AlignACE 3.0 10/20/99 AlignACE2 -i PA/PA_operons021_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944250059 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 PAB0359 43 hypothetical protein #1 rps13P 100 PAB0360 #2 rpoD 32 PAB2410 #3 rpl18E 166 PAB0364 #4 rpoN 44 PAB7131 #5 rpoK 120 PAB7132 #6 thrC-like 39 PAB0369 #7 PAB1867 78 PAB1867 #8 PAB1865 36 hypothetical protein #9 PAB1864 60 PAB1864 #10 putP-1 198 PAB0609 #11 hom 56 PAB0610 #12 PAB1675 40 PAB1675 #13 PAB1674 221 PAB1674 #14 PAB1673 174 PAB1673 #15 dapA 121 PAB0832 #16 ilvB 300 PAB0888 #17 leuA-1 30 PAB0890 #18 leuC-1 40 PAB0891 Motif 1 CCCACGGGCTCTCAAGGCCCGCGCCCTACCAGG 1 8 0 AGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCAAAT 1 31 1 CCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGA 1 49 1 GGCCAGGCTCGGCAACCCCCGCTCGG 3 1 0 GGGACGGGACCCTAAATCCCGCGCCTTTGGCCAGG 3 29 0 GGATTTGAACCCCGGAACCCCTACGGGACGGGACC 3 53 0 GGTTCCGGGGTTCAAATCCCCGCCCCCGCACCATT 3 69 1 ACCATTTATTCACGCTCACCCCGCCCTTGTCGGTT 3 98 1 CCCCGCCCTTGTCGGTTTCCCTGCGGCGCGAGAAT 3 116 1 GCGAAATTCCCCCTTCTAGAGTTTAAT 3 149 0 GGCTTGACCCCCACTTGTCTTCGAA 4 29 0 GCCAAGCTACCCCACGGCCCCGCCTAAATAAAGAA 5 19 0 GGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGCCG 5 42 1 GGGATTTGAACCCGGGTCACCGGCGCCCCAGGCCG 5 62 0 GGGTTCAAATCCCGGCGGCCCCACCAAAATATTGA 5 84 1 TTCATATCGCCCCCGCCTTTAGGCACA 10 181 0 CGATTTTTCAAGAATCCCTCCCAAACTTTTTA 11 7 1 CCCAAACTTTTTAATTTTCCCTTCCTAACTTTTTT 11 29 1 CTCACGTTCCCCTCTTGGGCGTTTT 13 206 0 CCCTAACCTTCATGAGCTCCCTTCCACTAACCCTC 16 152 1 GGGGTGTTTTTCCATGCCCTCCACCTCC 16 282 1 * ** ***** ** MAP Score: 25.0226 Motif 2 CCTGGTAGGGCGCGGGCCTTGAGAGC 1 6 1 AAATGGTGCGGGGGCGGGGATTTGAACCCC 3 75 0 CTCCCGGCCTGGGGCGCCGGTGACCCGGGT 5 58 1 TTTGTGCCTAAAGGCGGGGGCGATATGAA 10 179 1 TATTTAGGCGGGGCCGTGGGGTAGCTTGGC 5 24 1 AGCCTGGCCAAAGGCGCGGGATTTAGGGTC 3 27 1 TATTTTGGTGGGGCCGCCGGGATTTGAACC 5 85 0 CCGGCGCCCCAGGCCGGGAGGATAGCCAAG 5 48 0 GAAACCGACAAGGGCGGGGTGAGCGTGAAT 3 105 0 CGGTTTCCCTGCGGCGCGAGAATTAAACTC 3 128 1 TTCTGGCGCCGGGACGGGGATTTGAACCCC 1 55 0 TTTTAATTTGGAGGCGTGAGA 2 21 1 CCGAGCGGGGGTTGCCGAGCC 3 1 1 GAACCCCTACGGGACGGGACCCTAAATCCC 3 44 0 AAACGCCGATGGGGAGGAAGC 9 49 1 GGAGGTGGAGGGCATGGAAAA 16 289 0 GCCCAAGAGGGGAACGTGAG 13 211 1 ********** MAP Score: 24.0889 Motif 3 TGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCCG 1 12 1 GTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAA 1 44 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGG 3 5 1 GCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTC 3 33 1 GTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCATTT 3 64 1 GGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAA 5 51 1 CGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAAAA 5 72 1 CAAAAATTTTCGGGGGTGTTTTTCCATGCCCTCCACCTCC 16 270 1 **** * ** * * * MAP Score: 19.8462 Motif 4 ATAATTGTTGAAAAAGATTTAAATAAATATT 10 122 1 AGGGAAAATTAAAAAGTTTGGGAGGGATTCT 11 20 0 AATTTTATGTAAAAAGTTTAGTTGTTAGTAT 16 22 1 GGAAAAAAGTTAGGAAGGGAAAAT 11 42 0 CCTCCAAATTAAAAAGATAAGAGAA 2 4 0 TTGGAGGGTTAAAAATTTAAAGGTTAAAGTT 0 11 0 ACATTTATGAAAAAATATTTATTTAAATCTT 10 135 0 ATCGAAGCGGAAAAATTTATATTGTCTAAAA 15 45 0 GCGAAAAATTTATATAAGTTAATT 7 3 1 AAATTTTCCGAAAAATATTTATAGATTGGGA 16 79 1 GTTTGTCTCCAAAAATTTTCGGGGGTGTTTT 16 261 1 GGAGACAAACAAAACGATAAAATGTTGTAAT 16 240 0 TTTTAAAAACTTTTTATAATTCGAAG 4 5 1 AAAGAATAGGAAAACTTTTAACCTGAATGTC 10 36 0 TTTACATCTAAAAATGATATAATTGGGATTA 15 75 1 AAATATGTCGAAAATTATATAAAAAGAAAAC 13 180 1 TACTAAAAAGAAATAGATTTAAGAGCGTTT 8 9 0 GAATATTCCGAAATATTTTAGACAACTTTTT 10 76 0 ********* * MAP Score: 19.7317 Motif 5 TGTGCCTAAAGGCGGGGGCGATATGAA 10 181 1 TATCCTCCCGGCCTGGGGCGCCGGTGACCC 5 54 1 GGGTTCAAATCCCGGCGGCCCCACCAAAAT 5 84 1 GGATTTGAACCCCGGCGGGCAAACGCCCAC 1 38 0 TCTTTATTTAGGCGGGGCCGTGGGGTAGCT 5 20 1 GCCTTGAGAGCCCGTGGGCGTTTGCCCGCC 1 25 1 TTGTCGGTTTCCCTGCGGCGCGAGAATTAA 3 124 1 CCTGGTAGGGCGCGGGCCTTGAGAGCCC 1 8 1 TAAATGGTGCGGGGGCGGGGATTTGAACCC 3 76 0 AGGGTCCCGTCCCGTAGGGGTTCCGGGGTT 3 51 1 GGATTCTGGCGCCGGGACGGGGATTTGAAC 1 58 0 CCGAGCGGGGGTTGCCGAGCC 3 1 1 TTATGCATTAGCCTGAGGTGATGTGC 15 6 0 GGAGGTGGAGGGCATGGAAAAAC 16 287 0 ATAAACAAAGCCAGGAGGTGGTAGC 18 25 1 GCTTCCTCCCCATCGGCGTTTCGAAGGT 9 42 0 ********** MAP Score: 15.6648 Motif 6 CACGGGCTCTCAAGGCCCGCGCCCTACCAGG 1 8 0 CCCCGGCGGGCAAACGCCCACGGGCTCTCAAGG 1 26 0 TGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGT 1 39 1 GGTTCAAATCCCCGTCCCGGCGCCAGAATCCCA 1 57 1 CCGAGCGGGGGTTGCCGAGCCTGG 3 1 1 CCGAGCCTGGCCAAAGGCGCGGGATTTAGGGTC 3 24 1 GGAACCCCTACGGGACGGGACCCTAAATCCCGC 3 42 0 TTCCGGGGTTCAAATCCCCGCCCCCGCACCATT 3 71 1 GGGAAACCGACAAGGGCGGGGTGAGCGTGAATA 3 104 0 GAGTTTAATTCTCGCGCCGCAGGGAAACCGACA 3 125 0 AATTCGAAGACAAGTGGGGGTCAAGCC 4 27 1 GCCAAGCTACCCCACGGCCCCGCCTAAATAAAG 5 21 0 CACCGGCGCCCCAGGCCGGGAGGATAGCCAAGC 5 47 0 GACCCGGGTTCAAATCCCGGCGGCCCCACCAAA 5 79 1 AATCAACCTTCGAAACGCCGATGGGGAGGAAGC 9 37 1 ACATTTGTGCCTAAAGGCGGGGGCGATATGAA 10 176 1 AGAAAACGCCCAAGAGGGGAACGTGAG 13 204 1 ATGCAATAAACAAAGCCAGGAGGTGGTAGC 18 20 1 * ** ***** ** MAP Score: 11.9194 Motif 7 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGG 1 8 1 GATTTGAACCCCGGCGGGCAAACGCCCACGGGCTC 1 32 0 ATGGGATTCTGGCGCCGGGACGGGGATTTGAACCC 1 56 0 CCGAGCGGGGGTTGCCGAGCCTGGCCAAA 3 4 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCC 3 29 1 GTCCCGTCCCGTAGGGGTTCCGGGGTTCAAATCCC 3 54 1 GTGAATAAATGGTGCGGGGGCGGGGATTTGAACCC 3 76 0 AAACCGACAAGGGCGGGGTGAGCGTGAATAAATGG 3 99 0 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCT 5 20 1 GCTTGGCTATCCTCCCGGCCTGGGGCGCCGGTGAC 5 47 1 CGGCCTGGGGCGCCGGTGACCCGGGTTCAAATCCC 5 62 1 TCAATATTTTGGTGGGGCCGCCGGGATTTGAACCC 5 84 0 TGTGCCTAAAGGCGGGGGCGATATGAA 10 181 1 ** ***** *** MAP Score: 11.9133 Motif 8 GCCCACGGGCTCTCAAGGCCCGCGCCCTACCAGG 1 7 0 GCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAA 1 48 1 AGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCC 3 38 1 GGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCATTT 3 68 1 GCACCATTTATTCACGCTCACCCCGCCCTTGTCGGTT 3 96 1 CCCCGCCCTTGTCGGTTTCCCTGCGGCGCGAGAATTA 3 116 1 GGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAAAA 5 76 1 CTTTATCTTTCCCTTTTCCAATGTTTTTT 6 2 1 ATTTATATAAGTTAATTTCCCGATTCCCTTTGAAGAT 7 17 1 CACCCTAACCTTCATGAGCTCCCTTCCACTAACCCTC 16 150 1 CGGGGGTGTTTTTCCATGCCCTCCACCTCC 16 280 1 *** **** * ** MAP Score: 7.92853 Motif 9 TTTAAATTTTTAACCCTCCAAATACCCAAAGG 0 21 1 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCG 1 43 1 TTTATCCCCCTCCAAATGAATGGGATT 1 83 0 TCTCACGCCTCCAAATTAAAAAGATA 2 16 0 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCC 3 63 1 TTGACCCCCACTTGTCTTCGAATTATAAAAAGT 4 18 0 GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCC 5 71 1 CCTGTACTTACTGTTCTCCAAATTGTCTCTGTA 13 75 1 CTCTGTAGATTCTGAGTTCAACTTAATATCCAC 13 101 1 TATCGTTTTGTTTGTCTCCAAAAATTTTCGGGG 16 252 1 * * ******** MAP Score: 7.75124 Motif 10 CCTTTGGGTATTTGGAGGGTTAAAAATTT 0 24 0 CCTGGTAGGGCGCGGGCCTTGAGAGC 1 6 1 AATCCCATTCATTTGGAGGGGGATAAA 1 83 1 TATCTTTTTAATTTGGAGGCGTGAGA 2 16 1 AGCCTGGCCAAAGGCGCGGGATTTAGGGTC 3 27 1 GGAAACCGACAAGGGCGGGGTGAGCGTGAA 3 106 0 CTTTCTTTATTTAGGCGGGGCCGTGGGGTA 5 17 1 ACCTCAATATTTTGGTGGGGCCGCCGGGAT 5 92 0 CGAAACGCCGATGGGGAGGAAGC 9 47 1 AAGATTAATTATTGGGGGTGCCTT 10 4 0 ATTTGTGCCTAAAGGCGGGGGCGATATGAA 10 178 1 AATTAAAAAGTTTGGGAGGGATTCTTGAAA 11 15 0 GGAAAAAAGTTAGGAAGGGAAAATTAAAA 11 37 0 AGCGAGGGTTAGTGGAAGGGAGCTCATGAA 16 160 0 CAGAATTAGAATAGCGAGGGTTAGTGGAAG 16 172 0 ********** MAP Score: 7.1581 Motif 11 CAAACGCCCACGGGCTCTCAAGGCCCGCGCCCTACCAGG 1 9 0 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAG 1 43 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCG 3 5 1 CCCTACGGGACGGGACCCTAAATCCCGCGCCTTTGGCCAG 3 30 0 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCAT 3 63 1 TATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCG 5 24 1 CTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAATCCCG 5 58 1 CAAAAATTTTCGGGGGTGTTTTTCCATGCCCTCCACCTCC 16 270 1 **** * *** * * MAP Score: 4.68691 Motif 12 GCTCTCAAGGCCCGCGCCCTACCAGG 1 3 0 GGGGTTCAAATCCCCGTCCCGGCGCCAGAATCC 1 55 1 CCAGGCTCGGCAACCCCCGCTCGG 3 1 0 GATTTGAACCCCGGAACCCCTACGGGACGGGAC 3 54 0 GTTCCGGGGTTCAAATCCCCGCCCCCGCACCAT 3 70 1 CATTTATTCACGCTCACCCCGCCCTTGTCGGTT 3 100 1 GAGTTTAATTCTCGCGCCGCAGGGAAACCGACA 3 125 0 GGCTTGACCCCCACTTGTCTTCGAA 4 29 0 CCAAGCTACCCCACGGCCCCGCCTAAATAAAGA 5 20 0 GGTAGCTTGGCTATCCTCCCGGCCTGGGGCGCC 5 43 1 GCCTGGGGCGCCGGTGACCCGGGTTCAAATCCC 5 64 1 GTTCAAATCCCGGCGGCCCCACCAAAATATTGA 5 86 1 GCTTCCTCCCCATCGGCGTTTCGA 9 46 0 TTCATATCGCCCCCGCCTTTAGGCACA 10 181 0 CGATTTTTCAAGAATCCCTCCCAAACTTTTT 11 8 1 AATGTGAGAACAAGCACCCTAACCTTCATGAGC 16 136 1 AGCTCCCTTCCACTAACCCTCGCTATTCTAATT 16 166 1 GGTGTTTTTCCATGCCCTCCACCTCC 16 284 1 * ** ******* MAP Score: 2.82721 Motif 13 TAACTTTAACCTTTAAATTTTTAACCCTCCA 0 3 1 TTTTAAAAACTTTTTATAATTCGAAGACAAG 4 3 1 GCGAAAAATTTATATAAGTTAATTTCCCGA 7 2 1 AAACGCTCTTAAATCTATTTCTTTTTAGTATGTAC 8 7 1 GGACATTCAGGTTAAAAGTTTTCCTATTCTTTGGGTTT 10 35 1 AAAAAGTTGTCTAAAATATTTCGGAATATTCGAGTTCT 10 76 1 AAGAATCCCTCCCAAACTTTTTAATTTTCCCTTCCTAA 11 19 1 ACAAAAATAACCGAAAGGTTTATAAGTTCGAACTATAT 14 108 1 CTCAGGCTAATGCATAAGTTTGTATGTTTTAGACAATA 15 19 1 CTTGAAAATTTTAATTTTATGTAAAAAG 16 0 1 TTAATTTTATGTAAAAAGTTTAGTTGTTAGTATAATTT 16 20 1 CAAATTTTCCGAAAAATATTTATAGATTGGGAAAACAT 16 78 1 TTGTTTGTCTCCAAAAATTTTCGGGGGTGTTTTTCCAT 16 259 1 * *** *** * ** MAP Score: 1.02034 Motif 14 TGCCCGCCGGGGTTCAAATCCCCGTCCCGGC 1 47 1 GGGGTTCCGGGGTTCAAATCCCCGCCCCCGC 3 67 1 CGGTGACCCGGGTTCAAATCCCGGCGGCCCC 5 75 1 TAGGCACAAATGTTCATATCAGAACATTTAT 10 158 0 TATTTTTGTTGCTCTATATCCCAAGTATCTA 14 86 0 TTTCCGCTTCGATTTACATCTAAAAATGATA 15 63 1 ****** **** MAP Score: 0.266428