AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iphoB_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #2 TP0164 147 ABC transporter, ATP-binding protein (troB) #3 TP0802 45 T. pallidum predicted coding region TP0802 #4 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) Motif number 1 CTCTTCTTCTTGGGGGAAGAGAGGGCAGAAAAGATGC 1 16 1 TGGAGGGGCA 0.996738 -103 CTGGATATGAGCGGAAACAGAATGACGTGTTCTATCT 1 52 1 GGAAAAGACG 0.816262 -67 TTACGTTGGGTAGCGTAAGAGGGGGAGTGC 1 99 1 TGGAGGGGAG 0.995984 -20 AGAGTTGAGTGGGTAGAAGAGCCGTTGGTGGTCGGCT 2 21 1 GGAAGGGTTG 0.9582 -127 TCACCACGTCGTGAACAGGCGCTGCCGTACAGCCGAC 2 51 0 GGAAGGGCCG 0.989302 -97 ACGTGGTGATTAGTGAAGGAGGTGGCGCGCTCACCGC 2 79 1 TGGAGGGGCG 0.998521 -69 TTTCGCTCAATCGGGTAAGAGCCGTCAGCGGTGAGCG 2 106 0 TGGAGGGTCA 0.99239 -42 TTACCCGATTGAGCGAAAAGAAGGGAGCAGTAT 2 125 1 GGGAAAGGAG 0.975008 -23 CATCCCCCACGAGGGTATGGAGAGGAA 3 1 0 GGGAGAGGAA 0.987654 -45 GAAGCGTACACAGGGGGGCATCCCCCACGA 3 26 0 GGAAAGGGCA 0.979619 -20 TTACGCAAACGGGAGGTGGTGTTGTCATG 4 3 0 GGGTGGGTCA 0.970903 -75 CACCTCCCGTTTGCGTAAGGAAAGTAGTGTGTTGCGC 4 22 1 TGGAGAGTAG 0.971541 -56 * * * * * * **** Masking position 14 Map Score: 22.8314 Number of sites scoring better than the average of aligned sites = 1044 Number in coding regions = 945 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 AAAGTCTCTTCTTCTTGGGGGAAG 1 4 1 GTCTCTTCTC 0.993463 -115 CTTTTCTGCCCTCTCTTCCCCCAAGAAGAAG 1 18 0 CTCTCTTCCC 0.995833 -101 ATTCTGTTTCCGCTCATATCCAGCATCTTTT 1 44 0 CGCTCATATC 0.981699 -75 GCACTCCCCCTCTTACGCTACCCAACGT 1 101 0 CCCTCTTACC 0.99223 -18 GACCACCAACGGCTCTTCTACCCACTCAACT 2 23 0 GGCTCTTCTC 0.997083 -125 CACCGCTGACGGCTCTTACCCGATTGAGCGA 2 110 1 GGCTCTTACC 0.996856 -38 ********* * Masking position 7 Map Score: 11.1734 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 ACCCAACGTAACGCGCTCCACAGATAGAACACG 1 77 0 ACGCCTCACG 0.8793 -42 ACGTTGGGTAGCGTAAGAGGGGGAGTGC 1 101 1 GCGTAGAGGG 0.860981 -18 AATCACCACGTCGTGAACAGGCGCTGCCGTACA 2 57 0 TCGTAACGGG 0.989905 -91 AGGAGGTGGCGCGCTCACCGCTGACGGCTCTTA 2 95 1 GCGCCACGCG 0.997029 -53 TCCCTTCTTTTCGCTCAATCGGGTAAGAGCCGT 2 118 0 TCGCCAACGG 0.986988 -30 CAGGGGGGCATCCCCCACGAGGGTATGGAGAGG 3 13 0 TCCCCACAGG 0.973098 -33 GAAGCGTACACAGGGGGGCATCCCCC 3 30 0 GCGTCACGGG 0.997238 -16 TACTTTCCTTACGCAAACGGGAGGTGGTGTTGT 4 15 0 ACGCAACGGG 0.993802 -63 AAGTAGTGTGTTGCGCACCCGTGTTTCAAAAGG 4 43 1 TTGCCACCGG 0.974203 -35 **** *** ** * Masking position 13 Map Score: 10.317 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1176 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 ACACGTCATTCTGTTTCCGCTCATATCCAG 1 52 0 CTGTTTCCGC 0.904246 -67 GTGTTCTATCTGTGGAGCGCGTTACGTTGG 1 78 1 TGTGGAGCGC 0.980482 -41 CGCGTTACGTTGGGTAGCGTAAGAGGGGGA 1 95 1 TGGGTAGCGT 0.969374 -24 TAGCGTAAGAGGGGGAGTGC 1 109 1 GGGGGAGTGC 0.935 -10 GAGCCGTCAGCGGTGAGCGCGCCACCTCCT 2 95 0 CGGTGAGCGC 0.99651 -53 GGATGCCCCCCTGTGTACGCTTC 3 33 1 CTGTGTACGC 0.910061 -13 ACACCACCTCCCGTTTGCGTAAGGAAAGTA 4 18 1 CCGTTTGCGT 0.904323 -60 AGGAAAGTAGTGTGTTGCGCACCCGTGTTT 4 39 1 TGTGTTGCGC 0.969392 -39 ********** Masking position 9 Map Score: 5.21227 Number of sites scoring better than the average of aligned sites = 2339 Number in coding regions = 2151 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 CCCTCTCTTCCCCCAAGAAGAAGAGACTTT 1 11 0 CCCCAAGAAG 0.989773 -108 TCTTACGCTACCCAACGTAACGCGCTCCAC 1 89 0 CCCAACGTAA 0.962527 -30 CTTCACTAATCACCACGTCGTGAACAGGCG 2 67 0 CACCACGTCG 0.988393 -81 GGGGGGCATCCCCCACGAGGGTATGGAGAG 3 14 0 CCCCACGAGG 0.988371 -32 ********** Masking position 5 Map Score: 1.89682 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 86 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** No masking Map Score: 1.65857e-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: 1.65857e-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: 1.65857e-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