AlignACE 3.0 10/20/99 AlignACE2 -i AP/AP_operons037_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944234340 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 APE0805 130 362aa long hypothetical integrase/recombinase xerD #1 APE1339 269 211aa long hypothetical protein #2 APE1340 24 1376aa long hypothetical reverse gyrase #3 APE1376 239 1222aa long hypothetical reverse gyrase #4 APE1794 176 673aa long hypothetical DNA topoisomerase Motif 1 CTAGGAGCTTGGGTGGGGGCCGCCGGGGTAGGATTTGG 3 58 0 GCAAAAATAAGCCTGTGGGTCCCTGGTGCGTTGCGTCG 4 96 1 CAACTATTGAAGAGCGGGGGCTCAGCAGTCTTCCTTAG 3 106 1 ACGGCTTCATAGCTGGGGGGCGAGGTTGGGGTTGGAAG 1 215 1 CCAATGGTTAACACCAGGGCCCCCGAGGATTTTATCCG 4 12 1 CTCAAAGAAGGCTAGAGGGTGGCCGCGGTATAACCCTG 0 41 1 GGCTCCTAAAGGAAGAGGGGCAACCCGGGGTCGGGGGC 1 171 1 TCCGCAAACCAGGCCTGGGCCCAGGATGACCTAGCTTA 4 46 1 TAGCTCAGGAGGTGGAGGGCCACACCCACTAGAGTTAT 1 50 0 TGGGGTTGGAAGCCGAGGGTCAGCGTGGCGAGGATGCT 1 241 1 TCAATAGTTGACTTCCGGGTCTAGGAGCTTGGGTGGGG 3 78 0 CGGAGAGGGGTCGCAGCTACAGCTAGCCT 3 220 0 GGCAACCCGGGGTCGGGGGCGAATCCACGGCTTCATAG 1 189 1 GGTATACACCACGTCAGGGAGGCTCCTAAAGGAAGAGG 1 151 1 CCCTACCGCTGGAGCCGCGCCGACGCAACGCACCAGGG 4 116 0 TACGTATTTGGCGTGTAGGACACGAGACCCGTGACGGC 0 88 0 GCGCGGCTCCAGCGGTAGGGGTAGGTGCTTCAAGCCGG 4 134 1 GTCTAGATCCTCAAGGGGGCCTCAAAGAAGGCTAGAGG 0 21 1 AAGCCAATTATCTCGAGGACCACGGCAGGCAACAGCAT 1 107 0 ** * *** * * * * MAP Score: 40.2901 Motif 2 CGAGGTTGGGGTTGGAAGCCGAGGGTCAGCGTGG 1 235 1 GGATAAAATCCTCGGGGGCCCTGGTGTTAACCAT 4 15 0 CCATAATGCTGTTGCCTGCCGTGGTCCTCGAGAT 1 102 1 GAGCTTGGGTGGGGGCCGCCGGGGTAGGATTTGG 3 58 0 CGCCCCCCAGCTATGAAGCCGTGGATTCGCCCCC 1 203 0 AGGGGTAGGTGCTTCAAGCCGGCGGCATTCATCG 4 150 1 AAGAAGGCTAGAGGGTGGCCGCGGTATAACCCTG 0 45 1 CCATAAAATGCCGGGGGCCCAGAA 2 1 0 AGGTCATCCTGGGCCCAGGCCTGGTTTGCGGATA 4 44 0 GATAGGGCTGGTATGTAGCTCAGGAGGTGGAGGG 1 69 0 CCCCACCCAAGCTCCTAGACCCGGAAGTCAACTA 3 78 1 GTTCAGAGGCGTCTCGAGCTCTGGATGAACCCCT 1 16 0 CTACCCCTACCGCTGGAGCCGCGCCGACGCAACG 4 124 0 CCTTTAGGAGCCTCCCTGACGTGGTGTATACCAT 1 149 0 AAGCCGAGGGTCAGCGTGGCGAGGATGCT 1 250 1 AAAAATAAGCCTGTGGGTCCCTGGTGCGTTGCGT 4 98 1 GACACGAGACCCGTGACGGCCGGTATTTTCAGGG 0 74 0 TAACTCTAGTGGGTGTGGCCCTCCACCTCCTGAG 1 51 1 CTCTAGCCTTCTTTGAGGCCCCCTTGAGGATCTA 0 24 0 CTAAGGAAGACTGCTGAGCCCCCGCTCTTCAATA 3 110 0 GCCCCCGACCCCGGGTTGCCCCTCTTCCTTTAGG 1 175 0 TACGTATTTGGCGTGTAGGACACGAGACCCGTGA 0 92 0 CTTCCAACCCCAACCTCGCCCCCCAGCTATGAAG 1 219 0 ** ** **** ** MAP Score: 31.3761 Motif 3 GAGCTTGGGTGGGGGCCGCCGGGGTAGGATTT 3 60 0 CTTCATAGCTGGGGGGCGAGGTTGGGGTTGGA 1 219 1 TAAAATCCTCGGGGGCCCTGGTGTTAACCATT 4 14 0 TGAAAATACCGGCCGTCACGGGTCTCGTGTCC 0 77 1 ATAAAATGCCGGGGGCCCAGAA 2 0 0 ATCAGACTAAAGGAGCCTCGGGATTGAGTGGT 3 168 0 AAGGAAGAGGGGCAACCCGGGGTCGGGGGCGA 1 179 1 CGAGGACCACGGCAGGCAACAGCATTATGGAT 1 100 0 GGTTGGGGTTGGAAGCCGAGGGTCAGCGTGGC 1 238 1 CGTTGCGTCGGCGCGGCTCCAGCGGTAGGGGT 4 124 1 GAAGGCTAGAGGGTGGCCGCGGTATAACCCTG 0 47 1 TTATGTTCAGAGGCGTCTCGAGCTCTGGATGA 1 22 0 TTATCCGCAAACCAGGCCTGGGCCCAGGATGA 4 43 1 CCTTCTTTGAGGCCCCCTTGAGGATCTAGACT 0 20 0 CCGAGGGTCAGCGTGGCGAGGATGCT 1 253 1 CGATGAATGCCGCCGGCTTGAAGCACCTACCC 4 152 0 GGGGTCGGGGGCGAATCCACGGCTTCATAGCT 1 197 1 GGATAAGCTAGGTCATCCTGGGCCCAGGCCTG 4 55 0 TAGTTGACTTCCGGGTCTAGGAGCTTGGGTGG 3 80 0 TTGAAGAGCGGGGGCTCAGCAGTCTTCCTTAG 3 112 1 TTATCCCTTTGGGAGGCAAAAATAAGCCTGTG 4 81 1 CACCACGTCAGGGAGGCTCCTAAAGGAAGAGG 1 157 1 GCAACGCACCAGGGACCCACAGGCTTATTTTT 4 98 0 TATTCATCCAGCGAAGCTTCAACGACAATCTC 3 20 0 AGCTAACCCCGGAATACGTATTT 0 117 0 ******* *** MAP Score: 27.0678 Motif 4 GAGTCTAGATCCTCAAGGGGGCCTCAAAGAAGG 0 19 1 TCAAAGAAGGCTAGAGGGTGGCCGCGGTATAAC 0 42 1 GCTCCGAGGGGTTCATCCAGAGCT 1 1 1 CATAACTCTAGTGGGTGTGGCCCTCCACCTCCT 1 49 1 AATGCTGTTGCCTGCCGTGGTCCTCGAGATAAT 1 106 1 TCGCCCCCGACCCCGGGTTGCCCCTCTTCCTTT 1 178 0 AGGGGCAACCCGGGGTCGGGGGCGAATCCACGG 1 186 1 GTCGGGGGCGAATCCACGGCTTCATAGCTGGGG 1 200 1 CCACGGCTTCATAGCTGGGGGGCGAGGTTGGGG 1 213 1 TCGCCACGCTGACCCTCGGCTTCCAACCCCAAC 1 239 0 CCATAAAATGCCGGGGGCCCAGAA 2 4 0 TTTCCAAATCCTACCCCGGCGGCCCCCACCCAA 3 55 1 CAACTATTGAAGAGCGGGGGCTCAGCAGTCTTC 3 106 1 TCTACCACTCAATCCCGAGGCTCCTTTAGTCTG 3 165 1 CCAATGGTTAACACCAGGGCCCCCGAGGATTTT 4 12 1 ATCCGCAAACCAGGCCTGGGCCCAGGATGACCT 4 45 1 AGGCAAAAATAAGCCTGTGGGTCCCTGGTGCGT 4 94 1 GGTGCGTTGCGTCGGCGCGGCTCCAGCGGTAGG 4 120 1 * ** ******* MAP Score: 21.9955 Motif 5 GAAGGCTAGAGGGTGGCCGCGGTATAACCCTGAA 0 47 1 TGAAAATACCGGCCGTCACGGGTCTCGTGTCCTA 0 77 1 ATGTAGCTCAGGAGGTGGAGGGCCACACCCACTA 1 57 0 TAATGCTGTTGCCTGCCGTGGTCCTCGAGATAAT 1 105 1 AAGGAAGAGGGGCAACCCGGGGTCGGGGGCGAAT 1 179 1 CTTCATAGCTGGGGGGCGAGGTTGGGGTTGGAAG 1 219 1 GGTTGGGGTTGGAAGCCGAGGGTCAGCGTGGCGA 1 238 1 CCGAGGGTCAGCGTGGCGAGGATGCT 1 253 1 CCATAAAATGCCGGGGGCCCAGAA 2 6 0 GAGCTTGGGTGGGGGCCGCCGGGGTAGGATTTGG 3 58 0 TTGCGGATAAAATCCTCGGGGGCCCTGGTGTTAA 4 19 0 TTATCCGCAAACCAGGCCTGGGCCCAGGATGACC 4 43 1 GGTCCCTGGTGCGTTGCGTCGGCGCGGCTCCAGC 4 113 1 GCGTCGGCGCGGCTCCAGCGGTAGGGGTAGGTGC 4 128 1 GGCGATGAATGCCGCCGGCTTGAAGCACCT 4 156 0 ** **** *** * MAP Score: 12.4269 Motif 6 AGCCTTCTTTGAGGCCCCCTTGAGGATCTAGACTC 0 19 0 GGGTTATACCGCGGCCACCCTCTAGCCTTCTTTGA 0 42 0 CCCTGAAAATACCGGCCGTCACGGGTCTCGTGTCC 0 74 1 CTCGAGCTCTGGATGAACCCCTCGGAGC 1 3 0 TAGCTCAGGAGGTGGAGGGCCACACCCACTAGAGT 1 53 0 CCATAATGCTGTTGCCTGCCGTGGTCCTCGAGATA 1 102 1 TCTTCCTTTAGGAGCCTCCCTGACGTGGTGTATAC 1 152 0 CCTAAAGGAAGAGGGGCAACCCGGGGTCGGGGGCG 1 175 1 CCCGGGGTCGGGGGCGAATCCACGGCTTCATAGCT 1 194 1 CGGCTTCATAGCTGGGGGGCGAGGTTGGGGTTGGA 1 216 1 CGAGGTTGGGGTTGGAAGCCGAGGGTCAGCGTGGC 1 235 1 AGCATCCTCGCCACGCTGACCCTCGG 1 253 0 GATTGTCGTTGAAGCTTCGCTGGATGAATAGCGTT 3 22 1 GAGCTTGGGTGGGGGCCGCCGGGGTAGGATTTGGA 3 57 0 CTATTGAAGAGCGGGGGCTCAGCAGTCTTCCTTAG 3 109 1 TAGTCTGATCGGTGCCGGATTGGGGGTTTAGGCTA 3 191 1 GCTAGCTGTAGCTGCGACCCCTCTCCG 3 222 1 ATGGTTAACACCAGGGCCCCCGAGGATTTTATCCG 4 15 1 CGCAAACCAGGCCTGGGCCCAGGATGACCTAGCTT 4 48 1 GAGCCGCGCCGACGCAACGCACCAGGGACCCACAG 4 108 0 GCGTTGCGTCGGCGCGGCTCCAGCGGTAGGGGTAG 4 123 1 AGGGGTAGGTGCTTCAAGCCGGCGGCATTCATCGC 4 150 1 * *** *** *** MAP Score: 11.3887 Motif 7 AGGCTAGAGGGTGGCCGCGGTATAACCCTGAAAATACCGG 0 49 1 TTGGCGTGTAGGACACGAGACCCGTGACGGCCGGTATTTT 0 79 0 AATGCTGTTGCCTGCCGTGGTCCTCGAGATAATTGGCTTC 1 106 1 TATACACCACGTCAGGGAGGCTCCTAAAGGAAGAGGGGCA 1 153 1 AGGAAGAGGGGCAACCCGGGGTCGGGGGCGAATCCACGGC 1 180 1 CACGGCTTCATAGCTGGGGGGCGAGGTTGGGGTTGGAAGC 1 214 1 GTTGGGGTTGGAAGCCGAGGGTCAGCGTGGCGAGGATGCT 1 239 1 TTCTGGGCCCCCGGCATTTTATGG 2 4 1 TGTCGTTGAAGCTTCGCTGGATGAATAGCGTTTCCAAATC 3 25 1 TTGGGTGGGGGCCGCCGGGGTAGGATTTGGAAACGCTATT 3 48 0 GTCAACTATTGAAGAGCGGGGGCTCAGCAGTCTTCCTTAG 3 104 1 TCTACCACTCAATCCCGAGGCTCCTTTAGTCTGATCGGTG 3 165 1 TCCTTTAGTCTGATCGGTGCCGGATTGGGGGTTTAGGCTA 3 186 1 TAACACCAGGGCCCCCGAGGATTTTATCCGCAAACCAGGC 4 20 1 TATCCGCAAACCAGGCCTGGGCCCAGGATGACCTAGCTTA 4 44 1 CGCCGACGCAACGCACCAGGGACCCACAGGCTTATTTTTG 4 97 0 GGTGCGTTGCGTCGGCGCGGCTCCAGCGGTAGGGGTAGGT 4 120 1 CCAGCGGTAGGGGTAGGTGCTTCAAGCCGGCGGCATTCAT 4 142 1 * **** ** * ** MAP Score: 9.72312 Motif 8 AAGGCTAGAGGGTGGCCGCGGTATAACCCTGAAA 0 48 1 TGAAAATACCGGCCGTCACGGGTCTCGTGTCCTA 0 77 1 AGCTAACCCCGGAATACGTATTTGG 0 115 0 ATGTTCAGAGGCGTCTCGAGCTCTGGATGAACCC 1 18 0 CTCTAGTGGGTGTGGCCCTCCACCTCCTGAGCTA 1 54 1 TAATGCTGTTGCCTGCCGTGGTCCTCGAGATAAT 1 105 1 TTAGGAGCCTCCCTGACGTGGTGTATACCATGCG 1 146 0 CCCGACCCCGGGTTGCCCCTCTTCCTTTAGGAGC 1 172 0 AGCCGTGGATTCGCCCCCGACCCCGGGTTGCCCC 1 187 0 ACCCCAACCTCGCCCCCCAGCTATGAAGCCGTGG 1 213 0 GGTTGGGGTTGGAAGCCGAGGGTCAGCGTGGCGA 1 238 1 TTCTGGGCCCCCGGCATTTTATGG 2 3 1 GTTTCCAAATCCTACCCCGGCGGCCCCCACCCAA 3 54 1 CCCCGGCGGCCCCCACCCAAGCTCCTAGACCCGG 3 68 1 AGCCTAAACCCCCAATCCGGCACCGATCAGACTA 3 191 0 TAAAATCCTCGGGGGCCCTGGTGTTAACCATTGG 4 12 0 GGATTTTATCCGCAAACCAGGCCTGGGCCCAGGA 4 38 1 GGATAAGCTAGGTCATCCTGGGCCCAGGCCTGGT 4 53 0 AACGCACCAGGGACCCACAGGCTTATTTTTGCCT 4 94 0 TGGTGCGTTGCGTCGGCGCGGCTCCAGCGGTAGG 4 119 1 *** **** ** * MAP Score: 9.16573 Motif 9 TCTAGATCCTCAAGGGGGCCTCAAAGAAGGCTA 0 22 1 TCAAAGAAGGCTAGAGGGTGGCCGCGGTATAAC 0 42 1 AATACCGGCCGTCACGGGTCTCGTGTCCTACAC 0 81 1 CAAATACGTATTCCGGGGTTAGCT 0 116 1 GCTCCGAGGGGTTCATCCAGAGCTC 1 2 1 TCAGAGGCGTCTCGAGCTCTGGATGAACCCCTC 1 15 0 GAACATAACTCTAGTGGGTGTGGCCCTCCACCT 1 46 1 GTATGTAGCTCAGGAGGTGGAGGGCCACACCCA 1 60 0 GCTGTTGCCTGCCGTGGTCCTCGAGATAATTGG 1 109 1 GCATGGTATACACCACGTCAGGGAGGCTCCTAA 1 147 1 TTCGCCCCCGACCCCGGGTTGCCCCTCTTCCTT 1 179 0 CACGGCTTCATAGCTGGGGGGCGAGGTTGGGGT 1 214 1 CTGGGGGGCGAGGTTGGGGTTGGAAGCCGAGGG 1 227 1 GGGGTTGGAAGCCGAGGGTCAGCGTGGCGAGGA 1 242 1 CCATAAAATGCCGGGGGCCCAGAA 2 3 0 GGGTGGGGGCCGCCGGGGTAGGATTTGGAAACG 3 53 0 AATAGTTGACTTCCGGGTCTAGGAGCTTGGGTG 3 81 0 GACTGCTGAGCCCCCGCTCTTCAATAGTTGACT 3 103 0 CTCCTTTAGTCTGATCGGTGCCGGATTGGGGGT 3 185 1 CGGTGCCGGATTGGGGGTTTAGGCTAGCTGTAG 3 200 1 CGGAGAGGGGTCGCAGCTACAGCT 3 225 0 CAATGGTTAACACCAGGGCCCCCGAGGATTTTA 4 13 1 CCTGGGCCCAGGCCTGGTTTGCGGATAAAATCC 4 38 0 CGACGCAACGCACCAGGGACCCACAGGCTTATT 4 101 0 CCTGGTGCGTTGCGTCGGCGCGGCTCCAGCGGT 4 117 1 GTCGGCGCGGCTCCAGCGGTAGGGGTAGGTGCT 4 130 1 GGCGATGAATGCCGCCGGCTTGAAGCACCTACC 4 153 0 * ** ***** ** MAP Score: 8.71763 Motif 10 TTTCAGGGTTATACCGCGGCCACCCTCTAGCCTTCTT 0 45 0 ATGGTATACACCACGTCAGGGAGGCTCCTAAAGGAAG 1 149 1 GATTCGCCCCCGACCCCGGGTTGCCCCTCTTCCTTTA 1 177 0 GGGGGCGAATCCACGGCTTCATAGCTGGGGGGCGAGG 1 203 1 CCTCGGCTTCCAACCCCAACCTCGCCCCCCAGCTATG 1 222 0 AGCATCCTCGCCACGCTGACCCTCGGCTTCCA 1 247 0 CCATAAAATGCCGGGGGCCCAGAA 2 3 0 GTTTCCAAATCCTACCCCGGCGGCCCCCACCCAAGCT 3 54 1 GCGGCCCCCACCCAAGCTCCTAGACCCGGAAGTCAAC 3 73 1 GTGCTAAGGAAGACTGCTGAGCCCCCGCTCTTCAATA 3 110 0 GCCTAAACCCCCAATCCGGCACCGATCAGACTAAAGG 3 187 0 TTGCGGATAAAATCCTCGGGGGCCCTGGTGTTAACCA 4 16 0 TTATCCGCAAACCAGGCCTGGGCCCAGGATGACCTAG 4 43 1 CGCCGACGCAACGCACCAGGGACCCACAGGCTTATTT 4 100 0 TGGTGCGTTGCGTCGGCGCGGCTCCAGCGGTAGGGGT 4 119 1 AGGTGCTTCAAGCCGGCGGCATTCATCGCC 4 156 1 * * ** ** **** MAP Score: 7.93057 Motif 11 GAGTCTAGATCCTCAAGGGGGCCTCAAAGAAGGCT 0 19 1 TCAAAGAAGGCTAGAGGGTGGCCGCGGTATAACCC 0 42 1 CTAGAGTTATGTTCAGAGGCGTCTCGAGCTCTGGA 1 25 0 GAACATAACTCTAGTGGGTGTGGCCCTCCACCTCC 1 46 1 TAATGCTGTTGCCTGCCGTGGTCCTCGAGATAATT 1 105 1 GTATACACCACGTCAGGGAGGCTCCTAAAGGAAGA 1 152 1 GCTCCTAAAGGAAGAGGGGCAACCCGGGGTCGGGG 1 172 1 GGCAACCCGGGGTCGGGGGCGAATCCACGGCTTCA 1 189 1 CGGCTTCATAGCTGGGGGGCGAGGTTGGGGTTGGA 1 216 1 GGGGTTGGAAGCCGAGGGTCAGCGTGGCGAGGATG 1 242 1 TTTCCAAATCCTACCCCGGCGGCCCCCACCCAAGC 3 55 1 GTCAACTATTGAAGAGCGGGGGCTCAGCAGTCTTC 3 104 1 TTCTACCACTCAATCCCGAGGCTCCTTTAGTCTGA 3 164 1 TTTAGGCTAGCTGTAGCTGCGACCCCTCTCCG 3 217 1 CTGTGGGTCCCTGGTGCGTTGCGTCGGCGCGGCTC 4 108 1 CTACCCCTACCGCTGGAGCCGCGCCGACGCAACGC 4 123 0 GGCTCCAGCGGTAGGGGTAGGTGCTTCAAGCCGGC 4 138 1 * * *** ** *** MAP Score: 6.43239 Motif 12 GAGTCTAGATCCTCAAGGGGGCCTCAAAGAAGGC 0 19 1 AAGGCTAGAGGGTGGCCGCGGTATAACCCTGAAA 0 48 1 GTATAACCCTGAAAATACCGGCCGTCACGGGTCT 0 68 1 CGGCCGTCACGGGTCTCGTGTCCTACACGCCAAA 0 86 1 GCTCCGAGGGGTTCATCCAGAGCT 1 0 1 CAGCATTATGGATAGGGCTGGTATGTAGCTCAGG 1 79 0 TAATGCTGTTGCCTGCCGTGGTCCTCGAGATAAT 1 105 1 TTAGGAGCCTCCCTGACGTGGTGTATACCATGCG 1 146 0 AAGGAAGAGGGGCAACCCGGGGTCGGGGGCGAAT 1 179 1 CTTCATAGCTGGGGGGCGAGGTTGGGGTTGGAAG 1 219 1 GGTTGGGGTTGGAAGCCGAGGGTCAGCGTGGCGA 1 238 1 CCGAGGGTCAGCGTGGCGAGGATGCT 1 253 1 TTCTGGGCCCCCGGCATTTTATGG 2 3 1 GGGTGGGGGCCGCCGGGGTAGGATTTGGAAACGC 3 52 0 GGGTCTAGGAGCTTGGGTGGGGGCCGCCGGGGTA 3 66 0 GTCAACTATTGAAGAGCGGGGGCTCAGCAGTCTT 3 104 1 TTCTACCACTCAATCCCGAGGCTCCTTTAGTCTG 3 164 1 TGATCGGTGCCGGATTGGGGGTTTAGGCTAGCTG 3 196 1 CGGAGAGGGGTCGCAGCTACAGCTAG 3 223 0 TAAAATCCTCGGGGGCCCTGGTGTTAACCATTGG 4 12 0 GGATTTTATCCGCAAACCAGGCCTGGGCCCAGGA 4 38 1 GGATAAGCTAGGTCATCCTGGGCCCAGGCCTGGT 4 53 0 AACGCACCAGGGACCCACAGGCTTATTTTTGCCT 4 94 0 TGGTGCGTTGCGTCGGCGCGGCTCCAGCGGTAGG 4 119 1 GTAGGTGCTTCAAGCCGGCGGCATTCATCGCC 4 154 1 ** **** *** * MAP Score: 6.14403