AlignACE 3.0 10/20/99 AlignACE2 -i PA/PA_sum_all016_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944252924 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 rps13P 100 PAB0360 #1 rpoD 32 PAB2410 #2 rpl18E 166 PAB0364 #3 rpoN 44 PAB7131 #4 rpoK 120 PAB7132 #5 thrC-like 39 PAB0369 #6 PAB0370 34 hypothetical protein Motif 1 GGCAAACGCCCACGGGCTCTCAAGGCCCGCGCCCTACCAGG 0 9 0 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAA 0 43 1 CCTCCAAATGAATGGGATTCTGGCGCCGGGACGGGGATTTGA 0 60 0 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGGG 2 5 1 TGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTT 2 31 1 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCATTT 2 63 1 TGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAA 4 50 1 GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAAAA 4 71 1 * *** * * * * * * MAP Score: 24.7293 Motif 2 GTCCCGTCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGC 2 54 1 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCG 4 20 1 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTT 0 3 1 GCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGC 0 34 1 CTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTC 2 30 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGG 2 2 1 CAATATTTTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCGG 4 74 0 TTGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAA 4 49 1 GCGCCGCAGGGAAACCGACAAGGGCGGGGTGAGCGTGAATAAAT 2 101 0 CCCTCCAAATGAATGGGATTCTGGCGCCGGGACGGGGATTTGAA 0 59 0 * *** **** ** MAP Score: 22.4824 Motif 3 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTG 0 8 1 TGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGC 0 39 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGC 2 1 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGG 2 29 1 AAATGGTGCGGGGGCGGGGATTTGAACCCCGGAACCCCTAC 2 64 0 GTTTCCCTGCGGCGCGAGAATTAAACTCTAGAAGGGGGAAT 2 130 1 GGGCCGTGGGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGC 4 34 1 TTTTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCGGCG 4 72 0 * ** ** ** ** * MAP Score: 22.2971 Motif 4 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGG 0 9 1 CCTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGG 0 26 1 GGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCC 0 41 1 GGGATTCTGGCGCCGGGACGGGGATTTGAACCC 0 56 0 CCGAGCGGGGGTTGCCGAGCCTGGCCA 2 4 1 CTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCC 2 30 1 ATGGTGCGGGGGCGGGGATTTGAACCCCGGAAC 2 70 0 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGG 4 20 1 CGGCGCCCCAGGCCGGGAGGATAGCCAAGCTAC 4 44 0 TTGGTGGGGCCGCCGGGATTTGAACCCGGGTCA 4 78 0 ******* * ** MAP Score: 19.2538 Motif 5 CTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTT 0 11 1 CTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCA 0 27 1 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCG 0 43 1 AATCCCCGTCCCGGCGCCAGAATCCCATTCATTTGG 0 63 1 GGTTGCCGAGCCTGGCCAAAGGCGCGGGATTTAGGG 2 19 1 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCA 2 63 1 GGATAGCCAAGCTACCCCACGGCCCCGCCTAAATAA 4 23 0 ACCCGGGTCACCGGCGCCCCAGGCCGGGAGGATAGC 4 52 0 GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCA 4 71 1 ** **** * *** MAP Score: 18.7071 Motif 6 GCTCTCAAGGCCCGCGCCCTACCAGG 0 6 0 GGCGGGCAAACGCCCACGGGCTCTCAAGGC 0 25 0 CGTGGGCGTTTGCCCGCCGGGGTTCAAATC 0 37 1 GGGTTCAAATCCCCGTCCCGGCGCCAGAAT 0 56 1 TCTCACGCCTCCAAATTAAAAA 1 20 0 GGCTCGGCAACCCCCGCTCGG 2 1 0 GCGGGGGTTGCCGAGCCTGGCCAAAGGCGC 2 14 1 GGATTTAGGGTCCCGTCCCGTAGGGGTTCC 2 45 1 GGATTTGAACCCCGGAACCCCTACGGGACG 2 58 0 GGGGTTCAAATCCCCGCCCCCGCACCATTT 2 75 1 TTATTCACGCTCACCCCGCCCTTGTCGGTT 2 103 1 TTAATTCTCGCGCCGCAGGGAAACCGACAA 2 124 0 AGCTACCCCACGGCCCCGCCTAAATAAAGA 4 20 0 TTGGCTATCCTCCCGGCCTGGGGCGCCGGT 4 49 1 GAACCCGGGTCACCGGCGCCCCAGGCCGGG 4 60 0 CGGGTTCAAATCCCGGCGGCCCCACCAAAA 4 83 1 ********** MAP Score: 18.564 Motif 7 GGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCC 0 13 1 CGCCGGGACGGGGATTTGAACCCCGGCGGGCAAACGCCC 0 40 0 CCAAATGAATGGGATTCTGGCGCCGGGACGGGGATTTGA 0 60 0 CCTTTGGCCAGGCTCGGCAACCCCCGCTCGG 2 2 0 CCTACGGGACGGGACCCTAAATCCCGCGCCTTTGGCCAG 2 30 0 TGCGGGGGCGGGGATTTGAACCCCGGAACCCCTACGGGA 2 60 0 TCGCGCCGCAGGGAAACCGACAAGGGCGGGGTGAGCGTG 2 108 0 CCCCCTTCTAGAGTTTAATTCTCGCGCCGCAGGGAAACC 2 129 0 CCGGCCTGGGGCGCCGGTGACCCGGGTTCAAATCCCGGC 4 61 1 *** ** **** * MAP Score: 18.4199 Motif 8 GGCTCTCAAGGCCCGCGCCCTACCAGG 0 7 0 CGGGCAAACGCCCACGGGCTCTCAAGGCCC 0 23 0 GGGATTTGAACCCCGGCGGGCAAACGCCCA 0 39 0 AAATCCCCGTCCCGGCGCCAGAATCCCATT 0 62 1 ACCCCTACGGGACGGGACCCTAAATCCCGC 2 42 0 GGATTTGAACCCCGGAACCCCTACGGGACG 2 58 0 GTTCAAATCCCCGCCCCCGCACCATTTATT 2 78 1 TATTCACGCTCACCCCGCCCTTGTCGGTTT 2 104 1 TGTCGGTTTCCCTGCGGCGCGAGAATTAAA 2 125 1 GCCAAGCTACCCCACGGCCCCGCCTAAATA 4 24 0 CTTGGCTATCCTCCCGGCCTGGGGCGCCGG 4 48 1 ACCCGGGTCACCGGCGCCCCAGGCCGGGAG 4 58 0 GGTTCAAATCCCGGCGGCCCCACCAAAATA 4 85 1 ********** MAP Score: 18.3898 Motif 9 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTT 0 5 1 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAA 0 43 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGG 2 4 1 GGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTC 2 32 1 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCATTT 2 63 1 TCTCGCGCCGCAGGGAAACCGACAAGGGCGGGGTGAGCGTGA 2 107 0 TTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCG 4 22 1 GGATTTGAACCCGGGTCACCGGCGCCCCAGGCCGGGAGGATA 4 54 0 GCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAAAATA 4 73 1 * *** *** *** MAP Score: 15.9867 Motif 10 CCTGGTAGGGCGCGGGCCTTGAGAGCC 0 0 1 GCCTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTC 0 25 1 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGC 0 43 1 AAATCCCCGTCCCGGCGCCAGAATCCCATTCATTTGG 0 62 1 CCGAGCGGGGGTTGCCGAGCCTGGCCA 2 0 1 GGTTGCCGAGCCTGGCCAAAGGCGCGGGATTTAGGGT 2 19 1 CCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCA 2 62 1 CACCATTTATTCACGCTCACCCCGCCCTTGTCGGTTT 2 97 1 TTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCG 4 27 1 TGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGG 4 50 1 GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCAC 4 71 1 ** *** * **** MAP Score: 12.77 Motif 11 CCTGGTAGGGCGCGGGCCTTGAGAGCC 0 3 1 CCCCGGCGGGCAAACGCCCACGGGCTCTCAAGGC 0 25 0 GACGGGGATTTGAACCCCGGCGGGCAAACGCCCA 0 39 0 GGTTCAAATCCCCGTCCCGGCGCCAGAATCCCAT 0 57 1 TGGCCAGGCTCGGCAACCCCCGCTCGG 2 3 0 AAATCCCGCGCCTTTGGCCAGGCTCGGCAACCCC 2 17 0 ACCCCGGAACCCCTACGGGACGGGACCCTAAATC 2 46 0 GGTTCAAATCCCCGCCCCCGCACCATTTATTCAC 2 77 1 CATTTATTCACGCTCACCCCGCCCTTGTCGGTTT 2 100 1 TTGTCGGTTTCCCTGCGGCGCGAGAATTAAACTC 2 124 1 GCCAAGCTACCCCACGGCCCCGCCTAAATAAAGA 4 20 0 GTCACCGGCGCCCCAGGCCGGGAGGATAGCCAAG 4 48 0 GGATTTGAACCCGGGTCACCGGCGCCCCAGGCCG 4 62 0 GGTTCAAATCCCGGCGGCCCCACCAAAATATTGA 4 85 1 ** ******** MAP Score: 12.2249 Motif 12 GCTCTCAAGGCCCGCGCCCTACCAGG 0 0 0 TGAACCCCGGCGGGCAAACGCCCACGGGCTCTCAAG 0 27 0 CGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAATC 0 51 1 GTTGCCGAGCCTGGCCAAAGGCGCGGGATTTAGGGT 2 20 1 GCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCCG 2 40 1 TAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACC 2 65 1 ACCATTTATTCACGCTCACCCCGCCCTTGTCGGTTT 2 98 1 CCGCCCTTGTCGGTTTCCCTGCGGCGCGAGAATTAA 2 118 1 GTGGGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGC 4 39 1 GCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACC 4 73 1 * ** * * ***** MAP Score: 10.2654 Motif 13 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCC 0 10 1 CGGGCAAACGCCCACGGGCTCTCAAGGCCCGCGCCCTACCA 0 12 0 CGTGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGC 0 37 1 TTCTGGCGCCGGGACGGGGATTTGAACCCCGGCGGGCAAAC 0 44 0 CCTTTGGCCAGGCTCGGCAACCCCCGCTCGG 2 0 0 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGG 2 29 1 GAACCCCTACGGGACGGGACCCTAAATCCCGCGCCTTTGGC 2 33 0 CCGTCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGC 2 57 1 AATGGTGCGGGGGCGGGGATTTGAACCCCGGAACCCCTACG 2 63 0 CGGTTTCCCTGCGGCGCGAGAATTAAACTCTAGAAGGGGGA 2 128 1 CTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCC 4 21 1 CCGTGGGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGCCGG 4 37 1 TATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAATC 4 54 1 GGGATTTGAACCCGGGTCACCGGCGCCCCAGGCCGGGAGGA 4 56 0 TTTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCGGCGC 4 71 0 *** **** ** * MAP Score: 9.25315 Motif 14 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGG 0 9 1 CCTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGG 0 26 1 GGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTC 0 40 1 CCATTCATTTGGAGGGGGATAAA 0 87 1 CCGAGCGGGGGTTGCCGAGCCTGG 2 1 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTC 2 29 1 TCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCC 2 60 1 AATAAATGGTGCGGGGGCGGGGATTTGAACCCC 2 75 0 GTCGGTTTCCCTGCGGCGCGAGAATTAAACTCT 2 126 1 ATTCGAAGACAAGTGGGGGTCAAGCC 3 28 1 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGG 4 20 1 GGGCGCCGGTGACCCGGGTTCAAATCCCGGCGG 4 69 1 TATAGCTTTAGGGGTGGGCTAGA 6 21 1 * ******** * MAP Score: 8.35066 Motif 15 CTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCA 0 27 1 CGCCGGGACGGGGATTTGAACCCCGGCGGGCAAACG 0 43 0 CAAATGAATGGGATTCTGGCGCCGGGACGGGGATTT 0 62 0 CCCTAAATCCCGCGCCTTTGGCCAGGCTCGGCAACC 2 19 0 GCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCCGGG 2 42 1 TGCGGGGGCGGGGATTTGAACCCCGGAACCCCTACG 2 63 0 AAACCGACAAGGGCGGGGTGAGCGTGAATAAATGGT 2 98 0 CCGCCCTTGTCGGTTTCCCTGCGGCGCGAGAATTAA 2 118 1 TTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATC 4 22 1 CCGGGTCACCGGCGCCCCAGGCCGGGAGGATAGCCA 4 50 0 TGGGGCCGCCGGGATTTGAACCCGGGTCACCGGCGC 4 71 0 *** *** *** * MAP Score: 8.06782 Motif 16 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTT 0 3 1 GCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGC 0 34 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGG 2 2 1 AACCCCTACGGGACGGGACCCTAAATCCCGCGCCTTTGGCCAGG 2 29 0 GTCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCAT 2 59 1 CAAGGGCGGGGTGAGCGTGAATAAATGGTGCGGGGGCGGGGATT 2 83 0 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCG 4 20 1 TGGGGCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAA 4 67 1 * *** * * * *** MAP Score: 7.24445 Motif 17 CCTGGTAGGGCGCGGGCCTTGAGAGC 0 4 1 CGGGCCTTGAGAGCCCGTGGGCGTTTGCCCGC 0 22 1 GGGGATTTGAACCCCGGCGGGCAAACGCCCAC 0 38 0 GGGATTCTGGCGCCGGGACGGGGATTTGAACC 0 57 0 GCCAGGCTCGGCAACCCCCGCTCGG 2 3 0 CGAGCCTGGCCAAAGGCGCGGGATTTAGGGTC 2 25 1 GATTTAGGGTCCCGTCCCGTAGGGGTTCCGGG 2 46 1 GGGTTCAAATCCCCGCCCCCGCACCATTTATT 2 76 1 TTTATTCACGCTCACCCCGCCCTTGTCGGTTT 2 102 1 GAGTTTAATTCTCGCGCCGCAGGGAAACCGAC 2 126 0 CAAGCTACCCCACGGCCCCGCCTAAATAAAGA 4 20 0 CTTGGCTATCCTCCCGGCCTGGGGCGCCGGTG 4 48 1 TTGAACCCGGGTCACCGGCGCCCCAGGCCGGG 4 60 0 ATATTTTGGTGGGGCCGCCGGGATTTGAACCC 4 84 0 * * ******** MAP Score: 2.47622