AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_operons014_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944239368 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0162 174 Holliday junction DNA helicase (ruvB) #1 TP0251 153 DNA-binding protein II #2 TP0353 262 ribonuclease H (rnhA) #3 TP0417 26 apolipoprotein N-acyltransferase (cutE) #4 TP0519 300 response regulatory protein (atoC) #5 TP0543 41 Holliday junction DNA helicase (ruvA) #6 TP0544 24 T. pallidum predicted coding region TP0544 #7 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #8 TP0547 143 penicillin tolerance protein (lytB) #9 TP0642 140 phosphomannomutase (manB) Motif 1 AAAGAAAACGGCACTCTGGCGCGGACCTCTCGA 0 91 1 GCAACTGTAGCTGCTTATGCGAGGAAGATCAAA 0 143 0 GCATAAGCAGCTACAGTTGCGCCCTCTT 0 156 1 CGAGCCACAGCCTTTCTAGCGAAAACACCTTTC 1 32 0 ACACATTCGGGACTTCTGGCGAGCCACAGCCTT 1 51 0 ACGGTGTGTTCTCTTCACCCGAGGTGGTGCGCG 1 94 1 CAAACAGCCGCCTCAAACGCGCACCACCTCGGG 1 111 0 TTTGAGGCGGCTGTTTGCCCGCGTGTGTTTCTT 1 127 1 GCAAGGCGGTGTACACGTGCGCGTTGCACTTTC 2 68 0 AAAAACCAAACCGTCGTCCCGCGTACCAAAGTT 2 121 1 AGTTCCTGCACAATCCGTGCGCGCCTCATTCTC 2 150 1 GCCTCATTCTCCCTCCTTGCGAAAATATCTTCG 2 172 1 CAATACATTGTCCCCACGGCGCAAAACTGTTAC 2 226 1 AAAACTGTTACCGTAGGCGCGACT 2 248 1 CGTAGTGTTCGCTTCAGTGCGCCACACATAAAG 5 10 1 AGGACACTCCTCACGCGCAGTGTA 6 5 0 TTTCTATATTCCTCGCGCGGGTATCAGGG 7 6 1 TCCTCCTCATGTTCACCAGCGCATTCTGATTTG 7 58 0 AGACACGTTGCTTTTCCTGCGCGA 8 1 0 GAAGAACTCACCACCACGCCGCGCCCTTGCATG 8 55 1 GCCTTTGGTACACTCGGCGCGCCAGTTTTCTTC 8 96 1 ** *** ***** MAP Score: 21.2302 Motif 2 AAGTAGCGGATCACGCAGGAAACGTCAATTTTTCA 0 42 1 CTCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTT 0 90 0 ATTTGATCTTCCTCGCATAAGCAGCTACAGTTGCG 0 142 1 GGAAAGGTGTTTTCGCTAGAAAGGCTGTGGCTCGC 1 31 1 AAAGGCTGTGGCTCGCCAGAAGTCCCGAATGTGTA 1 50 1 GGTGTGTTCTCTTCACCCGAGGTGGTGCGCGTTTG 1 96 1 CCGAGGTGGTGCGCGTTTGAGGCGGCTGTTTGCCC 1 112 1 GCGGCTGTTTGCCCGCGTGTGTTTCTTGTC 1 133 1 AGTGCAGCATGTACACCCGAGGAGAAAGTGCAACG 2 45 1 AAAGTGCAACGCGCACGTGTACACCGCCTTGCAGA 2 69 1 AGGAACTTTGGTACGCGGGACGACGGTTTGGTTTT 2 122 0 GGAGAATGAGGCGCGCACGGATTGTGCAGGAACTT 2 149 0 AACTTTCCCCTGCCAGAAAAGCATTT 3 4 0 CTTCAGTGCGCCACACATAAAGAGGAGATA 5 21 1 TACACTGCGCGTGAGGAGTGTCCT 6 4 1 TTTCTATATTCCTCGCGCGGGTATCAGGGTGTGAG 7 10 1 TCGCGCAGGAAAAGCAACGTGTCTT 8 0 1 CACGCCGCGCCCTTGCATGACCTGGGTGCCTTTGG 8 69 1 GGTGCCTTTGGTACACTCGGCGCGCCAGTTTTCTT 8 93 1 TCTGTGCAATGCTCACAAAAAGTGCATGTCTTGAA 9 35 0 ** *** *** ** MAP Score: 19.0077 Motif 3 AGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTT 0 95 0 ACCCGAGGTGGTGCGCGTTTGAGGCGGCTGTT 1 110 1 CTGTGCCCTCTCCGTGTTAGCTTT 2 2 1 AGTGCAGCATGTACACCCGAGGAGAAAGTGCA 2 45 1 CGGTGTACACGTGCGCGTTGCACTTTCTCCTC 2 63 0 AGGAACTTTGGTACGCGGGACGACGGTTTGGT 2 125 0 TGCACAATCCGTGCGCGCCTCATTCTCCCTCC 2 156 1 CCAATACATTGTCCCCACGGCGCAAAACTGTT 2 225 1 AGTAAAACACGTACCCCGTCCAACAGTAGAGG 4 185 0 GTTCGCTTCAGTGCGCCACACATAAAGAGGAG 5 16 1 TACACTGCGCGTGAGGAGTGTCCT 6 4 1 TCACACCCTGATACCCGCGCGAGGAATATAGA 7 12 0 TCAAATCAGAATGCGCTGGTGAACATGAGGAG 7 57 1 GGTGCCTTTGGTACACTCGGCGCGCCAGTTTT 8 93 1 TTCCGGTTTAGTGCCCCAGTGAGTGAT 8 126 1 TTGAAAAAGTGTACCAGAGCCACTACACTG 9 8 0 ******* * ** MAP Score: 16.3896 Motif 4 AGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTC 0 94 0 AAGAGGGCGCAACTGTAGCTGCTTA 0 159 0 TCACCCGAGGTGGTGCGCGTTTGAGGCGGCTGT 1 108 1 TGAGGCGGCTGTTTGCCCGCGTGTGTTTCTTGT 1 129 1 GGAGAAAGTGCAACGCGCACGTGTACACCGCCT 2 65 1 CCTGCACAATCCGTGCGCGCCTCATTCTCCCTC 2 154 1 GTGTTCGCTTCAGTGCGCCACACATAAAGAGGA 5 14 1 TACACTGCGCGTGAGGAGTGTCCT 6 2 1 TTTCTATATTCCTCGCGCGGGTATCAGGGTGTG 7 10 1 TGTCAAATCAGAATGCGCTGGTGAACATGAGGA 7 55 1 CTCACCACCACGCCGCGCCCTTGCATGACCTGG 8 61 1 CTTTGGTACACTCGGCGCGCCAGTTTTCTTCCG 8 98 1 TCTTCCGGTTTAGTGCCCCAGTGAGTGAT 8 124 1 CTTCCCATTACAATGCCCCTCTATCCTGTGGTG 9 77 1 * ****** *** MAP Score: 16.1903 Motif 5 GTGACACTCCTTGGGTGAATTTTGATGCATCA 0 8 1 AAGTAGCGGATCACGCAGGAAACGTCAATTTTTC 0 42 1 TTTTCAGTACCCTTTCAGGAAAAGAAAACGGCAC 0 71 1 ATTTGATCTTCCTCGCATAAGCAGCTACAGTTGC 0 142 1 ACGCGCACCACCTCGGGTGAAGAGAACACACCGT 1 94 0 CAAGAAACACACGCGGGCAAACAGCCGCCTCAAA 1 127 0 GCATGTACACCCGAGGAGAAAGTGCAACGCGCAC 2 51 1 GTGTACACCGCCTTGCAGAATAAGACAGCGTACC 2 85 1 GTACCAAAGTTCCTGCACAATCCGTGCGCGCCTC 2 143 1 CATTCTCCCTCCTTGCGAAAATATCTTCGCTCCA 2 176 1 CAGTTTTGCGCCGTGGGGACAATGTATTGGTCCG 2 221 0 AACTTTCCCCTGCCAGAAAAGCATTT 3 5 0 CTCCTTTTACCCATAGATAAATTGGGACGATCGC 4 217 1 CTTCAGTGCGCCACACATAAAGAGGAGATA 5 21 1 AGGACACTCCTCACGCGCAGTGTA 6 2 0 TCGCGCAGGAAAAGCAACGTGTCT 8 0 1 CACGCCGCGCCCTTGCATGACCTGGGTGCCTTTG 8 69 1 ** **** *** * MAP Score: 15.918 Motif 6 TTTCTATATTCCTCGCGCGGGTATCAGGG 7 9 1 TCCTGCACAATCCGTGCGCGCCTCATTCTC 2 153 1 CACGTTGCTTTTCCTGCGCGA 8 1 0 GAAAACGGCACTCTGGCGCGGACCTCTCGA 0 94 1 AAATTGACGTTTCCTGCGTGATCCGCTACT 0 43 0 GTGACACTCCTTGGGTGAATTTTGATG 0 7 1 TTGCACTTTCTCCTCGGGTGTACATGCTGC 2 48 0 GGCGGCTGTTTGCCCGCGTGTGTTTCTTGT 1 132 1 TACACTGCGCGTGAGGAGTGT 6 1 1 AACGCGCACCACCTCGGGTGAAGAGAACAC 1 99 0 AGGCGGTGTACACGTGCGCGTTGCACTTTC 2 68 0 CCTTTGGTACACTCGGCGCGCCAGTTTTCT 8 97 1 CATTCGGGACTTCTGGCGAGCCACAGCCTT 1 51 0 CCACGCCGCGCCCTTGCATGACCTGGGTGC 8 68 1 GAACTCACCACCACGCCGCGCCCTTGCATG 8 58 1 CTGTGCCCTCTCCGTGTTAGCTTTCC 2 6 1 ********** MAP Score: 13.0245 Motif 7 AAAAGAAAACGGCACTCTGGCGCGGACCTCTCGAG 0 90 1 AGCGACTTGACACCGCTGCCCGGAAAGGTGTTT 1 8 1 TTTCGCTAGAAAGGCTGTGGCTCGCCAGAAGTCCC 1 41 1 CTCCTCGGGTGTACATGCTGCACTGTTTTTAGAGG 2 34 0 CGTGCGCGTTGCACTTTCTCCTCGGGTGTACATGC 2 51 0 CGACGGTTTGGTTTTTGCGGTACGCTGTCTTATTC 2 102 0 GGATTGTGCAGGAACTTTGGTACGCGGGACGACGG 2 131 0 CGCAAGGAGGGAGAATGAGGCGCGCACGGATTGTG 2 158 0 AAATGCTTTTCTGGCAGGGGAAAGTT 3 4 1 TACAGGAGAGGGAATTGATGCCCGAAATATTCACA 4 48 1 AAGACACGTTGCTTTTCCTGCGCGA 8 0 0 GGTGCCTTTGGTACACTCGGCGCGCCAGTTTTCTT 8 93 1 ATTGTAATGGGAAGGTGCTGCTCTGTGCAATGCTC 9 56 0 * ****** *** MAP Score: 12.1653 Motif 8 CAGCTACAGTTGCGCCCTCTT 0 163 1 TGTACAACGGTGTGTTCTCTTCACCCGAGG 1 88 1 GAGGCGGCTGTTTGCCCGCGTGTGTTTCTT 1 130 1 CTGTGCCCTCTCCGTGTTAGC 2 1 1 CGCGTTGCACTTTCTCCTCGGGTGTACATG 2 52 0 GCGCGCCTCATTCTCCCTCCTTGCGAAAAT 2 168 1 ACCAATACATTGTCCCCACGGCGCAAAACT 2 224 1 AACTTTCCCCTGCCAGAAAAGCA 3 13 0 CGGGCATCAATTCCCTCTCCTGTATCCGAA 4 42 0 GACACACTGATGTCACCGCCATGTTCTTTA 4 156 0 GTGACATCAGTGTGTCCTCTACTGTTGGAC 4 170 1 TATCTCCTCTTTATGTGTGG 5 31 0 TTGACACTTCTTTCCCCTCACACCCTGATA 7 31 0 ATTTCCTCCTCATGTTCACCAG 7 72 0 ********** MAP Score: 10.8123 Motif 9 CACTCTGGCGCGGACCTCTCGAGCTACATGATA 0 102 1 TGTGGCTCGCCAGAAGTCCCGAATGTGTAGACT 1 56 1 ACGGTGTGTTCTCTTCACCCGAGGTGGTGCGCG 1 94 1 TTTGAGGCGGCTGTTTGCCCGCGTGTGTTTCTT 1 127 1 ACAGTGCAGCATGTACACCCGAGGAGAAAGTGC 2 43 1 GAGGAGAAAGTGCAACGCGCACGTGTACACCGC 2 63 1 AAAAACCAAACCGTCGTCCCGCGTACCAAAGTT 2 121 1 AAAGTTCCTGCACAATCCGTGCGCGCCTCATTC 2 148 1 GCCTCATTCTCCCTCCTTGCGAAAATATCTTCG 2 172 1 AAAACTGTTACCGTAGGCGCGACT 2 248 1 TACACTGCGCGTGAGGAGTGTCCT 6 2 1 TTTCTATATTCCTCGCGCGGGTATCAGGG 7 6 1 AGACACGTTGCTTTTCCTGCGCGA 8 1 0 AGAACTCACCACCACGCCGCGCCCTTGCATGAC 8 57 1 GCCTTTGGTACACTCGGCGCGCCAGTTTTCTTC 8 96 1 TCAAGACATGCACTTTTTGTGAGCATTGCACAG 9 36 1 * ** * ****** MAP Score: 6.97351 Motif 10 GCTCGAGAGGTCCGCGCCAGAGTGCCGTTT 0 96 0 CGACTTGACACCGCTGCCCGGAAAGGTGTT 1 12 1 AGCCGCCTCAAACGCGCACCACCTCGGGTG 1 109 0 GAGAAAGTGCAACGCGCACGTGTACACCGC 2 66 1 TCCTGCACAATCCGTGCGCGCCTCATTCTC 2 153 1 TCATTCTCCCTCCTTGCGAAAATATCTTCG 2 175 1 CATTGTCCCCACGGCGCAAAACTGTTACCG 2 231 1 ACTGTTACCGTAGGCGCGACT 2 251 1 AACTTTCCCCTGCCAGAAAAGCATTT 3 10 0 CACACTGATGTCACCGCCATGTTCTTTAAT 4 154 0 AGTGTTCGCTTCAGTGCGCCACACATAAAG 5 13 1 TACACTGCGCGTGAGGAGTGT 6 1 1 TTTCTATATTCCTCGCGCGGGTATCAGGG 7 9 1 GACACTTCTTTCCCCTCACACCCTGATACC 7 29 0 CACGTTGCTTTTCCTGCGCGA 8 1 0 ACTCACCACCACGCCGCGCCCTTGCATGAC 8 60 1 TTTGGTACACTCGGCGCGCCAGTTTTCTTC 8 99 1 ********** MAP Score: 6.49375 Motif 11 TGAAAAATTGACGTTTCCTGCGTGATCCGC 0 47 0 AGTGCCGTTTTCTTTTCCTGAAAGGGTACT 0 76 0 AGAAGCATTTGATCTTCCTCGCATAAGCAG 0 136 1 GCCCGGAAAGGTGTTTTCGCTAGAAAGGCT 1 27 1 CTGTACAACGGTGTGTTCTCTTCACCCGAG 1 87 1 TTGCCCGCGTGTGTTTCTTGTC 1 141 1 CGTGCGCGTTGCACTTTCTCCTCGGGTGTA 2 56 0 AAATGCTTTTCTGGCAGGGGAAAG 3 4 1 GGTGACATCAGTGTGTCCTCTACTGTTGGA 4 169 1 CGCATTTCCTTATTCTTTACT 4 289 0 AAGACACGTTGCTTTTCCTGCGCGA 8 5 0 GTGGTGGTGAGTTCTTCTTCTTTTATTTAT 8 42 0 TGGCTCTGGTACACTTTTTCAAGACATGCA 9 18 1 TTCAAGACATGCACTTTTTGTGAGCATTGC 9 35 1 GAGCGCTTCCTCACCTTTAAAA 9 128 0 ********** MAP Score: 3.85109 Motif 12 AGTAGCGGATCACGCAGGAAACGTCAATTTT 0 43 1 AGTACCCTTTCAGGAAAAGAAAACGGCACTC 0 76 1 TGATCTTCCTCGCATAAGCAGCTACAGTTGC 0 145 1 CGCACCACCTCGGGTGAAGAGAACACACCGT 1 94 0 GAAACACACGCGGGCAAACAGCCGCCTCAAA 1 127 0 AAAGCTAACACGGAGAGGGCACAG 2 3 0 GATATTTTCGCAAGGAGGGAGAATGAGGCGC 2 170 0 ATTTCGGATACAGGAGAGGGAATTGATGCCC 4 40 1 CTAAGACATACGAGTAAAGAATAAGGAAATG 4 277 1 CAGTGCGCCACACATAAAGAGGAGATA 5 24 1 TACACTGCGCGTGAGGAGTGTCCT 6 7 1 CCCTGATACCCGCGCGAGGAATATAGAAA 7 8 0 TCAGGGTGTGAGGGGAAAGAAGTGTCAAATC 7 33 1 GCTGGTGAACATGAGGAGGAAAT 7 71 1 TCGCGCAGGAAAAGCAACGTGTCTTT 8 5 1 AAATAAATAAAAGAAGAAGAACTCACCACCA 8 40 1 AGGTCATGCAAGGGCGCGGCGTGGTGGTGAG 8 61 0 AGTACTTTTAAAGGTGAGGAAGCGCTC 9 123 1 **** ****** MAP Score: 2.02068 Motif 13 AGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTTCC 0 88 0 AAGAGGGCGCAACTGTAGCTGCTTATGCGAGGA 0 151 0 AGCGACTTGACACCGCTGCCCGGAAAGGTGTTTTCGCTA 1 10 1 CGGGTGAAGAGAACACACCGTTGTACAGTCTACACATTC 1 76 0 GGTGTGTTCTCTTCACCCGAGGTGGTGCGCGTTTGAGGC 1 96 1 GCGGCTGTTTGCCCGCGTGTGTTTCTTGTC 1 133 1 CTGTGCCCTCTCCGTGTTAGCTTTCCTCTAAAA 2 4 1 AGTGCAGCATGTACACCCGAGGAGAAAGTGCAACGCGCA 2 45 1 CTGCAAGGCGGTGTACACGTGCGCGTTGCACTTTCTCCT 2 64 0 AGGAACTTTGGTACGCGGGACGACGGTTTGGTTTTTGCG 2 118 0 TGCACAATCCGTGCGCGCCTCATTCTCCCTCCTTGCGAA 2 156 1 GCGAAAATATCTTCGCTCCATCACCAACTGTCGGACCAA 2 190 1 CGTAGTGTTCGCTTCAGTGCGCCACACATAAAGAG 5 6 1 TACACTGCGCGTGAGGAGTGTCCT 6 2 1 TTTCTATATTCCTCGCGCGGGTATCAGGGTGTGAGGGGA 7 10 1 AAAAGAAGAAGAACTCACCACCACGCCGCGCCCTTGCAT 8 48 1 CACGCCGCGCCCTTGCATGACCTGGGTGCCTTTGGTACA 8 69 1 GGTGCCTTTGGTACACTCGGCGCGCCAGTTTTCTTCCGG 8 93 1 CTTCCCATTACAATGCCCCTCTATCCTGTGGTGCCGTAA 9 77 1 * *** ** * * ** MAP Score: 0.805512