AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_fusions003_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944238369 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0314 22 T. pallidum predicted coding region TP0314 #1 TP0315 300 T. pallidum predicted coding region TP0315 #2 TP0617 95 T. pallidum predicted coding region TP0617 #3 TP0618 55 T. pallidum predicted coding region TP0618 #4 TP0620 57 tpr protein I (tprI) #5 TP0621 59 tpr protein J (tprJ) Motif 1 GCGGCTAGACGGGTGGGGGGGGTGAGGTAGAA 4 16 1 CTACTAGACAGGGCCGGGGGGGGGGGTGAGGT 5 34 1 AGCGCCCAGTGGGAACAGGGGGTGCTTGCTGA 1 200 1 TTAGAAAAGAAGGGTGAGGGGGCTACTAGACA 5 12 1 GGGAGGCGCCGGGAGGAACGGGTCCTGTCGAA 3 10 1 AGGTAGAAGTGAGAGGAGGGGGAGTGA 4 40 1 GAAGAATTGCGGGGAGGAGTGAAGGT 3 39 1 TTTATCTGTGGGGTGAAGGTGGT 1 287 1 GCCGGGGGGGGGGGTGAGGTAGC 5 46 1 ATTCTCGAGCGGGTGGGGCTTGCCCTCACGCT 1 112 1 CGTATCTGTCGGTAGCGGCGGGTTTTGAGTGC 2 13 1 CCCTCATTGGGGGCCTGGATGGTGATGTAATG 2 69 0 CGTCAGCGTAGAGACGAGCGTACCGTCCTGCA 1 143 0 *** ******* MAP Score: 32.5624 Motif 2 GGGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA 4 35 1 CACGCGGCTAGACGGGTGGGGGGGGTGAGGTAGAAG 4 13 1 TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGACAGG 5 10 1 TCCTGTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 32 1 GGGGCTACTAGACAGGGCCGGGGGGGGGGGTGAGGT 5 30 1 GGGAGGCGCCGGGAGGAACGGGTCCTGT 3 2 1 ATACGTATCTGTCGGTAGCGGCGGGTTTTGAGTGCA 2 10 1 GAACCCTCATTGGGGGCCTGGATGGTGATGTAATGG 2 68 0 ACGTTTATCTGTGGGGTGAAGGTGGT 1 284 1 TTGAATTTTTGCTGGGACAGATGGCGGAGTCCTCGA 1 77 1 GAGTCCTCGATTCTCGAGCGGGTGGGGCTTGCCCTC 1 103 1 ATAGTGGAGCTCAGCGCCCAGTGGGAACAGGGGGTG 1 188 1 GTACCGTCCTGCAGCGTGAGGGCAAGCCCCACCCGC 1 120 0 CCTTACATGGGTATTGCCGAGAGTATGTGGTCTGAG 1 236 1 * * * * ** **** MAP Score: 25.2743 Motif 3 GAGAAGTTTGACAGCGCGTTCGATGCCCTCAGGGTGGAGCA 1 13 1 AGAATCGAGGACTCCGCCATCTGTCCCAGCAAAAATTCAAG 1 76 0 GTGAGGGCAAGCCCCACCCGCTCGAGAATCGAGGACTCCGC 1 100 0 GCAGGACGGTACGCTCGTCTCTACGCTGACGAAGGTTGCCA 1 144 1 TGGGCGCTGAGCTCCACTATCAGTGGCAACCTTCGTCAGCG 1 167 0 TGATAGTGGAGCTCAGCGCCCAGTGGGAACAGGGGGTGCTT 1 186 1 CACTCAAAACCCGCCGCTACCGACAGATACGTAT 2 3 0 GGTTTTGAGTGCACTGCGCTCATCTACGACAGCTACCATTA 2 33 1 AGCTACCATTACATCACCATCCAGGCCCCCAATGAGGGTTC 2 63 1 TCGACAGGACCCGTTCCTCCCGGCGCCTCCC 3 0 0 ACCTTCACTCCTCCCCGCAATTCTTCGACAGGACCCGTTC 3 25 0 TTCTACCTCACCCCCCCCACCCGTCTAGCCGCGTGTGA 4 7 0 TCACTCCCCCTCCTCTCACTTCTACCTCACCCCCCCCAC 4 28 0 CTAGTAGCCCCCTCACCCTTCTTTTCTAACA 5 0 0 ACCCCCCCCCCCGGCCCTGTCTAGTAGCCCCCTCACCCTTC 5 20 0 ** ** ** * * ** MAP Score: 23.9829 Motif 4 ACAGCGCGTTCGATGCCCTCAGGGTGGAGCAATACCGTGTA 1 23 1 CGGAGTCCTCGATTCTCGAGCGGGTGGGGCTTGCCCTCACG 1 101 1 GCTGACGAAGGTTGCCACTGATAGTGGAGCTCAGCGCCCAG 1 168 1 GTGGAGCTCAGCGCCCAGTGGGAACAGGGGGTGCTTGCTGA 1 191 1 TACTTTGGCACGTTTATCTGTGGGGTGAAGGTGGT 1 275 1 ATACGTATCTGTCGGTAGCGGCGGGTTTTGAGTGC 2 4 1 GGGAGGCGCCGGGAGGAACGGGTCCTGTCGAA 3 1 1 CGGGTCCTGTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 28 1 TCACACGCGGCTAGACGGGTGGGGGGGGTGAGGTAG 4 5 1 TGGGGGGGGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA 4 29 1 TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGACAGG 5 5 1 GGGTGAGGGGGCTACTAGACAGGGCCGGGGGGGGGGGTGAG 5 23 1 TACTAGACAGGGCCGGGGGGGGGGGTGAGGTAGC 5 35 1 * * *** ***** MAP Score: 19.1287 Motif 5 CATGGGTATTGCCGAGAGTATGTGGTCTGAGCGT 1 241 1 GTCGGTAGCGGCGGGTTTTGAGTGCACTGCGCTC 2 20 1 GGGAGGCGCCGGGAGGAACGGGTCCTGTCGAAGA 3 10 1 GTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 36 1 CACGCGGCTAGACGGGTGGGGGGGGTGAGGTAGA 4 13 1 GGTGGGGGGGGTGAGGTAGAAGTGAGAGGAGGGG 4 27 1 GTAGAAGTGAGAGGAGGGGGAGTGA 4 42 1 TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGACA 5 10 1 ACTAGACAGGGCCGGGGGGGGGGGTGAGGTAGC 5 36 1 * **** ***** MAP Score: 13.5863 Motif 6 CTGAGGGCATCGAACGCGCTGTCAAACTTCT 1 14 0 GAGGACTCCGCCATCTGTCCCAGCAAAAATT 1 80 0 GAGGGCAAGCCCCACCCGCTCGAGAATCGAG 1 108 0 GCGGGTGGGGCTTGCCCTCACGCTGCAGGAC 1 120 1 TAGAGACGAGCGTACCGTCCTGCAGCGTGAG 1 136 0 TGATAGTGGAGCTCAGCGCCCAGTGGGAACA 1 186 1 CAGCAAGCACCCCCTGTTCCCACTGGGCGCT 1 200 0 GGGGTGCTTGCTGACGCTCCTTACATGGGTA 1 218 1 ACCACCTTCACCCCACAGATAAACGT 1 284 0 CACTCAAAACCCGCCGCTACCGACAGATACG 2 13 0 TCGTAGATGAGCGCAGTGCACTCAAAACCCG 2 31 0 CGCTCATCTACGACAGCTACCATTACATCAC 2 49 1 TACATCACCATCCAGGCCCCCAATGAGGGTT 2 72 1 CCGTTCCTCCCGGCGCCTCCC 3 0 0 CGCAATTCTTCGACAGGACCCGTTCCTCCCG 3 19 0 ACCTTCACTCCTCCCCGCAATTCTTCGACA 3 35 0 CTCACCCCCCCCACCCGTCTAGCCGCGTGTG 4 11 0 CTCACTTCTACCTCACCCCCCCCACCCGTCT 4 22 0 TCACTCCCCCTCCTCTCACTTCTACCT 4 40 0 TGTCTAGTAGCCCCCTCACCCTTCTTTTCTA 5 13 0 TCACCCCCCCCCCCGGCCCTGTCTAGTAGCC 5 32 0 GCTACCTCACCCCCCCCCCCGGCCCT 5 43 0 ** ******** MAP Score: 8.58426 Motif 7 ATTTTTGCTGGGACAGATGGCGGAGTCCTCGATT 1 81 1 ACCGTCCTGCAGCGTGAGGGCAAGCCCCACCCGC 1 120 0 TCACGCTGCAGGACGGTACGCTCGTCTCTACGCT 1 137 1 AGCGCCCAGTGGGAACAGGGGGTGCTTGCTGACG 1 200 1 CTCCTTACATGGGTATTGCCGAGAGTATGTGGTC 1 234 1 CGTTTATCTGTGGGGTGAAGGTGGT 1 285 1 ATACGTATCTGTCGGTAGCGGCGGGTTTTGAGT 2 9 1 GTGATGTAATGGTAGCTGTCGTAGATGAGCGCAG 2 46 0 CCTCATTGGGGGCCTGGATGGTGATGTAATGGTA 2 66 0 GGGAGGCGCCGGGAGGAACGGGTC 3 0 1 GGTCCTGTCGAAGAATTGCGGGGAGGAGTGAAGG 3 30 1 TCACACGCGGCTAGACGGGTGGGGGGGGTGAG 4 8 1 AGACGGGTGGGGGGGGTGAGGTAGAAGTGAGAGG 4 22 1 GTGAGGTAGAAGTGAGAGGAGGGGGAGTGA 4 37 1 TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGACA 5 10 1 GGGGGCTACTAGACAGGGCCGGGGGGGGGGGTGA 5 29 1 GGGCCGGGGGGGGGGGTGAGGTAGC 5 44 1 ** ** * ***** MAP Score: 5.93285 Motif 8 CTTGAATTTTTGCTGGGACAGATGGCGGAGTCCTCGAT 1 76 1 TCCTCGATTCTCGAGCGGGTGGGGCTTGCCCTCACGCT 1 106 1 AGCGCCCAGTGGGAACAGGGGGTGCTTGCTGACGCTCC 1 200 1 GGCACGTTTATCTGTGGGGTGAAGGTGGT 1 281 1 CGTATCTGTCGGTAGCGGCGGGTTTTGAGTGCACTGCG 2 13 1 GGGAGGCGCCGGGAGGAACGGGTCCTGTCGAA 3 4 1 GTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 36 1 TCACACGCGGCTAGACGGGTGGGGGGGGTGAGGT 4 6 1 CGGGTGGGGGGGGTGAGGTAGAAGTGAGAGGAGGGGGA 4 25 1 TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGA 5 4 1 GGGTGAGGGGGCTACTAGACAGGGCCGGGGGGGGGGGT 5 23 1 ACAGGGCCGGGGGGGGGGGTGAGGTAGC 5 41 1 ** * ** ** * ** MAP Score: 5.43891 Motif 9 GCTCCACCCTGAGGGCATCGAACGCGCTGTCAAA 1 19 0 AATTTTTGCTGGGACAGATGGCGGAGTCCTCGAT 1 80 1 GAGTCCTCGATTCTCGAGCGGGTGGGGCTTGCCC 1 103 1 TACCGTCCTGCAGCGTGAGGGCAAGCCCCACCCG 1 121 0 CCTTCGTCAGCGTAGAGACGAGCGTACCGTCCTG 1 145 0 TCAGCGCCCAGTGGGAACAGGGGGTGCTTGCTGA 1 198 1 GCACGTTTATCTGTGGGGTGAAGGTGGT 1 282 1 ATACGTATCTGTCGGTAGCGGCGGGTTTTGAGTG 2 10 1 AATGGTAGCTGTCGTAGATGAGCGCAGTGCACTC 2 39 0 CCCTCATTGGGGGCCTGGATGGTGATGTAATGGT 2 67 0 GGGAGGCGCCGGGAGGAACGGGTCCT 3 2 1 GTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 36 1 TCACACGCGGCTAGACGGGTGGGGGGGGTGA 4 7 1 CGGGTGGGGGGGGTGAGGTAGAAGTGAGAGGAGG 4 25 1 AGGTAGAAGTGAGAGGAGGGGGAGTGA 4 40 1 TAGAAAAGAAGGGTGAGGGGGCTACTAGACAGGG 5 13 1 GGGGCTACTAGACAGGGCCGGGGGGGGGGGTGAG 5 30 1 *** * ** *** * MAP Score: 4.16149 Motif 10 CGCGTTCGATGCCCTCAGGGTGGAGCAATACCG 1 27 1 ATTTTTGCTGGGACAGATGGCGGAGTCCTCGAT 1 81 1 GTCCTCGATTCTCGAGCGGGTGGGGCTTGCCCT 1 105 1 TGATAGTGGAGCTCAGCGCCCAGTGGGAACAGG 1 186 1 CGCCCAGTGGGAACAGGGGGTGCTTGCTGACGC 1 202 1 GTTTATCTGTGGGGTGAAGGTGGT 1 286 1 ACGTATCTGTCGGTAGCGGCGGGTTTTGAGTGC 2 12 1 GGTTTTGAGTGCACTGCGCTCATCTACGACAGC 2 33 1 TTGGGGGCCTGGATGGTGATGTAATGGTAGCTG 2 62 0 GGGAGGCGCCGGGAGGAACGGGTCCTG 3 4 1 TCCTGTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 32 1 CACGCGGCTAGACGGGTGGGGGGGGTGAGGTAG 4 13 1 GGGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA 4 35 1 TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGAC 5 10 1 CTACTAGACAGGGCCGGGGGGGGGGGTGAGGTA 5 34 1 ** * * ****** MAP Score: 1.38739 Motif 11 CGGGAGAAGTTTGACAGCGCGTTCGATGCCC 1 9 1 AGCGCGTTCGATGCCCTCAGGGTGGAGCAATA 1 25 1 GAGTCCTCGATTCTCGAGCGGGTGGGGCTTGC 1 103 1 GTACCGTCCTGCAGCGTGAGGGCAAGCCCCAC 1 124 0 CCACTGATAGTGGAGCTCAGCGCCCAGTGGGA 1 182 1 AGCACCCCCTGTTCCCACTGGGCGCTGAGCTC 1 194 0 CCGAGAGTATGTGGTCTGAGCGTTACTTTGGC 1 252 1 ACGTTTATCTGTGGGGTGAAGGTGGT 1 284 1 CGTATCTGTCGGTAGCGGCGGGTTTTGAGTGC 2 13 1 GGCGGGTTTTGAGTGCACTGCGCTCATCTACG 2 29 1 GAACCCTCATTGGGGGCCTGGATGGTGATGTA 2 72 0 GGGAGGCGCCGGGAGGAACGGG 3 0 1 TGTCGAAGAATTGCGGGGAGGAGTGAAGGT 3 35 1 CCCACCCGTCTAGCCGCGTGTGA 4 1 0 CACGCGGCTAGACGGGTGGGGGGGGTGAGGTA 4 13 1 GGGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA 4 35 1 TTAGAAAAGAAGGGTGAGGGGGCTACTAGACA 5 12 1 GGGGCTACTAGACAGGGCCGGGGGGGGGGGTG 5 30 1 CAGGGCCGGGGGGGGGGGTGAGGTAGC 5 42 1 ****** * *** MAP Score: 0.385945