AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_operons020_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944239679 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0010 300 T. pallidum predicted coding region TP0010 #1 TP0011 33 tpr protein B (tprB) #2 TP0015 190 phenylalanyl-tRNA synthetase beta subunit (pheT) #3 TP0848 32 ribosomal protein L20 (rplT) #4 TP0849 52 ribosomal protein L35 (rpmI) #5 TP0850 162 translation initiation factor 3 (infC) #6 TP0973 87 phenylalanyl-tRNA synthetase alpha subunit (pheS) Motif 1 GGGGTTCTCTCGCACAGTGCCGGTTGC 0 0 1 GCACAGTGCCGGTTGCCCCAAGCGGTGCTACGGGTAG 0 21 1 CGGGTAGCACGAAGTTCGCCTTCGCGCCTAAGTTAAT 0 51 1 AATGGTGACGGCCGGGCTCGCGTGCAGACGCGATACG 0 115 1 ACGCGATACGGTAGCGCGCCCTCGGAGTAAAAGTATA 0 142 1 CGGTACTTATGCCGTGCGCATATGAGCGCTCAGTTTA 2 29 1 TGACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGCA 2 84 1 ACGGTGTGGTGGCTGGCCCTTGTGGTGTCCTTTTTTT 2 133 1 TTGACCGTATACTGAGCACGGTCGGAGGGCTC 2 168 1 CTCCCTTTTGGATGCCCACTATAGGTGGTGAATTTTT 5 11 1 GACATATTAGGAATGGCTAGATTGGGGCCCAGTCTTG 5 111 1 CACTACGGCAGATGTACCCTGATGCAGAACGAAAAAT 6 21 1 * * ** * **** * MAP Score: 15.1262 Motif 2 GGGGTTCTCTCGCACAGTGCCGGTTGCCCCAAGCGGTGCT 0 5 1 AGTAAGACGAGTACTCCCCGAAATGGTGACGGCCGGGCTCGCGTG 0 94 1 GGGCTCGCGTGCAGACGCGATACGGTAGCGCGCCCTCGGAGTAAA 0 128 1 AGTGTACCGTGTTTTCACCACAGTTTAGTACAACGATGTCATGTG 0 217 1 TCATGCCTTTGTGCGCACGGTACTTATGCCGTGCGCATATGAGCG 2 12 1 GCGCATATGAGCGCTCAGTTTAAGAGTGTTACGCGTATTATGACT 2 44 1 GGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCTTGTGGTGTC 2 117 1 TTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC 2 164 1 GTGGCAAGCGTGAGAGGACGGAGGAGCGTGGT 3 3 1 CTATTTCTCCACACTACGGCAGATGTACCCTGATGCAGA 6 4 1 ** * * * * * * ** MAP Score: 8.75897 Motif 3 GCAACCGGCACTGTGCGAGAGAACCCC 0 0 0 CTACCCGTAGCACCGCTTGGGGCAACCGGCACTGTGC 0 21 0 ATTAACTTAGGCGCGAAGGCGAACTTCGTGCTACCCG 0 51 0 CGTATCGCGTCTGCACGCGAGCCCGGCCGTCACCATT 0 115 0 CGTGCAGACGCGATACGGTAGCGCGCCCTCGGAGTAA 0 135 1 ATGTATGTTGGTGTACATTAGATATTC 0 283 1 TAAGTACCGTGCGCACAAAGGCATGAGC 2 1 0 TTTGTGCGCACGGTACTTATGCCGTGCGCATATGAGC 2 19 1 TGCCACTACACGGCACACGTGCTCTACACTTTAGTCA 2 84 0 GTGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCC 2 115 1 AAAAAAAGGACACCACAAGGGCCAGCCACCACACCGT 2 133 0 ACCGTATACTGAGCACGGTCGGAGGGCTC 2 171 1 ACGCTCCTCCGTCCTCTCACGCTTGCCAC 3 2 0 CCTTTTGGATGCCCACTATAGGTGGTGAATTTTTACA 5 14 1 CAAGACTGGGCCCCAATCTAGCCATTCCTAATATGTC 5 111 0 TTGTTTTTTAGCGTGCATTAGAAGTGG 5 145 1 TATTTCTCCACACTACGGCAGATGTACCCTGATGCAG 6 11 1 * ***** ** * * MAP Score: 8.43134 Motif 4 GGGGTTCTCTCGCACAGTGCCGGTTGCCCCAAGCGG 0 1 1 CACGAAGTTCGCCTTCGCGCCTAAGTTAATGCCCCAAGTAAGACG 0 58 1 AGTAAGACGAGTACTCCCCGAAATGGTGACGGCCGGGCTCGCGTG 0 94 1 TCATGCCTTTGTGCGCACGGTACTTATGCCGTGCGCATATGAGCG 2 12 1 GTGCGCATATGAGCGCTCAGTTTAAGAGTGTTACGCGTATTATGA 2 42 1 CCGTGTAGTGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCT 2 108 1 TTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC 2 164 1 TCTCCCTTTTGGATGCCCACTATAGGTGGTGAATTTTTACATGTA 5 10 1 CTATTTCTCCACACTACGGCAGATGTACCCTGATGCAGA 6 4 1 AACGTATTTTCGCGCCGTTTAGATGTAGGCTGTTTCTCAATT 6 55 0 * * * * * * * * ** MAP Score: 5.7989 Motif 5 ACCGCTTGGGGCAACCGGCACTGTGCGAGAGAACCCC 0 10 0 CGAACTTCGTGCTACCCGTAGCACCGCTTGGGGCAAC 0 32 0 TCCCCGAAATGGTGACGGCCGGGCTCGCGTGCAGACG 0 108 1 CGTGCAGACGCGATACGGTAGCGCGCCCTCGGAGTAA 0 135 1 CTAGACGCATGCATACAGTAGTGTACCGTGTTTTCAC 0 198 1 ATGCCTTTGTGCGCACGGTACTTATGCCGTGCGCATA 2 14 1 GAGGATGCCACTACACGGCACACGTGCTCTACACTTT 2 89 0 ACCGTATACTGAGCACGGTCGGAGGGCTC 2 171 1 ATCCAACAACACGAACTGCAGTTACCCGACACTCCA 4 9 0 TATTTCTCCACACTACGGCAGATGTACCCTGATGCAG 6 11 1 * ******* ** MAP Score: 5.56649 Motif 6 TTGGGGCAACCGGCACTGTGCGAGAGAACCCC 0 1 0 GAAATGGTGACGGCCGGGCTCGCGTGCAGACGCGATACGGT 0 113 1 GCGTGCAGACGCGATACGGTAGCGCGCCCTCGGAGTAAAAG 0 134 1 GCTCATGCCTTTGTGCGCACGGTACTTATGCC 2 1 1 CGGTACTTATGCCGTGCGCATATGAGCGCTCAGTTTAAGAG 2 29 1 TATGACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGCATC 2 82 1 GTGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCTTGT 2 115 1 GAGCCCTCCGACCGTGCTCAGTATACGGTCA 2 169 0 GTGGCAAGCGTGAGAGGACGGAGGAGCGTGG 3 0 1 * * * * * * ** * * MAP Score: 4.73084 Motif 7 GTTGCCCCAAGCGGTGCTACGGGTAGCACGAAGTTCGCCT 0 32 1 ACGAGTACTCCCCGAAATGGTGACGGCCGGGCTCGCGTGC 0 100 1 GCGTGCAGACGCGATACGGTAGCGCGCCCTCGGAGTAAAA 0 134 1 GCTCATGCCTTTGTGCGCACGGTACTTATGC 2 1 1 CGGTACTTATGCCGTGCGCATATGAGCGCTCAGTTTAAGA 2 29 1 TATGACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGCAT 2 82 1 GTGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCTTG 2 115 1 CTTTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC 2 162 1 GTGGCAAGCGTGAGAGGACGGAGGAGCGTG 3 0 1 TGGAGTGTCGGGTAACTGCAGTTCGTGTTGTT 4 2 1 CTAATATGTCATGTCAAGTAAACATGCAGGAAATCACCAT 5 81 0 TTGAGAAACAGCCTACATCTAAACGGCGCGAAAATACGTT 6 57 1 *** ** * ** ** MAP Score: 2.60983 Motif 8 GGGGTTCTCTCGCACAGTGCCGGTTGCCCCAAGCGG 0 1 1 TGCCCCAAGCGGTGCTACGGGTAGCACGAAGTTCGCCTTCGCGCC 0 34 1 AGTAAGACGAGTACTCCCCGAAATGGTGACGGCCGGGCTCGCGTG 0 94 1 GTGACGGCCGGGCTCGCGTGCAGACGCGATACGGTAGCGCGCCCT 0 119 1 CCGTGTAGTGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCT 2 108 1 TTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC 2 164 1 GTGGCAAGCGTGAGAGGACGGAGGAGCGTGGT 3 2 1 TGGAGTGTCGGGTAACTGCAGTTCGTGTTGTTGGATAAAGGGGA 4 9 1 TCTCCCTTTTGGATGCCCACTATAGGTGGTGAATTTTTACATGTA 5 10 1 ATGTAAATAAGGAATTGGGGTTGTGATGGGGATGGTGATTTCCTG 5 50 1 TCCACACTACGGCAGATGTACCCTGATGCAGAACGAAAAATTGAG 6 17 1 ** * * * ** * ** MAP Score: 1.5505 Motif 9 CACAGTGCCGGTTGCCCCAAGCGGTGCTACGGGT 0 22 1 GTAGCACGAAGTTCGCCTTCGCGCCTAAGTTAAT 0 54 1 TCCCCGAAATGGTGACGGCCGGGCTCGCGTGCAG 0 108 1 CGCGCTACCGTATCGCGTCTGCACGCGAGCCCGG 0 126 0 CGATACGGTAGCGCGCCCTCGGAGTAAAAGTATA 0 145 1 TACTTATGCCGTGCGCATATGAGCGCTCAGTTTA 2 32 1 GACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGG 2 85 1 CGGTGTGGTGGCTGGCCCTTGTGGTGTCCTTTTT 2 134 1 ACCGTATACTGAGCACGGTCGGAGGGCTC 2 171 1 GCAAGCGTGAGAGGACGGAGGAGCGTGGT 3 13 1 * ****** * ** MAP Score: 1.28545 Motif 10 GGGTTCTCTCGCACAGTGCCGGTTGCCCCAAGCGGTGCTACGGGT 0 11 1 CGGTGCTACGGGTAGCACGAAGTTCGCCTTCGCGCCTAAGTTAAT 0 43 1 CTCCCCGAAATGGTGACGGCCGGGCTCGCGTGCAGACGCGATACG 0 107 1 GCGTGCAGACGCGATACGGTAGCGCGCCCTCGGAGTAAAAGTATA 0 134 1 TGTGCGCACGGTACTTATGCCGTGCGCATATGAGCGCTCAGTTTA 2 21 1 TGACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGCATCCTCTGC 2 84 1 GGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCTTGTGGTGTC 2 117 1 TCCTTTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC 2 160 1 GTGGCAAGCGTGAGAGGACGGAGGAGCGTGGT 3 2 1 * * * ** * * * ** MAP Score: 0.832607