AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -imetJ_tpal_opreg_300.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 TP0278 127 T. pallidum predicted coding region TP0278 #2 TP0279 45 ribosomal protein S1 (rpsA) #3 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #4 TP0284 104 T. pallidum predicted coding region TP0284 Motif number 1 GCGCTCGTCTTCCTCGGAAGACTGTG 1 2 1 CGCGTTTCCG 0.960775 -126 TGATCACCAGCGCACTCCCTTCCCCACATGGACTG 1 49 0 CGCTCCTCCC 0.992663 -79 GTTCTGAGACTGTTTGCGCTCCTCGTCTGTTGTCT 1 83 0 TGTGCCTCCG 0.990835 -45 CACCGCACGGCGCGAACGCTTCTCCTC 3 3 0 CGCACCTCCC 0.996288 -175 AGCTACACAACGTGCGCACCGCACGGCGCGAACGC 3 19 0 CGTGCCCCCG 0.714036 -159 TCGGTGTTCACGCGAGCTCTCTACGCTTCCTAGCT 3 50 0 CGCGCCTTCG 0.800844 -128 GCACCCACTCCGTCAACTCCTCGCGGAAAATCGGT 3 80 0 CGTACCCCCG 0.963464 -98 GCACGGCAACCCCTCACGTTGTTCAGGA 3 160 0 CGGACCCCCG 0.979085 -18 *** ** ** * ** Masking position 2 Map Score: 14.7382 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 386 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 CACAGTCTTCCGAGGAAGACGAGCGC 1 4 0 CGAGAAGCAG 0.91954 -124 AAGCGGCAGTCCATGTGGGGAAGGGAGTGCGCT 1 43 1 CCAGTGGGAG 0.978682 -85 ATCAGACAACAGACGAGGAGCGCAAACAGTCTC 1 80 1 AGAGAGGGGC 0.975729 -48 GGGTGAAAAACGAAGAAGGGAAGTACAGGGCAG 2 21 0 CGAGAAGGAG 0.988797 -25 GAGGAGAAGCGTTCGCGCCGTGCG 3 2 1 AGGGAAGGTC 0.94511 -176 AGCGTTCGCGCCGTGCGGTGCGCACGTTGTGTA 3 18 1 CCGGCGGGGC 0.984042 -160 CGTTGTGTAGCTAGGAAGCGTAGAGAGCTCGCG 3 42 1 CTAGAAGGAG 0.942822 -136 CACCGATTTTCCGCGAGGAGTTGACGGAGTGGG 3 79 1 CCGGAGGGTG 0.99422 -99 TTGTTCAGGAACATGCGGCGAACTACACAAAAA 3 137 0 ACAGCGGGAC 0.973098 -41 TTCCTGAACAACGTGAGGGGTTGCCGTGC 3 159 1 ACGGAGGGTG 0.986637 -19 *** **** * ** Masking position 8 Map Score: 11.5764 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 632 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 CGCTTATTTGCCACAGTCTTCCGAGGAAGACGAG 1 14 0 CCTCTTCCGA 0.987693 -114 TTGCGCTCCTCGTCTGTTGTCTGATCACCAGCGC 1 71 0 CCTTGTCTGA 0.983188 -57 ATCATCCGCCCATGAGTGTTCTGAGACTGTTTGC 1 101 0 CGTGTTCTGA 0.9646 -27 CTTCCGTTTTCTGCCCTGTACTTC 2 1 1 CCTTTTCTGC 0.996906 -45 TACTTCCCTTCTTCGTTTTTCACCCCT 2 29 1 CCTTTTCACC 0.906721 -17 CTCGCGTGAACACCGATTTTCCGCGAGGAGTTGA 3 69 1 CCTTTTCCGC 0.99455 -109 GTGTAGTTCGCCGCATGTTCCTGAACAACGTGAG 3 142 1 CCGTTCCTGA 0.966199 -36 GAACCTTGCTCAAAACTTTTCTGAACTTTAAAAG 4 75 0 CATTTTCTGA 0.970119 -30 AAGTTTTGAGCAAGGTTCTCCTGC 4 91 1 CGTCTCCTGC 0.969284 -14 * * ******** Masking position 11 Map Score: 9.17831 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 191 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 CAAATAAGCGGCAGTCCATGTGGGGAAGGG 1 38 1 GCAGTCCATG 0.97613 -90 TCCATCATCCGCCCATGAGTGTTCTGA 1 111 0 TCCGCCCATG 0.991449 -17 CACAACGTGCGCACCGCACGGCGCGAACGC 3 19 0 GCACCGCACG 0.985074 -159 TTTGTGTAGTTCGCCGCATGTTCCTGAACA 3 139 1 TCGCCGCATG 0.987594 -39 CATCACATACTCAGCTCATGCAAT 4 5 0 TCAGCTCATG 0.98639 -100 ********** Masking position 8 Map Score: 3.16774 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 202 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 CTGTGGCAAATAAGCGGCAGTCCATGTGGG 1 32 1 TAAGCGGCAG 0.971851 -96 TACAGGGCAGAAAACGGAAG 2 1 0 AAAACGGAAG 0.979724 -45 AGAAGGGAAGTACAGGGCAGAAAACGGAAG 2 11 0 TACAGGGCAG 0.965545 -35 AGGGGTGAAAAACGAAGAAGGGAAGTA 2 29 0 AAAAACGAAG 0.942286 -17 ACTACACAAAAAACAGGCAGCACTATTTAT 3 119 0 AAACAGGCAG 0.976551 -59 TCTGAACTTTAAAAGCACAGCCCCGAAGAT 4 60 0 AAAAGCACAG 0.920398 -45 ********** Masking position 2 Map Score: 1.36008 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 274 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ********** No masking Map Score: -2.24942e-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: -2.24942e-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: -2.24942e-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