AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_operons026_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944239860 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0116 150 excinuclease ABC, subunit B (uvrB) #1 TP0344 152 transcription-repair coupling factor (trcF) #2 TP0511 42 transcription factor (carD) #3 TP0512 44 conserved hypothetical protein #4 TP0513 73 K+ transport protein (trkA) #5 TP0514 113 excinuclease ABC, subunit A (uvrA) #6 TP0687 55 DNA recombinase (recG) #7 TP0689 35 GTP-binding protein #8 TP0691 27 conserved hypothetical protein #9 TP0692 260 recA protein (recA) #10 TP0693 159 T. pallidum predicted coding region TP0693 Motif 1 CTTTTCGTTAGGGACGTGCAGGACGACGCCGACAC 10 19 0 AGTCTGTAAAGGAGATGGCCGGAGG 7 20 1 TAGCTCAGTTGGTTAGAGCAGCGGACTCATAATCC 9 135 1 ACGCGGCTGTGGTGTGCGCTGCAGAATAAAGAGGT 10 123 1 GTCCGAAGGCCATAGTAGCACGAAATTTTTTT 4 51 0 CCCTTCCGGCGGGACTTGTAGCACGAAACAACACA 9 96 0 CCGCGTTGCTTGTCACCGCTGCAGGCAGCTCTGCA 3 16 1 TGAGCGAGAAGGATGCAGCAGGAGAGGGCAAGGGA 1 41 0 CTATTTCCACGCGCTGGCGGCCACTGA 8 7 0 GCGGTGACAAGCAACGCGGCGCGGG 3 0 0 CTATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCGC 9 204 1 CGCGTCTCTTGCGCCTTGCGCGGGGTTTTTCATGG 9 225 1 GTATGGGTGGTGTCGGCGTCGTCCTGCAC 10 4 1 GAGGAGAACAGGAAGGAGCACCGGTAGTAGTTG 1 8 0 GGACTCATAATCCGCGGGTCGCCGGTTCAAGTCCA 9 157 1 GTAGAAAGGGAGAACGTGTCGCAGGACGTTCGC 5 90 1 CAAATAGTATGGGCCCAGCTGGACTTGAACCGGCG 9 176 0 GTGGCAGGCGTTGTGCGCCGTGTTCTG 4 2 1 GCAATTCCACTCCCTTCGCGGCAGACCGCA 5 5 0 TGTCTTTGGTGGATATCGTAGGGTGGCTGTAACGA 10 65 1 TGCGCCGTGTTCTGCGCGCTGGCCATGCAAAAAAA 4 23 1 TTCTCGCTCAGGGACTAGCACAAGGCACAGTGCTC 1 66 1 GGTGTTCCCCGGGGTTTGTACAGCGTTTTGAAGAA 9 53 1 ** * ** ***** MAP Score: 27.0382 Motif 2 AACGTGCCTCCTCTTAAGCGGGGTCCACTCT 0 3 1 ACTACTACCGGTGCTCCTTCCTGTTCTCCTCCCTTGCC 1 12 1 TTGCCCTCTCCTGCTGCATCCTTCTCGCTCAGGGACTA 1 45 1 ACAAGGCACAGTGCTCCGTTACACTCGGCCGTGTGTCA 1 85 1 CATTTCTTGAGCGCGTGTTGACACACGGCCGAGTGTAA 1 103 0 GTACAAAAGGGTGCGCCAGTCTACACGTTCTTTGTGTT 2 14 1 CCCGCGCCGCGTTGCTTGTCACCGCTGCA 3 1 1 TTGCTTGTCACCGCTGCAGGCAGCTCTGCACGC 3 21 1 GGCAGGCGTTGTGCGCCGTGTTCTGCGCGCTGGCCATG 4 12 1 AAAAAATTTCGTGCTACTATGGCCTTCGGAC 4 52 1 TGCGGTCTGCCGCGAAGGGAGTGGAATTGCATAA 5 6 1 GCGAACGTCCTGCGACACGTTCTCCCTTTCTACGCGA 5 86 0 TCAGTGGCCGCCAGCGCGTGGAAATAG 8 1 1 GGATGAGAGGGTGTTCCCCGGGGTTTGTACAGCGTTTT 9 44 1 GTGTTGTTTCGTGCTACAAGTCCCGCCGGAAGGGCCTA 9 97 1 GTTAGAGCAGCGGACTCATAATCCGCGGGTCGCCGGTT 9 146 1 TACTATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCGCC 9 202 1 GGTAGCGCGTCTCTTGCGCCTTGCGCGGGGTTTTTCAT 9 220 1 TGGGTGGTGTCGGCGTCGTCCTGCACGTCCCTAACGAA 10 13 1 CGTAGGGTGGCTGTAACGAAGGGCCCGTGACGGTACTT 10 81 1 CACACCACAGCCGCGTGCTAAAGTACCGTCACGGGCCC 10 101 0 CCTCTTTATTCTGCAGCGCACACCACAGCCGCGTGCTA 10 119 0 **** * ** *** MAP Score: 23.9279 Motif 3 ATGCAGCAGGAGAGGGCAAGGGAGGAGAACAGGAAGG 1 27 0 GTTGACACACGGCCGAGTGTAACGGAGCACTGTGCCT 1 88 0 GTACGAGCGTGCATTTCTTGAGCGCGTGTTGACACAC 1 115 0 GCGTGCAGAGCTGCCTGCAGCGGTGACAAGCAACG 3 19 0 GTGGCAGGCGTTGTGCGCCGTGTTCTGCGC 4 3 1 AAATTTTTTTGCATGGCCAGCGCGCAGAACACGGCGC 4 24 0 TGCGGTCTGCCGCGAAGGGAGTGGAAT 5 0 1 GCCCTCTTATGGATGGGGATCGCGTAGAAAGGGAGAA 5 67 1 TGATGTTCTTGCGTTACCATTACGTATGCTCGCACAC 6 20 1 TCAGTGGCCGCCAGCGCGTGGAAATAG 8 2 1 GTGTTCCCCGGGGTTTGTACAGCGTTTTGAAGAATTG 9 54 1 CTGGACTTGAACCGGCGACCCGCGGATTATGAGTCCG 9 156 0 GCAGGTGGTAGCGCGTCTCTTGCGCCTTGCGCGGGGT 9 214 1 GTATGGGTGGTGTCGGCGTCGTCCTGCACGT 10 4 1 GGATATCGTAGGGTGGCTGTAACGAAGGGCCCGTGAC 10 75 1 TTTAGCACGCGGCTGTGGTGTGCGCTGCAGAATAAAG 10 117 1 ** ** * * *** * MAP Score: 23.6801 Motif 4 GTGGCAGGCGTTGTGCGCCGTGTTCTG 4 7 1 TGCGGTCTGCCGCGAAGGGAG 5 1 1 GCACGCGGCTGTGGTGTGCGCTGCAGAATA 10 121 1 CGTCTCTTGCGCCTTGCGCGGGGTTTTTCA 9 227 1 GTTGTGCGCCGTGTTCTGCGCGCTGGCCAT 4 19 1 ACTTGAACCGGCGACCCGCGGATTATGAGT 9 159 0 GCGAACGTCCTGCGACACGTTCTC 5 99 0 GCACACCACAGCCGCGTGCTAAAGTACCGT 10 110 0 TCAGTGGCCGCCAGCGCGTGGAAATA 8 6 1 GGAGCACTGTGCCTTGTGCTAGTCCCTGAG 1 72 0 TTCAGGCAGTGTGCGAGCATACGTA 6 40 0 GGTGGTGTCGGCGTCGTCCTGCACGTCCCT 10 15 1 GACAAGCAACGCGGCGCGGG 3 0 0 GGATGAGAGGGTGTTCCCCGGGGTTTGTAC 9 44 1 CCTCCGGCCATCTCCTTTACAGACTC 7 19 0 ATTTTTTTGCATGGCCAGCGCGCAGAACAC 4 29 0 GTCCTGCGACACGTTCTCCCTTTCTACGCG 5 87 0 GTGCAGAGCTGCCTGCAGCGGTGACAAGCA 3 22 0 ********** MAP Score: 22.3021 Motif 5 AACGTGCCTCCTCTTAAGCGGGGTCCACTC 0 3 1 AGAACAGGAAGGAGCACCGGTAGTAGTTG 1 2 0 AGGAGAGGGCAAGGGAGGAGAACAGGAAGGAGCACCG 1 20 0 GAGCGAGAAGGATGCAGCAGGAGAGGGCAAGGGAGGA 1 38 0 ACTGTGCCTTGTGCTAGTCCCTGAGCGAGAAGGATGC 1 60 0 CATTTCTTGAGCGCGTGTTGACACACGGCCGAGTGTA 1 104 0 AGGCTCCTGGGTACGAGCGTGCATTTC 1 135 0 CAGCGGTGACAAGCAACGCGGCGCGGG 3 0 0 GCGTGCAGAGCTGCCTGCAGCGGTGACAAGCAAC 3 20 0 GTGGCAGGCGTTGTGCGCCGTGTTCTG 4 0 1 TTTTTTGCATGGCCAGCGCGCAGAACACGGCGCACAA 4 20 0 TCTTATGGATGGGGATCGCGTAGAAAGGGAGAACGTG 5 71 1 GCGTAGAAAGGGAGAACGTGTCGCAGGACGTTCGC 5 88 1 TGAGTCTGTAAAGGAGATGGCCGGAGG 7 18 1 TGTTTATTTCGTAGATCGGGGTATGGGGATAGGATGA 9 13 1 GATAGGATGAGAGGGTGTTCCCCGGGGTTTGTACAGC 9 40 1 GGCCCTTCCGGCGGGACTTGTAGCACGAAACAACACA 9 96 0 CACAAATAGTATGGGCCCAGCTGGACTTGAACCGGCG 9 176 0 CGCAAGAGACGCGCTACCACCTGCACACAAATAGTAT 9 201 0 GAAAAACCCCGCGCAAGGCGCAAGAGACGCGCTACCA 9 219 0 TTTTCGTTAGGGACGTGCAGGACGACGCCGACACCAC 10 16 0 TGGCTGTAACGAAGGGCCCGTGACGGTACTTTAGCAC 10 88 1 GACGGTACTTTAGCACGCGGCTGTGGTGTGCGCTGCA 10 109 1 * ** ** * * *** MAP Score: 8.64133 Motif 6 GAGTGGACCCCGCTTAAGAGGAGGCACGTT 0 3 0 CAAAGGGAAAGGCACAGCATGTACTACAGATTTTTTA 0 90 1 AACAGGAAGGAGCACCGGTAGTAGTTG 1 0 0 CTGTTCTCCTCCCTTGCCCTCTCCTGCTGCATCCTTC 1 32 1 GCATCCTTCTCGCTCAGGGACTAGCACAAGGCACAGT 1 60 1 ACACAAAGAACGTGTAGACTGGCGCACCCTTTTGTAC 2 14 0 CCCGCGCCGCGTTGCTTGTCACCGCTGCAGGCAG 3 7 1 GCGTGCAGAGCTGCCTGCAGCGGTGACAAG 3 24 0 CAGAACACGGCGCACAACGCCTGCCAC 4 0 0 CAATTCCACTCCCTTCGCGGCAGACCGCA 5 2 0 CACGTTCTCCCTTTCTACGCGATCCCCATCCATAAGA 5 71 0 GCGAACGTCCTGCGACACGTTCTCCCTTTCTA 5 91 0 CTATTTCCACGCGCTGGCGGCCACTGA 8 1 0 GCTGTACAAACCCCGGGGAACACCCTCTCATCCTATC 9 40 0 TGTGTTGTTTCGTGCTACAAGTCCCGCCGGAAGGGCC 9 96 1 GTATGGGCCCAGCTGGACTTGAACCGGCGACCCGCGG 9 168 0 ATACTATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCG 9 201 1 TGGTAGCGCGTCTCTTGCGCCTTGCGCGGGGTTTTTC 9 219 1 TCGTTAGGGACGTGCAGGACGACGCCGACACCACCCA 10 13 0 CCGTCACGGGCCCTTCGTTACAGCCACCCTACGATAT 10 77 0 CCGTGACGGTACTTTAGCACGCGGCTGTGGTGTGCGC 10 105 1 *** * ** * ** * MAP Score: 8.60753 Motif 7 GAGTGGACCCCGCTTAAGAGGAGGCACGTT 0 3 0 AGAGCAAAATCAAAGGGAAAGGCACAGCATGTACTAC 0 80 1 AGGGAGGAGAACAGGAAGGAGCACCGGTAGTAGTTG 1 9 0 AGTCCCTGAGCGAGAAGGATGCAGCAGGAGAGGGCAA 1 45 0 GAGCACTGTGCCTTGTGCTAGTCCCTGAGCGAGAAGG 1 64 0 TACACTCGGCCGTGTGTCAACACGCGCTCAAGAAATG 1 104 1 AGTAGTACAAAAGGGTGCGCCAGTCTACACGTT 2 6 1 GCAGCGGTGACAAGCAACGCGGCGCGGG 3 1 0 GTTGCTTGTCACCGCTGCAGGCAGCTCTGCACGC 3 20 1 CAGAACACGGCGCACAACGCCTGCCAC 4 0 0 GCGTTGTGCGCCGTGTTCTGCGCGCTGGCCATGCAAA 4 17 1 CAATTCCACTCCCTTCGCGGCAGACCGCA 5 2 0 GCCCTCTTATGGATGGGGATCGCGTAGAAAGGGAGAA 5 67 1 CGCGTAGAAAGGGAGAACGTGTCGCAGGACGTTCGC 5 87 1 CTATTTCCACGCGCTGGCGGCCACTGA 8 1 0 GCTGTACAAACCCCGGGGAACACCCTCTCATCCTATC 9 40 0 TGTGTTGTTTCGTGCTACAAGTCCCGCCGGAAGGGCC 9 96 1 AGCGGACTCATAATCCGCGGGTCGCCGGTTCAAGTCC 9 154 1 CGCCGGTTCAAGTCCAGCTGGGCCCATACTATTTGTG 9 176 1 AAGGCGCAAGAGACGCGCTACCACCTGCACACAAATA 9 205 0 CCATGAAAAACCCCGCGCAAGGCGCAAGAGACGCGCT 9 223 0 GTGCAGGACGACGCCGACACCACCCATAC 10 2 0 GTGTCGGCGTCGTCCTGCACGTCCCTAACGAAAAGAA 10 19 1 GTGGCTGTAACGAAGGGCCCGTGACGGTACTTTAGCA 10 87 1 CCGTGACGGTACTTTAGCACGCGGCTGTGGTGTGCGC 10 105 1 ** * ** * *** * MAP Score: 4.95327 Motif 8 AACTACTACCGGTGCTCCTTCCTGTTCTCCTCCC 1 11 1 CTCCTCCCTTGCCCTCTCCTGCTGCATCCTTCTC 1 37 1 CTAGCACAAGGCACAGTGCTCCGTTACACTCGGC 1 80 1 GTGCTCCGTTACACTCGGCCGTGTGTCAACACGC 1 95 1 CCCGCGCCGCGTTGCTTGTCACCGCTG 3 3 1 GCGTGCAGAGCTGCCTGCAGCGGTGACAAGCAA 3 21 0 GTGGCAGGCGTTGTGCGCCGTGTTCTGCGCG 4 7 1 TGTGCGCCGTGTTCTGCGCGCTGGCCATGCAAAA 4 21 1 TGCGGTCTGCCGCGAAGGGAGTGGA 5 1 1 AGTCTGTAAAGGAGATGGCCGGAGG 7 20 1 ATTTCCACGCGCTGGCGGCCACTGA 8 1 0 ATAGGATGAGAGGGTGTTCCCCGGGGTTTGTACA 9 41 1 CTGAGCTATAGGCCCTTCCGGCGGGACTTGTAGC 9 109 0 TAGCTCAGTTGGTTAGAGCAGCGGACTCATAATC 9 135 1 TGGACTTGAACCGGCGACCCGCGGATTATGAGTC 9 158 0 CTATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCG 9 204 1 CGCGTCTCTTGCGCCTTGCGCGGGGTTTTTCATG 9 225 1 GTATGGGTGGTGTCGGCGTCGTCCTGCAC 10 5 1 GCACACCACAGCCGCGTGCTAAAGTACCGTCACG 10 106 0 ACGCGGCTGTGGTGTGCGCTGCAGAATAAAGAGG 10 123 1 ** * * ** **** MAP Score: 4.83429 Motif 9 CAACTACTACCGGTGCTCCTTCCTGTTC 1 0 1 TCCTCCCTTGCCCTCTCCTGCTGCATCCTTCTCGCTCA 1 38 1 ACGGAGCACTGTGCCTTGTGCTAGTCCCTGAGCGAGAA 1 66 0 CCCGCGCCGCGTTGCTTGTCACCGCTGCA 3 1 1 GCGTGCAGAGCTGCCTGCAGCGGTGACAAGCAACG 3 19 0 GTGGCAGGCGTTGTGCGCCGTGTTCTGC 4 0 1 TTTTTTGCATGGCCAGCGCGCAGAACACGGCGCACAAC 4 19 0 CAATTCCACTCCCTTCGCGGCAGACCGCA 5 1 0 GACACGTTCTCCCTTTCTACGCGATCCCCATCCATAAG 5 72 0 TAGAAAGGGAGAACGTGTCGCAGGACGTTCGC 5 91 1 TCAGTGGCCGCCAGCGCGTGGAAATAG 8 1 1 TAGGATGAGAGGGTGTTCCCCGGGGTTTGTACAGCGTT 9 42 1 TGAGCTATAGGCCCTTCCGGCGGGACTTGTAGCACGAA 9 104 0 GGACTTGAACCGGCGACCCGCGGATTATGAGTCCGCTG 9 153 0 CGCAAGAGACGCGCTACCACCTGCACACAAATAGTATG 9 200 0 GGTAGCGCGTCTCTTGCGCCTTGCGCGGGGTTTTTCAT 9 220 1 TGGGTGGTGTCGGCGTCGTCCTGCACGTCCCTAACGAA 10 13 1 TGCTAAAGTACCGTCACGGGCCCTTCGTTACAGCCACC 10 86 0 * ** ** ** * * * MAP Score: 3.59864 Motif 10 CAACTACTACCGGTGCTCCTTCCTGTTCTCCT 1 10 1 GTGCTCCTTCCTGTTCTCCTCCCTTGCCCTCT 1 22 1 CTCCTCCCTTGCCCTCTCCTGCTGCATCCTTC 1 37 1 CTAGCACAAGGCACAGTGCTCCGTTACACTCG 1 80 1 TAGTACAAAAGGGTGCGCCAGTCTACACGTTC 2 12 1 CCCGCGCCGCGTTGCTTGTCACC 3 1 1 CGTTGCTTGTCACCGCTGCAGGCAGCTCTGCA 3 19 1 CCGCTGCAGGCAGCTCTGCACGC 3 31 1 GTGGCAGGCGTTGTGCGCCGTGTTCTGCG 4 7 1 GTTGTGCGCCGTGTTCTGCGCGCTGGCCATGC 4 19 1 TGCGGTCTGCCGCGAAGGGAGTG 5 1 1 ACGTATGCTCGCACACTGCCTGAA 6 41 1 TCAGTGGCCGCCAGCGCGTGGAAAT 8 3 1 GGATGAGAGGGTGTTCCCCGGGGTTTGTACAG 9 44 1 TGGACTTGAACCGGCGACCCGCGGATTATGAG 9 160 0 CAAATAGTATGGGCCCAGCTGGACTTGAACCG 9 179 0 GTGGTAGCGCGTCTCTTGCGCCTTGCGCGGGG 9 218 1 GGTGGTGTCGGCGTCGTCCTGCACGTCCCTAA 10 15 1 CGGTACTTTAGCACGCGGCTGTGGTGTGCGCT 10 111 1 CGGCTGTGGTGTGCGCTGCAGAATAAAGAGGT 10 126 1 **** **** ** MAP Score: 0.519175 Motif 11 GAACAGGAAGGAGCACCGGTAGTAGTTG 1 8 0 GGCAAGGGAGGAGAACAGGAAGGAGCACCG 1 20 0 TTGACACACGGCCGAGTGTAACGGAGCACT 1 94 0 GTGTAGACTGGCGCACCCTTTTGTACTACT 2 10 0 GACAAGCAACGCGGCGCGGG 3 0 0 CAGGCGTTGTGCGCCGTGTTCTGCGCGCTG 4 14 1 TTTTTTGCATGGCCAGCGCGCAGAACACGG 4 27 0 TGCGGTCTGCCGCGAAGGGAGTGGAATT 5 8 1 ATCCATAAGAGGGCAGACTATGCGCAATTT 5 51 0 TCTTATGGATGGGGATCGCGTAGAAAGGGA 5 71 1 CCACGCGCTGGCGGCCACTGA 8 1 0 CTGAGCTATAGGCCCTTCCGGCGGGACTTG 9 113 0 CAGTTGGTTAGAGCAGCGGACTCATAATCC 9 140 1 TTGAACCGGCGACCCGCGGATTATGAGTCC 9 157 0 CAAATAGTATGGGCCCAGCTGGACTTGAAC 9 181 0 CAAGGCGCAAGAGACGCGCTACCACCTGCA 9 213 0 CGCGTCTCTTGCGCCTTGCGCGGGGTTTTT 9 225 1 TTTTTCATGGGAGGCTTGTG 9 250 1 GCAGGACGACGCCGACACCACCCATAC 10 7 0 CTTTTCGTTAGGGACGTGCAGGACGACGCC 10 24 0 TACCGTCACGGGCCCTTCGTTACAGCCACC 10 86 0 GCACACCACAGCCGCGTGCTAAAGTACCGT 10 110 0 TTATTCTGCAGCGCACACCACAGCCGCGTG 10 122 0 ********** MAP Score: 0.152747