AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_operons023_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944239753 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0278 127 T. pallidum predicted coding region TP0278 #1 TP0279 45 ribosomal protein S1 (rpsA) #2 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #3 TP0284 104 T. pallidum predicted coding region TP0284 #4 TP0289 22 T. pallidum predicted coding region TP0289 #5 TP0290 54 conserved hypothetical protein #6 TP0291 36 T. pallidum predicted coding region TP0291 #7 TP0296 85 conserved hypothetical protein #8 TP0298 132 exported protein (tpn38b) #9 TP0319 28 membrane lipoprotein (tmpC) #10 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) Motif 1 AGAGGGCAGTGCTTTTTTAGGG 6 1 1 CTGAACACTTGAGGACGGTGCGTGTTTGACG 7 51 1 GAGTGATCTTCGGGGCTGTGCTTTTAAAGTT 3 54 1 TCCATGTGGGGAAGGGAGTGCGCTGGTGATC 0 51 1 AGCGTTCGCGCCGTGCGGTGCGCACGTTGTG 2 17 1 CAATGCGTTTGGGGGCAGGGGTGAGGAGTAG 8 35 1 TAATGAACTTGAGGGAGGGGCT 10 63 1 CTCCTTCTCTCTGGGTGGTGCAATGCGTTTG 8 15 1 CGACCCGCCCGTGGTCAGTGGGTATGGGGAC 10 26 1 TCCCTCTCTCGCGTAGGGTGCACCCTACCGG 8 93 0 GGGATTTTTGGGGGGAGGTGTT 8 120 1 AGGAGTTGACGGAGTGGGTGCGAATATAAAT 2 93 1 AGTGGGGCGTGTGTCTCGACCC 10 1 1 GTCTTCCTCGGAAGACTGTGGCAAATAAGCG 0 16 1 TCTGGTCTTTTCAGGCTGTGGGTGCCGGTAG 8 69 1 TAGCTAGGAAGCGTAGAGAGCTCGCGTGAAC 2 48 1 TTTGTCGATAAAGGGGGGAGGATTCTT 9 11 1 CAACGTGAGGGGTTGCCGTGC 2 166 1 CGTGTTGTTTTTTGGGTGTGCACTTGTTCAA 5 16 1 * ********* MAP Score: 25.1601 Motif 2 GGCAAATAAGCGGCAGTCCATGTGGGGAAGGGAGTGCGCTGG 0 35 1 GAGGAGAAGCGTTCGCGCCGTGCGGTGCGCAC 2 0 1 GCGCCGTGCGGTGCGCACGTTGTGTAGCTAGGAAGCGTAGAG 2 24 1 AATATAAATAGTGCTGCCTGTTTTTTGTGTAGTTCGCCGCAT 2 115 1 ATTGCATGAGCTGAGTATGTGATGATTCTTTTTCTCACT 3 7 1 GTGATCTTCGGGGCTGTGCTTTTAAAGTTCAGAAAAGTTTTG 3 56 1 AGTTGCCGTGTTGTTTTTTGGGTGTGCACTTGTTCA 5 4 1 AGAGGGCAGTGCTTTTTTAGGGAAAAGGAAGATCG 6 3 1 ACACTTGAGGACGGTGCGTGTTTGACGTTACGCTCTCGCT 7 55 1 TCTCTGGGTGGTGCAATGCGTTTGGGGGCAGGGGTGAGGAGT 8 22 1 GAGGAGTAGTGCTCTGGTCTTTTCAGGCTGTGGGTGCCGGTA 8 57 1 CCCTACGCGAGAGAGGGATTTTTGGGGGGAGGTGTT 8 106 1 AGTGGGGCGTGTGTCTCGACCCGCCCGTGGTCA 10 1 1 CGACCCGCCCGTGGTCAGTGGGTATGGGGACGTCCAGTAATG 10 26 1 * ** * * *** * * MAP Score: 24.0158 Motif 3 GCAAATAAGCGGCAGTCCATGTGGGGAAGGGAGTGCGCTGG 0 36 1 GAAAAACGAAGAAGGGAAGTACAGGGCAGAAAACGGAAG 1 8 0 CCGATTTTCCGCGAGGAGTTGACGGAGTGGGTGCGAATATA 2 80 1 CTCACTCGGTTGAGTGATCTTCGGGGCTGTGCTTTTAAAGT 3 43 1 AGTTGCCGTGTTGTTTTTTGGGTGTGCACTTGTTCA 5 5 1 TCTGGGTGGTGCAATGCGTTTGGGGGCAGGGGTGAGGAGTA 8 24 1 AGGAGTAGTGCTCTGGTCTTTTCAGGCTGTGGGTGCCGGTA 8 58 1 CCCTACGCGAGAGAGGGATTTTTGGGGGGAGGTGTT 8 106 1 GTTTGTCGATAAAGGGGGGAGGATTCTT 9 0 1 CCCGCCCGTGGTCAGTGGGTATGGGGACGTCCAGTAATGAA 10 29 1 GGGACGTCCAGTAATGAACTTGAGGGAGGGGCT 10 52 1 * ** * **** * * MAP Score: 22.6833 Motif 4 TACTCCTCACCCCTGCCCCCAAACGCATTGCA 8 33 0 AACACCTCCCCCCAAAAATCCCTC 8 118 0 AGCCCCTCCCTCAAGTTCATTACT 10 61 0 CCAGCGCACTCCCTTCCCCACATGGACTGCCG 0 45 0 ACTTTAAAAGCACAGCCCCGAAGATCACTCAA 3 52 0 CGGGTCGAGACACACGCCCCACT 10 1 0 GGGCGTGTGTCTCGACCCGCCCGTGGTCAGTG 10 14 1 TACTGGACGTCCCCATACCCACTGACCACGGG 10 33 0 GTCAAACACGCACCGTCCTCAAGTGTTCAGAA 7 49 0 TCCATCATCCGCCCATGAGTGTTC 0 113 0 GGTGCACCCTACCGGCACCCACAGCCTGAAAA 8 76 0 AAGAATCCTCCCCCCTTTATCGACA 9 13 0 CCCCCAAACGCATTGCACCACCCAGAGAGAAG 8 18 0 GCGATCTTCCTTTTCCCTAAAAAAGCACTG 6 16 0 AGACCAGAGCACTACTCCTCACCCCTGCCCCC 8 45 0 TATATTCGCACCCACTCCGTCAACTCCTCGCG 2 89 0 GTGCGCACCGCACGGCGCGAACGCTTCTCCTC 2 10 0 TAGTTCGCCGCATGTTCCTGAACAACGTGAGG 2 144 1 GCACGGCAACCCCTCACGTTGTT 2 164 0 CCGTTTTCTGCCCTGTACTTCCCTTCTTCGTT 1 13 1 *** ******* MAP Score: 18.8943 Motif 5 CCGATTTTCCGCGAGGAGTTGACGGAGTGGGTGCGAATATAAATA 2 80 1 GAGGAGAAGCGTTCGCGCCGTGCGGTGCGCACGTTGTG 2 3 1 CGCACGTTGTGTAGCTAGGAAGCGTAGAGAGCTCGCGTGAACACC 2 37 1 GTGGGTGCCGGTAGGGTGCACCCTACGCGAGAGAGGGATTTTTGG 8 86 1 AAGCGGCAGTCCATGTGGGGAAGGGAGTGCGCTGGTGATCAGACA 0 42 1 GGTGCAATGCGTTTGGGGGCAGGGGTGAGGAGTAGTGCTCTGGTC 8 31 1 GCACATTCTGAACACTTGAGGACGGTGCGTGTTTGACGTTACGCT 7 44 1 TTTTCTCACTCGGTTGAGTGATCTTCGGGGCTGTGCTTTTAAAGT 3 39 1 CCATCATCCGCCCATGAGTGTTCTGAGACTGTTTGCGCTCCTCGT 0 91 0 AGTTGCCGTGTTGTTTTTTGGGTGTGCACTTGTTCAAGTTCA 5 7 1 TCTTTCTCCTTCTCTCTGGGTGGTGCAATGCGTTTG 8 1 1 GAGTAGTGCTCTGGTCTTTTCAGGCTGTGGGTGCCGGTAGGGTGC 8 60 1 GTCCCCATACCCACTGACCACGGGCGGGTCGAGACACACGCCCCA 10 12 0 GCGCTCGTCTTCCTCGGAAGACTGTGGCAAATAAGCGG 0 3 1 * * * ** * * * * * MAP Score: 10.9707 Motif 6 TGGGGAAGGGAGTGCGCTGGTGATCAGACA 0 57 1 TCCGCCCATGAGTGTTCTGAGACTGTTTGC 0 100 0 ACGAAGAAGGGAAGTACAGGGCAGAAAACG 1 14 0 CGCGCCGTGCGGTGCGCACGTTGTGTAGCT 2 23 1 GTAGCTAGGAAGCGTAGAGAGCTCGCGTGA 2 47 1 GCGGAAAATCGGTGTTCACGCGAGCTCTCT 2 62 0 TTTTCCGCGAGGAGTTGACGGAGTGGGTGC 2 84 1 CTGAACTTTAAAAGCACAGCCCCGAAGATC 3 58 0 CTGTGCTTTTAAAGTTCAGAAAAGTTTTGA 3 69 1 ATTACTTCAGCGTACTGCACCA 4 8 1 AACTTGAACAAGTGCACACCCAAAAAACAA 5 20 0 TTTCCCTAAAAAAGCACTGCCCTCT 6 5 0 AGGAATATCGGGTGTTCAGCACATTCTGAA 7 26 1 ACCGTCCTCAAGTGTTCAGAATGTGCTGAA 7 40 0 GGTGAGGAGTAGTGCTCTGGTCTTTTCAGG 8 54 1 ********** MAP Score: 9.38362 Motif 7 CGGCAGTCCATGTGGGGAAGGGAGTGCGCTGGTGATCA 0 45 1 GAGGAGAAGCGTTCGCGCCGTGCGGTGCGCACGTTGTG 2 10 1 TGTGTAGCTAGGAAGCGTAGAGAGCTCGCGTGAACACC 2 44 1 AACACCGATTTTCCGCGAGGAGTTGACGGAGTGGGTGC 2 76 1 CTCGGTTGAGTGATCTTCGGGGCTGTGCTTTTAAAGTT 3 47 1 AGAGGGCAGTGCTTTTTTAGGGAAAAGGAAGATCGC 6 10 1 GAACACTTGAGGACGGTGCGTGTTTGACGTTACGCTCT 7 53 1 GGTGGTGCAATGCGTTTGGGGGCAGGGGTGAGGAGTAG 8 28 1 GGGGCAGGGGTGAGGAGTAGTGCTCTGGTCTTTTCAGG 8 46 1 TCTGGTCTTTTCAGGCTGTGGGTGCCGGTAGGGTGCAC 8 69 1 AAAATCCCTCTCTCGCGTAGGGTGCACCCTACCGGCAC 8 90 0 ACGCGAGAGAGGGATTTTTGGGGGGAGGTGTT 8 110 1 CGTCCAGTAATGAACTTGAGGGAGGGGCT 10 56 1 ** * * *** * ** MAP Score: 5.81711 Motif 8 TTGCCACAGTCTTCCGAGGAAGACGAGCGC 0 1 0 TGTGGCAAATAAGCGGCAGTCCATGTGGGGAAGGGAGTG 0 32 1 GCTGGTGATCAGACAACAGACGAGGAGCGCAAACAGTCT 0 72 1 GGTGAAAAACGAAGAAGGGAAGTACAGGGCAGAAAACGG 1 13 0 GAGGAGAAGCGTTCGCGCCGTGCGGTGCGCACGT 2 5 1 GTAGCTAGGAAGCGTAGAGAGCTCGCGTGAACACCGATT 2 47 1 GATTTTCCGCGAGGAGTTGACGGAGTGGGTGCGAATATA 2 82 1 TAACGTCAAACACGCACCGTCCTCAAGTGTTCAGAATGT 7 46 0 CTCTCTGGGTGGTGCAATGCGTTTGGGGGCAGGGGTGAG 8 21 1 GTAGTGCTCTGGTCTTTTCAGGCTGTGGGTGCCGGTAGG 8 62 1 GTGGGTGCCGGTAGGGTGCACCCTACGCGAGAGAGGGAT 8 86 1 TCGACCCGCCCGTGGTCAGTGGGTATGGGGACGTCCAGT 10 25 1 ATGGGGACGTCCAGTAATGAACTTGAGGGAGGGGCT 10 49 1 * * * * ** * *** MAP Score: 4.98819 Motif 9 GCGCTCGTCTTCCTCGGAAGACTGTGGCAAAT 0 0 1 CTGATCACCAGCGCACTCCCTTCCCCACATGGACTGCCGCTT 0 42 0 AACGTGCGCACCGCACGGCGCGAACGCTTCTCCTC 2 3 0 CACCGATTTTCCGCGAGGAGTTGACGGAGTGGGTGCGAATAT 2 78 1 GTGTAGTTCGCCGCATGTTCCTGAACAACGTGAGGGGTTGCC 2 141 1 AGTTGCCGTGTTGTTTTTTGGGTGTGCACTTGTTCAA 5 5 1 TCAGCGCAAGATACGCAGGAATATCGGGTGTTCAG 7 3 1 CAAACACGCACCGTCCTCAAGTGTTCAGAATGTGCTGAACAC 7 37 0 TGAGGACGGTGCGTGTTTGACGTTACGCTCTCGCT 7 60 1 GTGGTGCAATGCGTTTGGGGGCAGGGGTGAGGAGTAGTGCTC 8 29 1 GTGAGGAGTAGTGCTCTGGTCTTTTCAGGCTGTGGGTGCCGG 8 55 1 TCCCTCTCTCGCGTAGGGTGCACCCTACCGGCACCCACAGCC 8 82 0 GTGTCTCGACCCGCCCGTGGTCAGTGGGTATGGGGACGTCCA 10 20 1 TGGGGACGTCCAGTAATGAACTTGAGGGAGGGGCT 10 50 1 **** * * ** ** MAP Score: 4.05775 Motif 10 TCCATCATCCGCCCATGAGTGTTCTG 0 111 0 ACAACGTGCGCACCGCACGGCGCGAACGCT 2 17 0 ACTCCGTCAACTCCTCGCGGAAAATCGGTG 2 78 0 GCACGGCAACCCCTCACGTTGTTCAGGAA 2 158 0 TCACCCCTGCCCCCAAACGCATTGCACCAC 8 29 0 CAGAGCACTACTCCTCACCCCTGCCCCCAA 8 43 0 GGTGCACCCTACCGGCACCCACAGCCTGAA 8 78 0 CAAAAATCCCTCTCTCGCGTAGGGTGCACC 8 100 0 AACACCTCCCCCCAAAAATCCC 8 120 0 AAGAATCCTCCCCCCTTTATCGAC 9 14 0 GTGTGTCTCGACCCGCCCGTGGTCAGTGGG 10 18 1 AGCCCCTCCCTCAAGTTCATTACTGG 10 59 0 ********** MAP Score: 3.41468 Motif 11 GCGCTCGTCTTCCTCGGAAGACTGTGGCAAATAAG 0 8 1 AGCGGCAGTCCATGTGGGGAAGGGAGTGCGCTGGTGA 0 43 1 TCAGAACACTCATGGGCGGATGATGGA 0 110 1 GAGGAGAAGCGTTCGCGCCGTGCGGTGCGCACGTTG 2 9 1 ACCGATTTTCCGCGAGGAGTTGACGGAGTGGGTGCGA 2 79 1 GCCGCATGTTCCTGAACAACGTGAGGGGTTGCCGTGC 2 150 1 ATTGCATGAGCTGAGTATGTGATGATTCTTT 3 4 1 ATTCTGAACACTTGAGGACGGTGCGTGTTTGACGTTA 7 48 1 TCTTTCTCCTTCTCTCTGGGTGGTGCAATGCGTT 8 7 1 TGGTGCAATGCGTTTGGGGGCAGGGGTGAGGAGTAGT 8 30 1 AGTGCTCTGGTCTTTTCAGGCTGTGGGTGCCGGTAGG 8 64 1 GTAGGGTGCACCCTACGCGAGAGAGGGATTTTTGGGG 8 96 1 GAGAGAGGGATTTTTGGGGGGAGGTGTT 8 114 1 GGGCGTGTGTCTCGACCCGCCCGTGGTCAGTGGGTAT 10 14 1 * ** ** * * *** MAP Score: 0.77612 Motif 12 CACCAGCGCACTCCCTTCCCCACATGGACTG 0 48 0 ACGTGCGCACCGCACGGCGCGAACGCTTCTC 2 13 0 TTTATATTCGCACCCACTCCGTCAACTCCTC 2 92 0 GCACGGCAACCCCTCACGTTGTTCAGG 2 160 0 AACTTTAAAAGCACAGCCCCGAAGATCACTC 3 54 0 TTTCCCTAAAAAAGCACTGCCCTCT 6 4 0 TAACGTCAAACACGCACCGTCCTCAAGTGTT 7 54 0 CTACTCCTCACCCCTGCCCCCAAACGCATTG 8 35 0 ACCCTACCGGCACCCACAGCCTGAAAAGACC 8 72 0 AACACCTCCCCCCAAAAATCCCT 8 119 0 AAGAATCCTCCCCCCTTTATCGACA 9 13 0 CGGGTCGAGACACACGCCCCACT 10 2 0 GGGCGTGTGTCTCGACCCGCCCGTGGTCAGT 10 14 1 TACTGGACGTCCCCATACCCACTGACCACGG 10 34 0 AGCCCCTCCCTCAAGTTCATTA 10 63 0 ***** ***** MAP Score: 0.358818