AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ifis_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 TP0406 190 glutamate racemase (murI) #2 TP0407 127 phosphoglycolate phosphatase (gph-1) #3 TP0408 78 T. pallidum predicted coding region TP0408 #4 TP0409 39 T. pallidum predicted coding region TP0409 #5 TP0410 264 protein-export membrane protein (secD) #6 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) #7 TP1009 96 glycerol-3-phosphate dehydrogenase (gpsA) #8 TP1010 125 nucleoside-diphosphate kinase (ndk) #9 TP1011 34 peptidyl-tRNA hydrolase (pth) #10 TP1012 204 RNA polymerase sigma-43 factor (sigA) Motif number 1 CATGTTCGAACCCACACCGTATTGCTCTAC 1 57 0 CCCACACCGT 0.916333 -134 TTCGAACATGCGCGCAAAGCTTATACGGGC 1 77 1 CGCGCAAAGC 0.965303 -114 TGACACCACACCCGTCCAGCCCGTATAAGC 1 95 0 CCCGTCCAGC 0.912962 -96 CCCCAGGTCCTGCACACCGCATACATTGAC 1 121 0 TGCACACCGC 0.914587 -70 ATATCGGGTGCGTGCACTGTGTGTGTTTGT 2 23 1 CGTGCACTGT 0.859446 -105 CGCACGCAGCACCGCGCTGTCTATCAGCCT 2 73 0 ACCGCGCTGT 0.805265 -55 GCCCATTGTACGCACGCAGCACCGCGCTGT 2 83 0 CGCACGCAGC 0.969905 -45 CCGAACCCCACACGTCCAGCGTGGCGCCCG 3 15 1 CACGTCCAGC 0.868647 -64 CCTTCGTCTTCACGCGACGCACAGCGGGTA 3 49 0 CACGCGACGC 0.967049 -30 CCAACGCGCGCGTGCGCTGCATTAATC 4 8 0 CGTGCGCTGC 0.962948 -32 CACCACGCTTACCACCCCGTGGATACCGCC 5 81 0 ACCACCCCGT 0.78845 -184 GCTGTGCTCCCGCACCACGCTTACCACCCC 5 93 0 CGCACCACGC 0.976762 -172 TGACTTCGAGCGTGCCATGCTCATTCACCT 5 133 0 CGTGCCATGC 0.897824 -132 TATGCGCGCAATCGCACTGCGGCTGACTTC 5 156 0 ATCGCACTGC 0.717459 -109 CGAAAAAGAACACGCACCGCAGACCCTAAA 7 15 0 CACGCACCGC 0.991614 -82 GGTACGCTGGCGCGCCACGTGTATTAGCTA 8 91 1 CGCGCCACGT 0.98164 -35 CGCGTCCTGCTCCTATTTCA 9 25 0 CGCGTCCTGC 0.976197 -10 CGTATGCCTACACGCACCGCGCGGGGCGCA 10 51 1 CACGCACCGC 0.991614 -154 ATGTATAGAATGCGCCCCGCGCGGTGCGTG 10 61 0 TGCGCCCCGC 0.989173 -144 AGAGAACTGTAGCGCGCCGTGGGAAAGGGA 10 108 1 AGCGCGCCGT 0.967127 -97 ********** Masking position 9 Map Score: 33.6039 Number of sites scoring better than the average of aligned sites = 3439 Number in coding regions = 3154 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 2 AGCTCATGCATACGTCAACACACATACACGGC 1 9 0 TCGACACACA 0.890642 -182 TGCGCGCATGTTCGAACCCACACCGTATTGCTCT 1 59 0 TCGCCACACC 0.978866 -132 CACCGCATACATTGACACCACACCCGTCCAGCCC 1 103 0 ATGCCACACC 0.880771 -88 GGCACTGGATATCGGGTGCGTGCACTGTGTGTGT 2 15 1 ACGGCGTGCA 0.786472 -113 TCTCTTATCTACCGCCTCCACACAAACACACACA 2 40 0 ACGCCACACA 0.94921 -88 CCCATGGCCCATTGTACGCACGCAGCACCGCGCT 2 85 0 ATGGCACGCA 0.935528 -43 CGCGACGCACAGCGGGTACCCGCGGGCGCCACGC 3 33 0 ACGACCCGCG 0.899079 -46 TCCACTCACCTTCGTCTTCACGCGACGCACAGCG 3 53 0 TCGTCACGCG 0.942134 -26 GATTAATGCAGCGCACGCGCGCGTTGGTAAAGA 4 10 1 ACGGCGCGCG 0.98997 -30 ATGACAAGGCTGTGCTCCCGCACCACGCTTACCA 5 97 0 TTGCCGCACC 0.924551 -168 TCAGCCGCAGTGCGATTGCGCGCATAAACGACAG 5 160 1 TCGGCGCGCA 0.954644 -105 CAGATTGCGATTCGAAGCCCGGCGTGCCCCTGAC 5 217 1 TCGCCCGGCG 0.804641 -48 CTGGCGATCTCCTTGTCCACACCTGTCAGGGGC 5 242 0 TCTCCACACC 0.860832 -23 CACGGGGGTGTTTTCTTCCGCGCGTCTCTGTGGG 6 11 1 TTTCCGCGCG 0.858408 -116 ATATCTCTCCGTCCGAACGCGGATTATGGGC 6 106 0 TCGGAACGCG 0.871864 -21 GAATGGTGGGTACGCTGGCGCGCCACGTGTATTA 8 83 1 TCGGCGCGCC 0.99307 -43 GTTTGCGCCGTATGCCTACACGCACCGCGCGGGG 10 43 1 TTGACACGCA 0.862937 -162 GAATCAAGAGAACTGTAGCGCGCCGTGGGAAAGG 10 102 1 ACTGCGCGCC 0.940761 -103 * ** ******* Masking position 13 Map Score: 23.7965 Number of sites scoring better than the average of aligned sites = 1891 Number in coding regions = 1760 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 TATACGGGCTGGACGGGTGTGGTGTCAATGT 1 98 1 GGACGGTGTG 0.836433 -93 GCGGTGTGCAGGACCTGGGGATAACACGGTT 1 131 1 GGACCGGGGA 0.98497 -60 ACACGGCACTGGATATCGGGTGCGT 2 5 1 GGCACGGATA 0.76369 -123 GCGTACAATGGGCCATGGGGAAGCCGAGGTT 2 100 1 GGCCAGGGGA 0.95075 -28 GCGCCACGCTGGACGTGTGGGGTTCGGCAGA 3 11 0 GGACGGTGGG 0.940668 -68 CCAGCGTGGCGCCCGCGGGTACCCGCTGTGC 3 30 1 GCCCGGGGTA 0.744593 -49 TCTGCGGGAACAGAAAAGGACGCAGGC 5 7 1 GGAACGAAAA 0.684863 -258 TGACAGGTGTGGACAAGGAGATCGCCAG 5 247 1 GGACAGGAGA 0.979025 -18 TCTCTGTGGGGGAAGCGTAAAGAACGAGTCT 6 35 1 GGAAGGTAAA 0.928675 -92 GTCTAGGAGTGGAAGTGAGAACTCTTACCCA 6 62 1 GGAAGGAGAA 0.860683 -65 ATCCGCGTTCGGACGGAGAGATAT 6 113 1 GGACGAGAGA 0.830384 -14 CCTTTCTTCAGCAAGAGGAAACATGATCACC 7 49 0 GCAAGGGAAA 0.881276 -48 AGAAAGGTGAGGATCAGGGGAGGGGTTAGGA 7 73 1 GGATCGGGGA 0.851325 -24 GGACAGGGTGACTCACCATAC 8 1 1 GGACAGGTGA 0.855712 -125 ATACGGTGAAGGAAGGGTAAAAAGAGAAAGT 8 28 1 GGAAGGTAAA 0.928675 -98 GTATTAGCTAGGACGAGGAAATCAT 8 111 1 GGACGGGAAA 0.983786 -15 GGCATACGGCGCAAACGTGAAGATATGACTC 10 28 0 GCAAAGTGAA 0.583209 -177 TTCTTCAAAAGGAAATGTATAGAATGCGCCC 10 74 0 GGAAAGTATA 0.763629 -131 GCGCGCCGTGGGAAAGGGAGGTATGCACAGA 10 119 1 GGAAAGGAGG 0.902422 -86 ***** ***** Masking position 1 Map Score: 20.168 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 785 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 CGGTGTGCAGGACCTGGGGATAACACGGTT 1 132 1 GACCTGGGGA 0.935187 -59 CAAAGAACAGGCTAGGATGATGTCT 1 176 1 GCTAGGATGA 0.902698 -15 CGTACAATGGGCCATGGGGAAGCCGAGGTT 2 101 1 GCCATGGGGA 0.967366 -27 CGATAGTAACGACAGGATCACCCTTTTTTA 5 52 0 GACAGGATCA 0.878627 -213 GTCCACACCTGTCAGGGGCACGCCGGGCTT 5 231 0 GTCAGGGGCA 0.933041 -34 GACAGGTGTGGACAAGGAGATCGCCAG 5 248 1 GACAAGGAGA 0.887971 -17 GTTCTTTTTCGATACGGTGATCATGTTTCC 7 34 1 GATACGGTGA 0.885926 -63 GAAAGGTGAGGATCAGGGGAGGGGTTAGGA 7 74 1 GATCAGGGGA 0.862855 -23 GGACAGGGTGACTCACCATAC 8 2 1 GACAGGGTGA 0.98477 -124 ACGTGTATTAGCTAGGACGAGGAAATCAT 8 107 1 GCTAGGACGA 0.806921 -19 GATATGACTCGTTATGAGGAGGAACGC 10 8 0 GTTATGAGGA 0.726125 -197 CCAGTGGCGTGATAGGGACACCGAACAGAT 10 154 1 GATAGGGACA 0.882568 -51 ********** Masking position 10 Map Score: 7.3163 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 318 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 GGTGTGGGTTCGAACATGCGCGCAAAGCTTA 1 69 1 CGAACTGCGC 0.961615 -122 GGCACTGGATATCGGGTGCGTGCACTGTGTG 2 15 1 ATCGGTGCGT 0.742884 -113 ATTGTACGCACGCAGCACCGCGCTGTCTATC 2 78 0 CGCAGACCGC 0.770788 -50 ATGGGGAAGCCGAGGTTTCGTGCA 2 114 1 CGAGGTTCGT 0.869394 -14 ACAGCGGGTACCCGCGGGCGCCACGCTGGAC 3 28 0 CCCGCGGCGC 0.947225 -51 GCTCCACTCACCTTCGTCTTCACGCGA 3 62 0 CTCACTTCGT 0.747116 -17 TTTACCAACGCGCGCGTGCGCTGCATTAATC 4 11 0 CGCGCTGCGC 0.997557 -29 GTTCTTAATAAGAGCCTGCGTCCTTTTCTGT 5 20 0 AGAGCTGCGT 0.89121 -245 GTCGTTTATGCGCGCAATCGCACTGCGGCTG 5 161 0 CGCGCATCGC 0.98119 -104 ATACACGTGGCGCGCCAGCGTACCCACCATT 8 84 0 CGCGCAGCGT 0.989817 -42 GTCATATCTTCACGTTTGCGCCGTATGCCTA 10 30 1 CACGTTGCGC 0.835835 -175 ***** ***** Masking position 9 Map Score: 7.44609 Number of sites scoring better than the average of aligned sites = 2287 Number in coding regions = 2144 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 AAAAATTTCACAGGAACCGTGTTATCCCCAG 1 145 0 CAGGAACGTG 0.937874 -46 GCATAAACGACAGGAGAGGTGTTTCGAATCC 5 181 1 CAGGAGAGTG 0.993351 -84 ACGAGTCTAGGAGTGGAAGTGAGAACTCTTA 6 58 1 GAGTGGAGTG 0.90433 -69 TCTTCAGCAAGAGGAAACATGATCACCGTAT 7 45 0 GAGGAAAATG 0.900392 -52 TCCTCTTGCTGAAGAAAGGTGAGGATCAGGG 7 61 1 GAAGAAAGTG 0.930387 -36 AGGTGAGGATCAGGGGAGGGGTTAGGAATC 7 77 1 CAGGGGAGGG 0.957416 -20 TTTGAAGAATCAAGAGAACTGTAGCGCGCCG 10 96 1 CAAGAGACTG 0.935138 -109 CGATAAACCAGAGGAGATCTGTTCGGTGTCC 10 169 0 GAGGAGACTG 0.984391 -36 ******* *** Masking position 2 Map Score: 4.12022 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 187 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GCTAAGCTCATGCATACGTCAACACACATA 1 17 0 TGCATACGTC 0.987962 -174 CCCCAGGTCCTGCACACCGCATACATTGAC 1 121 0 TGCACACCGC 0.985476 -70 TACCACCCCGTGGATACCGCCGATAGTAAC 5 72 0 TGGATACCGC 0.977028 -193 CTGCTCCTATTTCATACGCCTCTGATGT 9 9 0 TTCATACGCC 0.914429 -26 GGTGCGTGTAGGCATACGGCGCAAACGTGA 10 39 0 GGCATACGGC 0.984104 -166 GGACCCTCTGTGCATACCTCCCTTTCCCAC 10 126 0 TGCATACCTC 0.987995 -79 ********** Masking position 6 Map Score: 5.73081 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 68 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 CAATACGGTGTGGGTTCGAACATGCGCGCA 1 63 1 TGGGTTCGAA 0.974516 -128 CTGGACGTGTGGGGTTCGGCAGA 3 4 0 GGGGTTCGGC 0.98868 -75 AATCTGTCTTAGGATTCGAAACACCTCTCC 5 193 0 AGGATTCGAA 0.879927 -72 GGGGCACGCCGGGCTTCGAATCGCAATCTG 5 217 0 GGGCTTCGAA 0.977351 -48 GCCCATAATCCGCGTTCGGACGGAGAGATA 6 106 1 CGCGTTCGGA 0.953345 -21 GATCAGGGGAGGGGTTAGGAATC 7 84 1 GGGGTTAGGA 0.973657 -13 ********** Masking position 5 Map Score: 2.1101 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 37 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ********** No masking Map Score: 1.50878e-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 10 GAAATTTTTCAAAGAACAGGCTAGGATGAT 1 167 1 AAAGAACAGG 0.978036 -24 GCGCGTTGGTAAAGAAGAGAT 4 29 1 AAAGAAGAGA 0.819215 -11 TCTGCGGGAACAGAAAAGGACGCAGGCTC 5 10 1 ACAGAAAAGG 0.897052 -255 GGGGAAGCGTAAAGAACGAGTCTAGGAGTG 6 43 1 AAAGAACGAG 0.950139 -84 CCGTATCGAAAAAGAACACGCACCGCAGAC 7 21 0 AAAGAACACG 0.943218 -76 GGAAGGGTAAAAAGAGAAAGTGTGGGGAGG 8 38 1 AAAGAGAAAG 0.84713 -88 GGACTTGCATAAAGAAAGAATGGTGGGTAC 8 66 1 AAAGAAAGAA 0.767763 -60 ********** Masking position 5 Map Score: 0.120508 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 141 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ********** No masking Map Score: 1.50878e-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 12 ********** No masking Map Score: 1.50878e-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 13 ********** No masking Map Score: 1.50878e-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