AlignACE 3.0 10/20/99 AlignACE2 -i PA/PA_sum_all026_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944253415 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 Motif 1 CCTGGTAGGGCGCGGGCCTTGAGAGCCCG 1 7 1 GGCCTTGAGAGCCCGTGGGCGTTTGCCCGCCG 1 24 1 GTGGGCGTTTGCCCGCCGGGGTTCAAATCCCC 1 38 1 TCTGGCGCCGGGACGGGGATTTGAACCCCGGC 1 52 0 ATCCCCGTCCCGGCGCCAGAATCCCATTCATT 1 64 1 CCGAGCGGGGGTTGCCGAGCCT 3 0 1 GCCTGGCCAAAGGCGCGGGATTTAGGGTCCCG 3 28 1 AACCCCTACGGGACGGGACCCTAAATCCCGCG 3 41 0 AATGGTGCGGGGGCGGGGATTTGAACCCCGGA 3 72 0 AAACCGACAAGGGCGGGGTGAGCGTGAATAAA 3 102 0 GGTTTCCCTGCGGCGCGAGAATTAAACTCTAG 3 129 1 ATTAAACTCTAGAAGGGGGAATTTCGC 3 149 1 TTCTTTATTTAGGCGGGGCCGTGGGGTAGCTT 5 19 1 CGGCGCCCCAGGCCGGGAGGATAGCCAAGCTA 5 45 0 TCCCGGCCTGGGGCGCCGGTGACCCGGGTTCA 5 59 1 ATTTTGGTGGGGCCGCCGGGATTTGAACCCGG 5 82 0 TTGTGCCTAAAGGCGGGGGCGATATGAA 10 180 1 TAAAAAGTTTGGGAGGGATTCTTGAAAAATCG 11 10 0 AAAAAAGTTAGGAAGGGAAAATTAAAAAGTTT 11 32 0 ********* * MAP Score: 27.9479 Motif 2 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCC 1 43 1 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACC 3 63 1 TGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGT 5 50 1 GGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGG 3 32 1 CTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTG 1 11 1 GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACC 5 71 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCG 3 5 1 CTCCAAATGAATGGGATTCTGGCGCCGGGACGGGGATT 1 63 0 TCCCTGCGGCGCGAGAATTAAACTCTAGAAGGGGGAAT 3 133 1 ***** * * ** * MAP Score: 19.3421 Motif 3 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTT 1 8 1 TGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCG 1 39 1 TTCAAATCCCCGTCCCGGCGCCAGAATCCCATTCATTTGG 1 59 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGG 3 1 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGG 3 29 1 GTCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCA 3 59 1 TCACGCTCACCCCGCCCTTGTCGGTTTCCCTGCGGCGCGA 3 107 1 GCTTGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGG 5 47 1 TGGGGCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCA 5 67 1 * **** ** *** MAP Score: 14.2408 Motif 4 TTCGAATTATAAAAAGTTTTTAAAA 4 2 0 TACATCCCAAAAAAACATTGGAAAAGGGAAAGA 6 15 0 GCGAAAAATTTATATAAGTTAATTTC 7 3 1 GGTACATACTAAAAAGAAATAGATTTAAGAGCG 8 13 0 TGGGTTTATCAAAAAGTTGTCTAAAATATTTCG 10 66 1 AAGTTGTCTAAAATATTTCGGAATATTCGAGTT 10 79 1 ATAATTGTTGAAAAAGATTTAAATAAATATTTT 10 122 1 AGATTTAAATAAATATTTTTTCATAAATGTTCT 10 136 1 AGGGAAAATTAAAAAGTTTGGGAGGGATTCTTG 11 18 0 GGAAAAAAGTTAGGAAGGGAAAATTA 11 40 0 CCTCGTTGCCAAAAGGTTTTCGAGAGA 12 4 0 TTAAAGTCCTAAAAATATGTCGAAAATTATATA 13 168 1 CTATATAGTTAAATATATCGATACTTATTAAAT 14 56 0 ATCGAAGCGGAAAAATTTATATTGTCTAAAACA 15 43 0 ******** * * MAP Score: 13.9266 Motif 5 TCTCACGCCTCCAAATTAAAAAGATAAGAGAA 2 5 0 GGTCCCGTCCCGTAGGGGTTCCGGGGTTCAAATCCCC 3 53 1 GCAGGGAAACCGACAAGGGCGGGGTGAGCGTGAATAA 3 103 0 TTTTATAATTCGAAGACAAGTGGGGGTCAAGCC 4 21 1 GGCGGCCCCACCAAAATATTGAGGTGAGGCGGC 5 97 1 CTACATCCCAAAAAAACATTGGAAAAGGGAAAGAT 6 14 0 GGAGAATCTTCAAAGGGAATCGGGAAATTAACTTATA 7 22 0 GACCACTTTCCAGAATAGGATTGGAGAATCTTCAAAG 7 44 0 AAAAAGTTGTCTAAAATATTTCGGAATATTCGAGTTC 10 76 1 AACATTTGTGCCTAAAGGCGGGGGCGATATGAA 10 175 1 CACCTCGTTGCCAAAAGGTTTTCGAGAGA 12 2 0 AAACGACTTTCAAAAAGAAAAAGAAGAAAAAA 13 5 0 TCAGAATCTACAGAGACAATTTGGAGAACAGTAAGTA 13 79 0 AAGAAAACGCCCAAGAGGGGAACGTGAG 13 203 1 ATATTGAGAACAAAATTAAGGAGGAGATCGAA 14 152 1 * **** * ** ** MAP Score: 12.3841 Motif 6 CCTGGTAGGGCGCGGGCCTTGAGAGCCC 1 8 1 GCCTTGAGAGCCCGTGGGCGTTTGCCCGCC 1 25 1 GGGCGTTTGCCCGCCGGGGTTCAAATCCCC 1 40 1 AATCCCCGTCCCGGCGCCAGAATCCCATTC 1 63 1 CCGAGCGGGGGTTGCCGAGCC 3 1 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCC 3 29 1 ATAAATGGTGCGGGGGCGGGGATTTGAACC 3 77 0 AAACCGACAAGGGCGGGGTGAGCGTGAATA 3 104 0 CGGTTTCCCTGCGGCGCGAGAATTAAACTC 3 128 1 TCTTTATTTAGGCGGGGCCGTGGGGTAGCT 5 20 1 CTCCCGGCCTGGGGCGCCGGTGACCCGGGT 5 58 1 GGTTCAAATCCCGGCGGCCCCACCAAAATA 5 85 1 TGTGCCTAAAGGCGGGGGCGATATGAA 10 181 1 ********** MAP Score: 11.4627 Motif 7 GGGCTCTCAAGGCCCGCGCCCTACCAGG 1 2 0 CCTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTC 1 26 1 GCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGC 1 42 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAG 3 4 1 CTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGT 3 30 1 ATGGTGCGGGGGCGGGGATTTGAACCCCGGAACCCC 3 67 0 TTTAATTCTCGCGCCGCAGGGAAACCGACAAGGGCG 3 119 0 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTA 5 20 1 CGGCGCCCCAGGCCGGGAGGATAGCCAAGCTACCCC 5 41 0 CTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAAT 5 58 1 TTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCG 5 75 0 TGTGCCTAAAGGCGGGGGCGATATGAA 10 181 1 ******* * ** MAP Score: 10.3114 Motif 8 CCTGGTAGGGCGCGGGCCTTGAGAGCCC 1 4 1 CTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTT 1 27 1 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGG 1 43 1 GAATGGGATTCTGGCGCCGGGACGGGGATTTGAA 1 59 0 CCGAGCGGGGGTTGCCGAGCCTGGCCAAA 3 5 1 GTCCCGTCCCGTAGGGGTTCCGGGGTTCAAATCC 3 54 1 GTGAATAAATGGTGCGGGGGCGGGGATTTGAACC 3 77 0 GAGTTTAATTCTCGCGCCGCAGGGAAACCGACAA 3 124 0 TCGAAGACAAGTGGGGGTCAAGCC 4 30 1 CTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCT 5 21 1 ACCCGGGTCACCGGCGCCCCAGGCCGGGAGGATA 5 54 0 CAATATTTTGGTGGGGCCGCCGGGATTTGAACCC 5 84 0 TCGAAACGCCGATGGGGAGGAAGC 9 46 1 GTGCCTAAAGGCGGGGGCGATATGAA 10 182 1 AAACGCCCAAGAGGGGAACGTGAG 13 207 1 * ***** * *** MAP Score: 9.02501 Motif 9 TTCTGGCGCCGGGACGGGGATTTGAACCCCG 1 54 0 CCATTCATTTGGAGGGGGATAAA 1 87 1 CCGAGCGGGGGTTGCCGAGCCT 3 1 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCG 3 29 1 AAATGGTGCGGGGGCGGGGATTTGAACCCCG 3 74 0 GTTTCCCTGCGGCGCGAGAATTAAACTCTAG 3 130 1 TTAAACTCTAGAAGGGGGAATTTCGC 3 150 1 AATTCGAAGACAAGTGGGGGTCAAGCC 4 27 1 TTTAGGCGGGGCCGTGGGGTAGCTTGGCTAT 5 26 1 AAAAACATTGGAAAAGGGAAAGATAAAG 6 7 0 TCTTCAAAGGGAATCGGGAAATTAACTTATA 7 22 0 TTCCAGAATAGGATTGGAGAATCTTCAAAGG 7 43 0 TCGAAACGCCGATGGGGAGGAAGC 9 46 1 TAAACCCAAAGAATAGGAAAACTTTTAACCT 10 43 0 AAAAAGTTAGGAAGGGAAAATTAAAAAGTTT 11 32 0 AGAAAACGCCCAAGAGGGGAACGTGAG 13 204 1 GATGTAAATCGAAGCGGAAAAATTTATATTG 15 52 0 **** ****** MAP Score: 8.27564 Motif 10 TCACGCCTCCAAATTAAAAAGATAAGAGAA 2 3 0 TCTTCGAATTATAAAAAGTTTTTAAAA 4 0 0 CTACATCCCAAAAAAACATTGGAAAAGGGAAAGATA 6 13 0 GGGAATCGGGAAATTAACTTATATAAATTTTTCGC 7 8 0 GAAAGCTTAAAAATCAACCTTCGAAACGCCGATGGGG 9 26 1 ATAATTGTTGAAAAAGATTTAAATAAATATTTTTTCA 10 122 1 CGACTTTCAAAAAGAAAAAGAAGAAAAAA 13 2 0 CTGCCTTGATAAAACAAGTCGAGTAAAGGTAAAACGA 13 36 0 TTCCTACTAGAAATAAAACTCTTAATAGTAAAGTGGA 13 129 0 TCTAGTAGGAATATTAAAGTCCTAAAAATATGTCGAA 13 155 1 AATTATATAAAAAGAAAACGCCCAAGAGGGGAACGTG 13 192 1 GGCAAGCTTTATATTAAAACTCAAAAACTCGATA 14 7 0 GATACTTGGGATATAGAGCAACAAAAATAACCGAAAG 14 88 1 TTTTAGATGTAAATCGAAGCGGAAAAATTTATATTGT 15 51 0 **** ** **** MAP Score: 7.87536 Motif 11 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTG 1 3 1 TGGGATTCTGGCGCCGGGACGGGGATTTGAACCCCGGCGGGCAAAC 1 44 0 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGGGATTTAGGGT 3 10 1 TGAATAAATGGTGCGGGGGCGGGGATTTGAACCCCGGAACCCCTAC 3 64 0 TTATTCACGCTCACCCCGCCCTTGTCGGTTTCCCTGCGGCGCGAGA 3 103 1 AGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGC 5 29 1 GGCCTGGGGCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACC 5 63 1 * * * ** * *** * MAP Score: 7.27498 Motif 12 TTCGAATTATAAAAAGTTTTTAAAA 4 2 0 GCGAAAAATTTATATAAGTTAATTTCC 7 4 1 ATACTAAAAAGAAATAGATTTAAGAGCGTTT 8 8 0 GGGTTTATCAAAAAGTTGTCTAAAATATTTCGG 10 67 1 GATAATTGTTGAAAAAGATTTAAATAAATATTT 10 121 1 AACATTTATGAAAAAATATTTATTTAAATCTTT 10 134 0 TAAAGTCCTAAAAATATGTCGAAAATTATATAA 13 169 1 TTGCCGAAATAGAATATATTTAATAAGTATCGA 14 39 1 AAAAATAACCGAAAGGTTTATAAGTTCGAACTA 14 110 1 AATCGAAGCGGAAAAATTTATATTGTCTAAAAC 15 44 0 ATTTACATCTAAAAATGATATAATTGGGATTAT 15 74 1 **** ** * *** MAP Score: 5.78358 Motif 13 CTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTT 1 11 1 ATTTGAACCCCGGCGGGCAAACGCCCACGGGCTCTC 1 30 0 AAATCCCCGTCCCGGCGCCAGAATCCCATTCATTTG 1 62 1 CCGAGCGGGGGTTGCCGAGCCTGGCC 3 0 1 GGTTGCCGAGCCTGGCCAAAGGCGCGGGATTTAGGG 3 19 1 CCCGGAACCCCTACGGGACGGGACCCTAAATCCCGC 3 42 0 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCA 3 63 1 TTAATTCTCGCGCCGCAGGGAAACCGACAAGGGCGG 3 118 0 TTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATC 5 22 1 TGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGG 5 50 1 GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCA 5 71 1 ** *** ** *** MAP Score: 5.33155 Motif 14 TCACGCCTCCAAATTAAAAAGATAAGAGAA 2 3 0 TCGGGAAATTAACTTATATAAATTTTTCGC 7 3 0 GTACATACTAAAAAGAAATAGATTTAAGAGCGTTT 8 8 0 CTAGCTTAAGAACTCGAATATTCCGAAATATTTTAGA 10 85 0 TAGGAAGGGAAAATTAAAAAGTTTGGGAGGGATTCTT 11 19 0 ACGACTTTCAAAAAGAAAAAGAAGAAAAAA 13 3 0 AATATGTCGAAAATTATATAAAAAGAAAACGCCCAAG 13 181 1 TTTATATTAAAACTCAAAAACTCGATA 14 0 0 AAGCTTGCCGAAATAGAATATATTTAATAAGTATCGA 14 35 1 GATATAGAGCAACAAAAATAACCGAAAGGTTTATAAG 14 97 1 TCTCAATATGAACTAATATAGTTCGAACTTATAAACC 14 124 0 TCATATTGAGAACAAAATTAAGGAGGAGATCGAA 14 150 1 TTACATCTAAAAATGATATAATTGGGATTATGCAAAT 15 76 1 GGGATTATGCAAATAATAAACTGGTGAAATAC 15 99 1 **** ***** * MAP Score: 5.23713 Motif 15 CAAACGCCCACGGGCTCTCAAGGCCCGCGCCCTACCAGG 1 4 0 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAATCC 1 43 1 CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGG 3 1 1 GGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCCGG 3 32 1 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCATTTATT 3 63 1 GCCGGGAGGATAGCCAAGCTACCCCACGGCCCCGCCTAAATAAAG 5 21 0 GCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAATCCC 5 52 1 GCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAAAATATTG 5 73 1 * ** ** * *** * MAP Score: 5.08527 Motif 16 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGT 1 3 1 GCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCCGCCG 1 19 1 GCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCCCCG 1 34 1 TGGGATTCTGGCGCCGGGACGGGGATTTGAACCCCGG 1 53 0 CCGAGCGGGGGTTGCCGAGCCTGGCCAA 3 1 1 GACCCTAAATCCCGCGCCTTTGGCCAGGCTCGGCAAC 3 20 0 GATTTAGGGTCCCGTCCCGTAGGGGTTCCGGGGTTCA 3 46 1 TGAATAAATGGTGCGGGGGCGGGGATTTGAACCCCGG 3 73 0 GGGAAACCGACAAGGGCGGGGTGAGCGTGAATAAATG 3 100 0 CGCCCTTGTCGGTTTCCCTGCGGCGCGAGAATTAAAC 3 119 1 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTAT 5 20 1 GGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGCCGGT 5 42 1 CTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAATC 5 58 1 CAATATTTTGGTGGGGCCGCCGGGATTTGAACCCGGG 5 81 0 ATCAACCTTCGAAACGCCGATGGGGAGGAAGC 9 38 1 ACATTTGTGCCTAAAGGCGGGGGCGATATGAA 10 176 1 CTCACGTTCCCCTCTTGGGCGTTTTCTTTTTA 13 199 0 * **** **** * MAP Score: 3.79706 Motif 17 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGG 1 9 1 GGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCC 1 41 1 ATGGGATTCTGGCGCCGGGACGGGGATTTGAAC 1 58 0 CCATTCATTTGGAGGGGGATAAA 1 87 1 CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTC 3 29 1 CCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCC 3 61 1 GTGAATAAATGGTGCGGGGGCGGGGATTTGAAC 3 78 0 GTTTAATTCTCGCGCCGCAGGGAAACCGACAAG 3 123 0 TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGG 5 20 1 ACCGGCGCCCCAGGCCGGGAGGATAGCCAAGCT 5 46 0 GGGCGCCGGTGACCCGGGTTCAAATCCCGGCGG 5 69 1 ATATTTTGGTGGGGCCGCCGGGATTTGAACCCG 5 83 0 TTCGAAACGCCGATGGGGAGGAAGC 9 45 1 TGTGCCTAAAGGCGGGGGCGATATGAA 10 181 1 ** ***** * ** MAP Score: 0.608183