AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_operons013_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944239332 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0284 104 T. pallidum predicted coding region TP0284 #1 TP0289 22 T. pallidum predicted coding region TP0289 #2 TP0290 54 conserved hypothetical protein #3 TP0291 36 T. pallidum predicted coding region TP0291 #4 TP0372 121 general stress protein (ctc) #5 TP0673 177 glutamyl-tRNA synthetase (gltX) #6 TP0979 169 conserved hypothetical protein #7 TP1011 34 peptidyl-tRNA hydrolase (pth) #8 TP1012 204 RNA polymerase sigma-43 factor (sigA) Motif 1 AGCTGGGCCGTGCGCGCATGTCCGC 6 4 1 CGGCGTACCAGGGCGGTACGCGCGAGCGCCT 6 125 1 TACACGCACCGCGCGGGGCGCATTCTATACA 8 58 1 CTTCACGTTTGCGCCGTATGCCTACACGCAC 8 36 1 TATGAAATAGGAGCAGGACGCG 7 22 1 AGAGGGCAGTGCTTTTTTAGGG 3 1 1 TGAGTGCTGTGAGGCGCTCGCGCGTACCGCC 6 136 0 GAAGCGCAACGCGCGGCACACACGCGCGGTA 6 94 0 GTCCCAGTTTGCGGCGTGTTCGCTTTCTGTG 4 84 1 GCGAACTAGAACGGCCGACGCGGACATGCGC 6 23 0 ATCCCCCTCCGGGGCGCAAGCATCCCTGTGA 5 124 0 ATCGGCCCCCGGGGAGGGCGAGCG 5 163 1 ATTGCGGGCACAGGGGCACGCGAACTAGAAC 6 42 0 ACATCAGAGGCGTATGAAATAGGAGCA 7 6 1 CCGTGGGAAAGGGAGGTATGCACAGAGGGTC 8 123 1 GCGCCCCGGAGGGGGATGTGCGATAATCGGC 5 138 1 GAGTGATCTTCGGGGCTGTGCTTTTAAAGTT 0 54 1 CCTTCCTACCACGCAGGATGCCGCTTCACGC 5 43 0 GGAAGACAGGGAGGCGGTCACGGTGCATGAG 5 74 1 ACTCGTTATGAGGAGGAACGC 8 0 0 CGCGGTATTTGCGGAGAACAAAGCAACCATT 6 70 0 GCCCTCCCCGGGGGCCGATTATCGCACATCC 5 151 0 CCGCCCTGGTACGCCGGAAGCGCAACGCGCG 6 110 0 TGGTGCAGTACGCTGAAGTAAT 1 9 0 TCCCTTTCCCACGGCGCGCTACAGTTCTCTT 8 106 0 ****** **** MAP Score: 35.9384 Motif 2 GAGTGATCTTCGGGGCTGTGCTTTTAAAGTTC 0 54 1 GTCCCAGTTTGCGGCGTGTTCGCTTTCTGTGC 4 84 1 GGGGAAGACAGGGAGGCGGTCACGGTGCATGA 5 72 1 ATCCCCCTCCGGGGCGCAAGCATCCCTGTGAG 5 123 0 GCGCCCCGGAGGGGGATGTGCGATAATCGGCC 5 138 1 CGCCCTCCCCGGGGGCCGATTATCGCACATCC 5 151 0 CGGCCCCCGGGGAGGGCGAGCG 5 165 1 AGCTGGGCCGTGCGCGCATGTCCG 6 2 1 ACGGCCGACGCGGACATGCGCGCACGGCCCAG 6 12 0 GCATGTCCGCGTCGGCCGTTCTAGTTCGCGTG 6 25 1 CGGGCACAGGGGCACGCGAACTAGAACGGCCG 6 37 0 CGGCACACACGCGCGGTATTTGCGGAGAACAA 6 80 0 TACCGCGCGTGTGTGCCGCGCGTTGCGCTTCC 6 94 1 CGGCGTACCAGGGCGGTACGCGCGAGCGCCTC 6 125 1 CCTGAGTGCTGTGAGGCGCTCGCGCGTACCGC 6 137 0 CTTCACGTTTGCGCCGTATGCCTACACGCACC 8 36 1 AATGCGCCCCGCGCGGTGCGTGTAGGCATACG 8 50 0 CGCACCGCGCGGGGCGCATTCTATACATTTCC 8 62 1 GAGAACTGTAGCGCGCCGTGGGAAAGGGAGGT 8 108 1 CCGTGGGAAAGGGAGGTATGCACAGAGGGTCC 8 123 1 AGAGGGTCCAGTGGCGTGATAGGGACACCGAA 8 146 1 *** **** *** MAP Score: 24.0851 Motif 3 CCCAGTTTGCGGCGTGTTCGCTTTCTGTGCATGGAGGATT 4 86 1 TGCAATCAACCGCGTGAAGCGGCATCCTGCGTGGTAGGAA 5 32 1 AAGACAGGGAGGCGGTCACGGTGCATGAGGAGTGTAATTT 5 76 1 TAATTTTCAGGGCCTCACAGGGATGCTTGCGCCCCGGAGG 5 110 1 GGGATGCTTGCGCCCCGGAGGGGGATGTGCGATAATCGGC 5 129 1 TGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 156 1 AGCTGGGCCGTGCGCGCATGTCCGCGTCGGCCGTT 6 5 1 TGTCCGCGTCGGCCGTTCTAGTTCGCGTGCCCCTGTGCCC 6 28 1 CCGCAAATACCGCGCGTGTGTGCCGCGCGTTGCGCTTCCG 6 87 1 TGCCGCGCGTTGCGCTTCCGGCGTACCAGGGCGGTACGCG 6 107 1 AGTGCTGTGAGGCGCTCGCGCGTACCGCCCTGGTACGCCG 6 125 0 CCCCGCGCGGTGCGTGTAGGCATACGGCGCAAACGTGAAG 8 36 0 AGAACTGTAGCGCGCCGTGGGAAAGGGAGGTATGCACAGA 8 109 1 AGGGTCCAGTGGCGTGATAGGGACACCGAACAGATCTCCT 8 148 1 **** ** ** ** MAP Score: 20.5895 Motif 4 TGGTACCGTCATTCCGTAGGTTCGAATCCTACCGTCCCA 4 51 1 AATCCTCCATGCACAGAAAGCGAACACGCCGCAAACTGG 4 87 0 GCAGGATGCCGCTTCACGCGGTTGATTGCACAGACAGGT 5 23 0 GTGAAGCGGCATCCTGCGTGGTAGGAAGGGGAAGACAGG 5 45 1 AGGAAGGGGAAGACAGGGAGGCGGTCACGGTGCATGAGG 5 67 1 AATTTTCAGGGCCTCACAGGGATGCTTGCGCCCCGGAGG 5 111 1 GGATGCTTGCGCCCCGGAGGGGGATGTGCGATAATCGGC 5 130 1 GCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 157 1 AGCTGGGCCGTGCGCGCATGTCCGCGTCGGCCG 6 4 1 CGGGCACAGGGGCACGCGAACTAGAACGGCCGACGCGGA 6 30 0 TTCTCCGCAAATACCGCGCGTGTGTGCCGCGCGTTGCGC 6 83 1 CCGCCCTGGTACGCCGGAAGCGCAACGCGCGGCACACAC 6 102 0 CGGCGTACCAGGGCGGTACGCGCGAGCGCCTCACAGCAC 6 125 1 CTTCACGTTTGCGCCGTATGCCTACACGCACCGCGCGGG 8 36 1 GAACTGTAGCGCGCCGTGGGAAAGGGAGGTATGCACAGA 8 110 1 AGGGAGGTATGCACAGAGGGTCCAGTGGCGTGATAGGGA 8 132 1 ** *** * * * ** MAP Score: 19.8474 Motif 5 GTTTTGAGCAAGGTTCTCCTGC 0 92 1 CGCAGGATGCCGCTTCACGCGGTTGATTGCAC 5 31 0 AGGGGAAGACAGGGAGGCGGTCACGGTGCATG 5 71 1 TGTAATTTTCAGGGCCTCACAGGGATGCTTGC 5 108 1 CATCCCCCTCCGGGGCGCAAGCATCCCTGTGA 5 124 0 TGCGCCCCGGAGGGGGATGTGCGATAATCGGC 5 137 1 GTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 155 1 AGCTGGGCCGTGCGCGCATGTCCGC 6 3 1 CGAACTAGAACGGCCGACGCGGACATGCGCGC 6 21 0 TTGCGGGCACAGGGGCACGCGAACTAGAACGG 6 40 0 CACACACGCGCGGTATTTGCGGAGAACAAAGC 6 77 0 GCGCAACGCGCGGCACACACGCGCGGTATTTG 6 90 0 CGCCCTGGTACGCCGGAAGCGCAACGCGCGGC 6 108 0 CCGGCGTACCAGGGCGGTACGCGCGAGCGCCT 6 124 1 GGTACGCGCGAGCGCCTCACAGCACTCAGGAT 6 139 1 CGCGTCCTGCTCCTATTTCATA 7 22 0 TGTAGGCATACGGCGCAAACGTGAAGATATGA 8 30 0 TTTGCGCCGTATGCCTACACGCACCGCGCGGG 8 43 1 GTATAGAATGCGCCCCGCGCGGTGCGTGTAGG 8 56 0 AGAGAACTGTAGCGCGCCGTGGGAAAGGGAGG 8 107 1 GCCGTGGGAAAGGGAGGTATGCACAGAGGGTC 8 122 1 GTATGCACAGAGGGTCCAGTGGCGTGATAGGG 8 138 1 **** * ***** MAP Score: 19.5423 Motif 6 ATTGCATGAGCTGAGTATGTGATGATTCT 0 3 1 TACCGTCCCAGTTTGCGGCGTGTTCGCTTTCTGTGC 4 80 1 GCGTGAAGCGGCATCCTGCGTGGTAGGAAGGGGAAG 5 43 1 AGACAGGGAGGCGGTCACGGTGCATGAGGAGTGTAA 5 77 1 TCACAGGGATGCTTGCGCCCCGGAGGGGGATGTGCG 5 124 1 TGTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 154 1 ACGCGGACATGCGCGCACGGCCCAGCT 6 1 0 GCGCATGTCCGCGTCGGCCGTTCTAGTTCGCGTGCC 6 23 1 GTTCTAGTTCGCGTGCCCCTGTGCCCGCAATGGTTG 6 42 1 TACCGCGCGTGTGTGCCGCGCGTTGCGCTTCCGGCG 6 94 1 CGCGCGTTGCGCTTCCGGCGTACCAGGGCGGTACGC 6 110 1 GCGTACCAGGGCGGTACGCGCGAGCGCCTCACAGCA 6 127 1 ATATCTTCACGTTTGCGCCGTATGCCTACACGCACC 8 32 1 CCGTATGCCTACACGCACCGCGCGGGGCGCATTCTA 8 49 1 GAGAACTGTAGCGCGCCGTGGGAAAGGGAGGTATGC 8 108 1 ** *** *** * * MAP Score: 11.3356 Motif 7 ATTACTTCAGCGTACTGCACCA 1 4 1 TCTGTGCAATCAACCGCGTGAAGCGGCATCCTGCGTG 5 28 1 TTACACTCCTCATGCACCGTGACCGCCTCCCTGTCTT 5 76 0 CACAGGGATGCTTGCGCCCCGGAGGGGGATGTGCGAT 5 125 1 GTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 155 1 AGCTGGGCCGTGCGCGCATGTCCGCGTC 6 1 1 GGCACGCGAACTAGAACGGCCGACGCGGACATGCGCG 6 22 0 CGTTCTAGTTCGCGTGCCCCTGTGCCCGCAATGGTTG 6 41 1 GCGCGGCACACACGCGCGGTATTTGCGGAGAACAAAG 6 78 0 CCTGGTACGCCGGAAGCGCAACGCGCGGCACACACGC 6 100 0 TTCCGGCGTACCAGGGCGGTACGCGCGAGCGCCTCAC 6 122 1 GGGCTAATATCCTGAGTGCTGTGAGGCGCTCGCGCGT 6 142 0 CATATCTTCACGTTTGCGCCGTATGCCTACACGCACC 8 31 1 CGTATGCCTACACGCACCGCGCGGGGCGCATTCTATA 8 50 1 ATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAGGT 8 103 1 * * **** **** MAP Score: 11.1992 Motif 8 TTCTCACTCGGTTGAGTGATCTTCGGGGCTGTGCTTTTAAAGTTC 0 41 1 TTGTTTTTTGGGTGTGCACTTGTTCAAGTTCAGAGGTGATGTTG 2 20 1 AAAAAACCTGTCTGTGCAATCAACCGCGTGAAGCGGCATCCTGCG 5 18 1 TTACACTCCTCATGCACCGTGACCGCCTCCCTGTCTTCCCCTTCC 5 68 0 ATCCCCCTCCGGGGCGCAAGCATCCCTGTGAGGCCCTGAAAATTA 5 110 0 CCCGGAGGGGGATGTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 142 1 AGCTGGGCCGTGCGCGCATGTCCGCGTCGGCCGTTC 6 1 1 GTTGCTTTGTTCTCCGCAAATACCGCGCGTGTGTGCCGCGCGTTG 6 74 1 TGTGCCGCGCGTTGCGCTTCCGGCGTACCAGGGCGGTACGCGCGA 6 105 1 TATCTTCACGTTTGCGCCGTATGCCTACACGCACCGCGCGGGGCG 8 33 1 CACTGGACCCTCTGTGCATACCTCCCTTTCCCACGGCGCGCTACA 8 114 0 * ** ** ** *** MAP Score: 9.74405 Motif 9 TCTGTGCAATCAACCGCGTGAAGCGGCATCCTGCG 5 28 1 CGGGGCGCAAGCATCCCTGTGAGGCCCTGAAAATT 5 111 0 AGGGATGCTTGCGCCCCGGAGGGGGATGTGCGATA 5 128 1 CGCTCGCCCTCCCCGGGGGCCGATTATCGCA 5 156 0 CCGACGCGGACATGCGCGCACGGCCCAGCT 6 5 0 TCTAGTTCGCGTGCCCCTGTGCCCGCAATGGTTGC 6 44 1 CCGCGCGTGTGTGCCGCGCGTTGCGCTTCCGGCGT 6 96 1 CTGTGAGGCGCTCGCGCGTACCGCCCTGGTACGCC 6 126 0 GCTAATATCCTGAGTGCTGTGAGGCGCTCGCGCGT 6 142 0 TATCTTCACGTTTGCGCCGTATGCCTACACGCACC 8 33 1 ATGCCTACACGCACCGCGCGGGGCGCATTCTATAC 8 53 1 CAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAGGT 8 105 1 GGGAAAGGGAGGTATGCACAGAGGGTCCAGTGGCG 8 127 1 * ***** * *** MAP Score: 9.5464 Motif 10 GAGTGATCTTCGGGGCTGTGCTTTTAAAGTT 0 54 1 ATTACTTCAGCGTACTGCACCA 1 7 1 AGAGGGCAGTGCTTTTTTAGGG 3 1 1 CACAGAAAGCGAACACGCCGCAAACTGGGAC 4 84 0 GCAATCAACCGCGTGAAGCGGCATCCTGCGT 5 33 1 AAGGGGAAGACAGGGAGGCGGTCACGGTGCA 5 70 1 GCAAGCATCCCTGTGAGGCCCTGAAAATTAC 5 109 0 GCACATCCCCCTCCGGGGCGCAAGCATCCCT 5 128 0 CTCGCCCTCCCCGGGGGCCGATTATCGCACA 5 154 0 AGCTGGGCCGTGCGCGCATGTCC 6 2 1 GAACGGCCGACGCGGACATGCGCGCACGGCC 6 15 0 ATTGCGGGCACAGGGGCACGCGAACTAGAAC 6 42 0 AATACCGCGCGTGTGTGCCGCGCGTTGCGCT 6 92 1 GGTACGCCGGAAGCGCAACGCGCGGCACACA 6 103 0 GCGCGTACCGCCCTGGTACGCCGGAAGCGCA 6 117 0 ATCCTGAGTGCTGTGAGGCGCTCGCGCGTAC 6 140 0 TATGAAATAGGAGCAGGACGCG 7 22 1 GTGCGTGTAGGCATACGGCGCAAACGTGAAG 8 36 0 GTATGCCTACACGCACCGCGCGGGGCGCATT 8 51 1 ATCAAGAGAACTGTAGCGCGCCGTGGGAAAG 8 103 1 ACAGAGGGTCCAGTGGCGTGATAGGGACACC 8 144 1 * ********* MAP Score: 9.52685 Motif 11 TCTTCGGGGCTGTGCTTTTAAAGTTCAGAAAAGTTTTGAGCAA 0 60 1 GTTTTTTGGGTGTGCACTTGTTCAAGTTCAGAGGTGATGTTG 2 22 1 AAAACCTGTCTGTGCAATCAACCGCGTGAAGCGGCATCCTGCG 5 20 1 CAGGGATGCTTGCGCCCCGGAGGGGGATGTGCGATAATCGGCC 5 127 1 TGTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 154 1 AGCTGGGCCGTGCGCGCATGTCCGCGTCGGCCGTTC 6 3 1 TGCCGCGCGTTGCGCTTCCGGCGTACCAGGGCGGTACGCGCGA 6 107 1 TCTTCACGTTTGCGCCGTATGCCTACACGCACCGCGCGGGGCG 8 35 1 GAAAGGGAGGTATGCACAGAGGGTCCAGTGGCGTGATAGGGAC 8 129 1 ** ** * * * *** MAP Score: 8.85809 Motif 12 GTTTTTTGGGTGTGCACTTGTTCAAGTTCAGAGGTGATGTTG 2 22 1 CGAATCCTACCGTCCCAGTTTGCGGCGTGTTCGCTTTCTGTGC 4 73 1 AAAACCTGTCTGTGCAATCAACCGCGTGAAGCGGCATCCTGCG 5 20 1 CAGGGATGCTTGCGCCCCGGAGGGGGATGTGCGATAATCGGCC 5 127 1 CGGAGGGGGATGTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 144 1 AGCTGGGCCGTGCGCGCATGTCCGCGTCGGCCGTTCTAGTTCG 6 10 1 CACAGGGGCACGCGAACTAGAACGGCCGACGCGGACATGCGCG 6 22 0 CCGCAAATACCGCGCGTGTGTGCCGCGCGTTGCGCTTCCGGCG 6 87 1 TGCCGCGCGTTGCGCTTCCGGCGTACCAGGGCGGTACGCGCGA 6 107 1 GTGAGGCGCTCGCGCGTACCGCCCTGGTACGCCGGAAGCGCAA 6 116 0 TCTTCACGTTTGCGCCGTATGCCTACACGCACCGCGCGGGGCG 8 35 1 CTACACGCACCGCGCGGGGCGCATTCTATACATTTCCTTTTGA 8 57 1 AGAACTGTAGCGCGCCGTGGGAAAGGGAGGTATGCACAGAGGG 8 109 1 AAGGGAGGTATGCACAGAGGGTCCAGTGGCGTGATAGGGACAC 8 131 1 ***** * * * * * MAP Score: 7.0876 Motif 13 TGTTTTTTGGGTGTGCACTTGTTCAAGTTCAGAGGTGATGTT 2 21 1 CCAGTTTGCGGCGTGTTCGCTTTCTGTGCATGGAGGATTGGA 4 87 1 GTGCAATCAACCGCGTGAAGCGGCATCCTGCGTGGTAGGAAG 5 31 1 TCCCCCTCCGGGGCGCAAGCATCCCTGTGAGGCCCTGAAAAT 5 112 0 GGAGGGGGATGTGCGATAATCGGCCCCCGGGGAGGGCGAGCG 5 145 1 AGCTGGGCCGTGCGCGCATGTCCGCGTCGGCCGTTCTAG 6 7 1 GTTCTAGTTCGCGTGCCCCTGTGCCCGCAATGGTTGCTTTGT 6 42 1 TCCGCAAATACCGCGCGTGTGTGCCGCGCGTTGCGCTTCCGG 6 86 1 GTTGCGCTTCCGGCGTACCAGGGCGGTACGCGCGAGCGCCTC 6 115 1 TGTATAGAATGCGCCCCGCGCGGTGCGTGTAGGCATACGGCG 8 47 0 GAGAACTGTAGCGCGCCGTGGGAAAGGGAGGTATGCACAGAG 8 108 1 ****** * * * * MAP Score: 1.63383