AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -itrpR_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 TP0708 65 T. pallidum predicted coding region TP0708 #2 TP0823 300 desulfoferrodoxin (rbo) #3 TP0943 48 flagellar protein (fliS) #4 TP0944 170 conserved hypothetical protein Motif number 1 TTTGTTTCGTCAAGGACCTGTTTCCAAGCG 1 24 0 CAAGGACCTG 0.926319 -42 AAACAAAAAACCAGCTGCAGACTAGCTCC 1 47 1 CCAGCTGCAG 0.904713 -19 TAGTTTCCGCTACGCTCCTGCCAGCTTGGA 2 66 0 TACGCTCCTG 0.972642 -235 GAGCCTGTGCTACGCACGAGTATACCTTGA 2 105 0 TACGCACGAG 0.979679 -196 ACTCGCTCCTTCCGAGCCTGTGCTACGCAC 2 118 0 TCCGAGCCTG 0.9465 -183 GGTAAAGCGTCACCCACCTGTACGCATTCA 2 152 0 CACCCACCTG 0.933713 -149 ACGCTTTACCCACGGACCTGATTTAGGTAG 2 172 1 CACGGACCTG 0.974372 -129 TTAGGTAGAATCAGCGCCTCTGCGGGGCTG 2 194 1 TCAGCGCCTC 0.825913 -107 GCGGAAACCGCCCGCGCCAGAGCACAGCCC 2 218 0 CCCGCGCCAG 0.993671 -83 GCGGGCGGTTTCCGCACGCGGAGGCACGAC 2 233 1 TCCGCACGCG 0.926066 -68 ACGACAGGCGTCCGCACGAGAACAAAATCA 2 258 1 TCCGCACGAG 0.98167 -43 ATTGTTTTGCTACGATGGAGGCTGCT 3 33 1 TACGATGGAG 0.527646 -16 CTATGCATAGCAAGAAGCAGTATCCCCGCA 4 68 0 CAAGAAGCAG 0.813943 -103 CTGTCGCGTGCAAGCACCACGCAGCAAAAA 4 105 0 CAAGCACCAC 0.927526 -66 GTGGTGCTTGCACGCGACAGTGGTTGTTCG 4 115 1 CACGCGACAG 0.93397 -56 ********** Masking position 4 Map Score: 19.3527 Number of sites scoring better than the average of aligned sites = 2836 Number in coding regions = 2608 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 GGAGCTAGTCTGCAGCTGGTTTTTTGTTT 1 47 0 CTGCAGCTGG 0.918906 -19 TTTTCTTTTCTTTCCGCAGGGCACGTAGAA 2 24 1 TTTCCGCAGG 0.958924 -277 TCCTGAGGAGTTTCTACGTGCCCTGCGGAA 2 35 0 TTTCTACGTG 0.868177 -266 AGAATCAGCGCCTCTGCGGGGCTGTGCTCT 2 200 1 CCTCTGCGGG 0.991737 -101 GGGCTGTGCTCTGGCGCGGGCGGTTTCCGC 2 218 1 CTGGCGCGGG 0.986868 -83 GCCTGTCGTGCCTCCGCGTGCGGAAACCGC 2 237 0 CCTCCGCGTG 0.989937 -64 AGCGCTTGTTTTTCTGCGGGGATACTGCTT 4 54 1 TTTCTGCGGG 0.99248 -117 GGGTTAGTTTTTGCTGCGTGGTGCTTGCAC 4 98 1 TTGCTGCGTG 0.98857 -73 CGAACAACCACTGTCGCGTGCAAGCACCAC 4 115 0 CTGTCGCGTG 0.967841 -56 ********** Masking position 7 Map Score: 14.928 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 504 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 AAAAGAAAAAAGCAAAAGATAG 2 3 0 AGCAAAAGAT 0.90194 -298 CCCTGCGGAAAGAAAAGAAAAAAGCAAAAG 2 15 0 AGAAAAGAAA 0.772755 -286 ACTCGTGCGTAGCACAGGCTCGGAAGGAGC 2 114 1 AGCACAGGCT 0.927584 -187 CCCGCGCCAGAGCACAGCCCCGCAGAGGCG 2 208 0 AGCACAGCCC 0.960629 -93 CGTCCGCACGAGAACAAAATCAGACCAACA 2 266 1 AGAACAAAAT 0.87721 -35 GAACAAAATCAGACCAACATAGGAGATGCT 2 277 1 AGACCAACAT 0.804112 -24 CCTCCATCGTAGCAAAACAATAGCGCCAAT 3 24 0 AGCAAAACAA 0.954755 -25 GTATCCCCGCAGAAAAACAAGCGCTCTAGT 4 49 0 AGAAAAACAA 0.917319 -122 AGCACCACGCAGCAAAAACTAACCCCTATG 4 93 0 AGCAAAAACT 0.888497 -78 ATAACTTGCACGAACAACCACTGTCGCGTG 4 125 0 CGAACAACCA 0.757045 -46 ATGTTTGTAAAGCAGAGCACTT 4 159 1 AGCAGAGCAC 0.856778 -12 ********** Masking position 6 Map Score: 6.45973 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 467 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 TTCGTCAAGGACCTGTTTCCAAGCGTGTAG 1 19 0 ACCTGTTTCC 0.94458 -47 TGGATTCCTGAGGAGTTTCTACGTGCCCTG 2 40 0 AGGAGTTTCT 0.918926 -261 TGACCATTTGGGTAGTTTCCGCTACGCTCC 2 78 0 GGTAGTTTCC 0.96036 -223 TGTGCTACGCACGAGTATACCTTGACCATT 2 100 0 ACGAGTATAC 0.861486 -201 CTCGGAAGGAGCGAGTTTACTGAATGCGTA 2 132 1 GCGAGTTTAC 0.933391 -169 CTCTGGCGCGGGCGGTTTCCGCACGCGGAG 2 226 1 GGCGGTTTCC 0.975292 -75 AGCAGCCTCCATCGTAGCAA 3 39 0 AGCAGCCTCC 0.926562 -10 CATAGCAAGAAGCAGTATCCCCGCAGAAAA 4 63 0 AGCAGTATCC 0.983051 -108 ********** Masking position 8 Map Score: 5.02153 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 242 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TTTACTGAATGCGTACAGGTGGGTGACGCT 2 147 1 GCGTACAGGT 0.954209 -154 CTGCGGGGCTGTGCTCTGGCGCGGGCGGTT 2 213 1 GTGCTCTGGC 0.986673 -88 GTCGATATTGGCGCTATTGTTTTGCTACGA 3 18 1 GCGCTATTGT 0.849591 -31 GGTGTTCAGGTGTAAGGAGAC 4 2 1 GTGTTCAGGT 0.97614 -169 AGAAAAACAAGCGCTCTAGTACCCTATGAG 4 39 0 GCGCTCTAGT 0.987144 -132 AACCACTGTCGCGTGCAAGCACCACGCAGC 4 110 0 GCGTGCAAGC 0.854694 -61 AAGTGCTCTGCTTTACAAACAT 4 159 0 GTGCTCTGCT 0.95486 -12 ********** Masking position 3 Map Score: 4.39931 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 627 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 CGCGGAGGCACGACAGGCGTCCGCACGAGA 2 249 1 CGACAGGCGT 0.979474 -52 TGTTGTGGTCGATATTGGCGCTATTGTTT 3 10 1 CGATATTGGC 0.954159 -39 TGTTTTGCTACGATGGAGGCTGCT 3 35 1 CGATGGAGGC 0.965217 -14 ACCCTATGAGCGACAGGGTCTCCTTACACC 4 19 0 CGACAGGGTC 0.986402 -152 TGCTTGCACGCGACAGTGGTTGTTCGTGCA 4 119 1 CGACAGTGGT 0.990878 -52 ********** Masking position 3 Map Score: 1.99222 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 87 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ********** No masking Map Score: -1.28365e-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: -1.28365e-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: -1.28365e-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