.972877 -53 TGCCTTAGGGAGCGGAGAGTCTGCCTGCG 7 10 1 GAGCGGAGAG 0.923478 -63 CCCCCCTTCCTTGCGAAGAGGAGTATGCCA 8 87 0 TTGCGAAGAG 0.984576 -25 ********** Masking position 10 Map Score: 1.77631 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 224 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: 1.41641e-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 8 ********** No masking Map Score: 1.41641e-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: 1.41641e-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