AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_tpal_reg_300.orf -o00380_tpal_300.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 TP0629 170 T. pallidum predicted coding region TP0629 #2 TP0630 169 chemotaxis protein methyltransferase (cheR) #3 TP0631 46 protein-glutamate methylesterase (cheB) #4 TP0632 104 tryptophanyl-tRNA synthetase (trsA) Motif number 1 CTGGTTATTTTGCGCGCTCCACAGCAGCACG 1 22 1 TCGCGCTCCA 0.965204 -149 GCGCGCCTGCACCGTGCTGCTGTGGAGCGCG 1 34 0 ACGTGCTGCT 0.922768 -137 CTCACTCTCCTTTGCGCGCCTGCACCGTGCT 1 47 0 TTGCGCGCCT 0.945765 -124 TTGACAGAAGTACCCGCTCCCTTCTAGAGTG 1 94 1 TCCCGCTCCC 0.993687 -77 TAGAGTGGCAGCGGCGCTCCTCGTTTGTGGT 1 118 1 GGGCGCTCCT 0.959562 -53 TCCTCGTTCTGACCTCCTGCGTGTACAAGAC 1 147 0 GCCTCCTGCG 0.868261 -24 GCTTGCAGAGATCATGCGCCGTC 2 3 0 ACATGCGCCG 0.950718 -167 CTCTGCAAGCGTCACGCTCCTGACACACCGT 2 24 1 GCACGCTCCT 0.991184 -146 CCCTTGAAGGTGCACGCGCCGCACGGTGTGT 2 46 0 TCACGCGCCG 0.987218 -124 GCGCCGACACGGTCTGCTCCCTTGAAGGTGC 2 64 0 GTCTGCTCCC 0.957754 -106 TGCCTGGCACCTCGCGCGCCGACACGGTCTG 2 79 0 CCGCGCGCCG 0.992418 -91 CGAGGTGCCAGGCACGCTTCCGTAAGACACA 2 96 1 GCACGCTTCC 0.942369 -74 TATACGCTCTGGTGTGCAGCC 3 1 0 GTGTGCAGCC 0.844152 -46 GGTAGTCTGTGGCCCCCTGCCTGTATACGCT 3 24 0 GCCCCCTGCC 0.939293 -23 GACGGACACGCACCCGTGATATAGA 4 5 1 GCACGCACCC 0.988804 -100 ACGTGCGCCGACCGCGCAGCCCTCCTCTATA 4 30 0 ACGCGCAGCC 0.959082 -75 GGCGCAGGAACACGTGCGCCGACCGCGCAGC 4 41 0 CCGTGCGCCG 0.981276 -64 GGCGCACGTGTTCCTGCGCCTGCACTCTTGA 4 52 1 TCCTGCGCCT 0.968699 -53 * ********* Masking position 7 Map Score: 33.27 Number of sites scoring better than the average of aligned sites = 2625 Number in coding regions = 2397 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 CCTTTGCGCGCCTGCACCGTGCTGCTGTGGA 1 39 0 CCTGCACGTG 0.983974 -132 TAGAAGGGAGCGGGTACTTCTGTCAAGCCAT 1 89 0 CGGGTACTCT 0.647036 -82 CGTTTGTGGTCTTGTACACGCAGGAGGTCAG 1 139 1 CTTGTACCGC 0.883984 -32 CGTCACGCTCCTGACACACCGTGCGGCGCGT 2 33 1 CTGACACCCG 0.962718 -137 CCGTGCGGCGCGTGCACCTTCAAGGGAGCAG 2 51 1 CGTGCACTTC 0.961427 -119 ACCTCGCGCGCCGACACGGTCTGCTCCCTTG 2 71 0 CCGACACGTC 0.974526 -99 GGAAGCGTGCCTGGCACCTCGCGCGCCGACA 2 86 0 CTGGCACTCG 0.940243 -84 ACAGTGAGAACCGACACTGTGTCTTACGGAA 2 113 0 CCGACACGTG 0.978553 -57 TCACTGTCGTTGTACACCCGGTAGCAATTAC 2 137 1 TGTACACCGG 0.80534 -33 CCTGCACACGGGGTAATTGCT 2 159 0 CCTGCACCGG 0.991508 -11 CACACCAGAGCGTATACAGGCAGGGGGCCAC 3 16 1 CGTATACGGC 0.876501 -31 GACGGACACGCACCCGTGATATA 4 3 1 CGGACACCAC 0.933078 -102 TGTTCCTGCGCCTGCACTCTTGAATACTGGA 4 60 1 CCTGCACCTT 0.954015 -45 ******* *** Masking position 6 Map Score: 14.3503 Number of sites scoring better than the average of aligned sites = 2267 Number in coding regions = 2071 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 3 GTCAACAGATGCTGGTTATTTTGCGCGCT 1 10 1 TGCTGGTTAT 0.952891 -161 GTCAAGCCATTGCTCTTTTTTCTCACTCTC 1 69 0 TGCTCTTTTT 0.969334 -102 GCAGCGGCGCTCCTCGTTTGTGGTCTTGTA 1 125 1 TCCTCGTTTG 0.97905 -46 CGCTCCTCGTTCTGACCTCCTGC 1 158 0 TCCTCGTTCT 0.98866 -13 CGCGCAGCCCTCCTCTATATCACGGGTGCG 4 19 0 TCCTCTATAT 0.93331 -86 ********** Masking position 4 Map Score: 1.27552 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 59 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GTACCCGCTCCCTTCTAGAGTGGCAGCGGC 1 103 1 CCTTCTAGAG 0.975302 -68 GCGCATGATCTCTGCAAGCGTCACGCTCCT 2 15 1 TCTGCAAGCG 0.989779 -155 GGCGCGTGCACCTTCAAGGGAGCAGACCGT 2 57 1 CCTTCAAGGG 0.987793 -113 CCTGCACACGGGGTAATTGC 2 160 0 CCTGCACACG 0.948436 -10 GTCCGTCCAGTATTCAAGAGTGCAGGCGCA 4 66 0 TATTCAAGAG 0.91746 -39 ********** Masking position 3 Map Score: 1.2331 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 291 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ********** No masking Map Score: -8.99385e-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 6 ********** No masking Map Score: -8.99385e-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: -8.99385e-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