AlignACE 3.0 10/20/99 AlignACE2 -i PA/PA_operons001_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944248918 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 PAB3002 52 PAB3002 #1 PAB2351 68 PAB2351 #2 PAB2350 300 hypothetical protein #3 PAB2260 157 PAB2260 #4 PAB2178 50 PAB2178 #5 PAB2177 53 PAB2177 #6 PAB2174_PAB0180 87 PAB2174: hypothetical protein, PAB0180: PAB0180 #7 glpk 26 PAB2406 #8 PAB0182 21 hypothetical protein #9 glpA 143 PAB0183 #10 rpl37AE 60 PAB7067 #11 PAB2357 42 hypothetical protein #12 fus 80 PAB0187 #13 PAB2140 64 PAB2140 #14 PAB2139 48 PAB2139 #15 PAB2119 139 hypothetical protein #16 PAB2118 68 hypothetical protein #17 PAB2117 54 hypothetical protein #18 PAB2116 294 hypothetical protein #19 PAB0252 121 hypothetical protein #20 PAB2040 69 PAB2040 #21 PAB2039 124 hypothetical protein #22 gltX 300 PAB0323 #23 PAB0359 43 hypothetical protein #24 rps13P 100 PAB0360 #25 PAB0422 300 hypothetical protein #26 rpoH 241 PAB7151 #27 tuf 281 PAB0465 #28 rps10P 36 PAB0466 #29 PAB1701 47 PAB1701 #30 PAB1637 74 PAB1637 #31 adkE 60 PAB0739 #32 PAB1434 41 PAB1434 #33 PAB1433 58 hypothetical protein Motif 1 TAGGCAGAAATTTGGAGGTGATTTAA 27 265 1 ATCCCATTCATTTGGAGGGGGATAAA 24 84 1 AATGCACCTCTCTGGAGGTGTTGAA 6 72 1 AATCCTCTATTTTGGGGGTGTTTG 13 50 1 TCTATAAGGTTTGGGGGGTGCATT 19 107 1 TCCTTTTTAGTTTTGAGGTGGAGCCT 9 127 1 TGCAAAAAAGTCTGGTGGGGCCGCCGGGAT 25 188 0 AATAACAAAATGTGGAGGTGTGGATG 18 6 0 ATTTAAATACTTCGGAGGTGAAGAAACTTC 19 55 1 AGCAAACACTTCTGGAGGCGAGAGCC 20 53 1 AGCAAGCTTATCGGGTGGTGAAA 12 67 1 CTTCTTTAATTCTTGGGGTGATTTGA 28 20 1 GGAGATATAGTTGTGAGGTGGTCAAAAATG 22 196 0 GGTAGCCTAGCCTGGTGGGGCGGGGGACTT 25 53 1 AAGAAAATCCCTTGGAGGGCAACA 15 125 1 GGTAATCGCGTTTGAGGGGGATGGTATATC 2 13 1 CTAAAAAACTTTTCGGGGGGCAATTCTCC 26 222 1 CCTTTGGGTATTTGGAGGGTTAAAAATTTA 23 23 0 TTTTCTTGGTCTTGGAGCTGTTTTGGTGTT 15 102 0 CTTAATAAACCTGGGAGGTCGCGAG 29 5 0 TCTTTGAAGTTTTTAAGGTGATTGGTGGGC 6 27 0 TATATATATCCTTGATGGTGCTTTGGC 31 43 1 ********** MAP Score: 27.8786 Motif 2 TTGGAGGGTTAAAAATTTAAAGGTTAAAGTT 23 11 0 CCGATGTCCGAAAATTTTAAAAGGCTATCCC 27 223 1 AAGGCTGAGGAAAGATTTAAAACCTGGAAAT 9 90 1 TCCAATTCCGAAAAGTTTATATATCTCTATT 18 65 0 ATTACCGAAAATTTTATATACTTTCTAC 26 7 1 GAACTTGGGAAAAGCTTTATAACTCTACCTT 12 23 1 AAAGGTTTATATATTAACTGC 25 0 1 AAATGTTAATAAAATTTTAGAGGAGATATAG 22 216 0 AGGTTGAGCTAAAATTTTAGAAACGAAATGT 22 241 0 TATTTAATTTAAAAATTTTAAGAAAAG 0 6 0 ACAAACAGGTAAAAGTTTTAATATGATAACT 25 256 1 AAGGAAGGGAAAAGTTTTTAATTGAAAATGG 3 80 0 CCATTTTGCAAAAATTTTTTAAGAATTTTTA 15 24 1 TGCCCCCCGAAAAGTTTTTTAGGATGAACTT 26 213 0 AAATCTTATGAAAAATTGAAACAGAA 16 5 0 AATCTTTGGCAAAGTTTGATATGGATGAGTT 2 72 1 AAATTAAAATAAAATTTGAGA 14 0 0 CAATTTTTCATAAGATTTAAATATGCCCCTT 16 18 1 TCATGGATTCTAAATTTTATATTTCTAATGA 2 234 0 GATTAACTTTAAAAGTTGTGAAGATGAATTG 21 80 1 CTAAGTTTTTAACCTCTTCTTC 11 1 1 CCAACTTAGTTAAGTTTTTAAACTCCCCTTT 27 132 1 **** ****** MAP Score: 26.3587 Motif 3 TTATATACTTCCTCCCTTCAAATCCTCTCTTAGATTTAACCCT 1 16 1 GGAGAGGCCTCAAGGGAGTTAAGCCTGATATTCGAACGCTATT 18 150 0 TCGCGCCATATCGCGTTTGCTATCCCGTAAAACTCTGGAATGC 22 41 1 AGGAAGTTATCGACGTTGGGGATCCTGGGCTAGACAGCATTCC 22 77 0 TGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCCGCC 24 12 1 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAAT 24 43 1 TTCTCGGTGCCCCGGTAGCCTAGCCTGGTGGGGCGGGGGACTT 25 40 1 ATCCCCAGGTCGCGGGTTCAAATCCCGCCCGGGGCTCCAAGAG 25 86 1 GTCTATCCTGCGGGCTTTGGGAGCCCGTGACCCGGGTTCAAAT 25 147 1 GAGCCCGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAGACT 25 167 1 CGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGCGGCCGCTTG 26 52 1 AGCGGCAGGTCCCGGGTTCAAAGCCCGGCCGGGGCTCCATTCT 26 98 1 CATCGGCTCCCTCCGGCGGGAAACCCGCCACAGAGGAGGAAGC 27 186 0 * ** * * **** * MAP Score: 25.7481 Motif 4 GCCTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCC 24 25 1 CTTGGTCTATCCTGCGGGCTTTGGGAGCCCGTGACCCGGGTTC 25 143 1 AGCGGCAGGTCCCGGGTTCAAAGCCCGGCCGGGGCTCCATTCT 26 98 1 TATTAGTTTCCCTGAGAGAAATCCCAAACGGTGGTTCCC 5 24 1 CGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGCGGCCGCTTG 26 52 1 TTCTCGGTGCCCCGGTAGCCTAGCCTGGTGGGGCGGGGGACTT 25 40 1 TCGGCTCCCTCCGGCGGGAAACCCGCCACAGAGGAGGAAGCCT 27 184 0 CTCTTGGAGCCCCGGGCGGGATTTGAACCCGCGACCTGGGGAT 25 86 0 GAGCCCGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAGACT 25 167 1 CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGG 24 0 1 CCTATACCACCTGATAGCATATACGCGTAAAGGGGCATATTT 16 36 0 TATTAAAACTCGAGGTGTCTATAAGGTTTGGGGGGTGCATT 19 90 1 ** * * ** * * * * MAP Score: 17.6574 Motif 5 TTCTAATGACTTCCTCCTTTTTAGCTTCCG 2 213 0 TCTTCTCCTTTTCCTCCTTCGTGAACTCCT 22 138 1 CAAATGAGGCTTCCTCCTCTGTGGCGGGTT 27 178 1 ATTTATATACTTCCTCCCTTCAAATCCTCT 1 14 1 ACTCCTTCCCCTTTTCCACTTTTAG 3 5 1 TTAATTTATTTTCCCCTTTCAATGTAAAGG 18 255 0 ATCTTAATTAATCCTCTTTCCCTTTACATT 18 235 1 TTTATCCCCCTCCAAATGAATGG 24 87 0 CCCTTTCCCCCACTCTTAACCTTG 0 38 0 TTCCCCCACCTCCTTTTAGA 19 0 1 TTGCTTGTAAATCCTCTATTAAAACTTAAT 30 47 0 GCACATTAAAATCCTCTATTTTGGGGGTGT 13 41 1 CTCCCTTCAAATCCTCTCTTAGATTTAACC 1 27 1 TTTCGAAGGTTTCCACCTTCTGTGATTAAA 15 51 0 TTCTTCTTCTTTTTTAAACAATA 20 3 1 AGCACCATAGTTCTTCCCTTTTATGCTCAA 9 27 1 AGTTTTTAAACTCCCCTTTTAATCTCAAAC 27 144 1 TATTAATGCAATCCACTTTTACAAACAGGT 25 236 1 ATCTCCAAGATCTTCCATTTTGCAAAAAT 15 9 1 ATCTTCCACCGAAACTATTT 33 48 0 TTTATATACTTTCTACCTCTGAGGAATTCT 26 22 1 ********** MAP Score: 17.3552 Motif 6 CCCTTTCCCCCACTCTTAACCTTGGT 0 36 0 GCTCCAACCCTCCCTTATCAGGG 1 55 0 AAATATACGCTAATGCACCTCTCTGGAGGTGT 6 61 1 TTCAACACCTCCAGAGAGGTGC 6 75 0 TCTCAACACCTGCTGGAATGGTG 14 35 0 CATCCACACCTCCACATTTTGTT 18 1 1 TTCCCCCACCTCCTTTTAGATAC 19 1 1 TTTTTGAAGTTTCTTCACCTCCGAAGTATTTA 19 58 0 CTTTTCCTCCTTCGTGAACTCCTTTATTTTTC 22 145 1 GCTCCCACCACTCTTCACGAACGA 22 286 0 TTTATCCCCCTCCAAATGAATGG 24 87 0 ATTACAAGTCCCCCGCCCCACCAGGCTAGGCT 25 56 0 CAAGCTACCCTACGGCCCCTCTTGGAGCCCCG 25 115 0 GGGCTTTGAACCCGGGACCTGCCGCTTACCAA 26 92 0 TAGGATGAACTTCACCAACTCCCGGCTTAAGC 26 193 0 TTAAATCACCTCCAAATTTCTGC 27 268 0 CTCGCGACCTCCCAGGTTTATT 29 0 1 *** ******* MAP Score: 16.0862 Motif 7 CCTGGTAGGGCGCGGGCCTTGAGAGCCC 24 7 1 GCGGGCAAACGCCCACGGGCTCTCAAGGCCC 24 23 0 GGATTTGAACCCCGGCGGGCAAACGCCCACG 24 37 0 ATGGGATTCTGGCGCCGGGACGGGGATTTGA 24 60 0 ACCAGGCTAGGCTACCGGGGCACCGAGAAAT 25 38 0 TAGCCTGGTGGGGCGGGGGACTTGTAATCCC 25 60 1 GTAATCCCCAGGTCGCGGGTTCAAATCCCGC 25 83 1 TCTTGGAGCCCCGGGCGGGATTTGAACCCGC 25 97 0 GGCTCCCAAAGCCCGCAGGATAGACCAAGCT 25 141 0 TTTGAACCCGGGTCACGGGCTCCCAAAGCCC 25 158 0 GTCTGGTGGGGCCGCCGGGATTTGAACCCGG 25 178 0 CTCGGCTAATGCCCCGGTGGCTCAGCCTGGT 26 50 1 GTAAGCGGCAGGTCCCGGGTTCAAAGCCCGG 26 95 1 AGAATGGAGCCCCGGCCGGGCTTTGAACCCG 26 110 0 CTTCCTCCTCTGTGGCGGGTTTCCCGCCGGA 27 187 1 CTCGCGACCTCCCAGGTTTATTAAGGTG 29 7 1 ********* * MAP Score: 9.03933 Motif 8 GCTCTCAAGGCCCGCGCCCTACCAGG 24 3 0 GATTTGAACCCCGGCGGGCAAACGCCCACGGGC 24 34 0 GGGGTTCAAATCCCCGTCCCGGCGCCAGAATCC 24 55 1 TTTCCATTTCTCGGTGCCCCGGTAGCCTAGCCT 25 33 1 GATTACAAGTCCCCCGCCCCACCAGGCTAGGCT 25 56 0 GGGATTTGAACCCGCGACCTGGGGATTACAAGT 25 79 0 CAAATCCCGCCCGGGGCTCCAAGAGGGGCCGTA 25 104 1 GGGATTTGAACCCGGGTCACGGGCTCCCAAAGC 25 160 0 GGTTCAAATCCCGGCGGCCCCACCAGACTTTTT 25 181 1 GGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGC 26 53 1 GGGCTTTGAACCCGGGACCTGCCGCTTACCAAG 26 91 0 CAAAGCCCGGCCGGGGCTCCATTCTAATAAAGC 26 116 1 ATAGTGGTCACCGCTGAGCCACCAACTTAGTTA 27 111 1 TCCTCTGTGGCGGGTTTCCCGCCGGAGGGAGCC 27 192 1 ****** *** * MAP Score: 6.24211 Motif 9 GCAAACACTTCTGGAGGCGAGAGCC 20 54 1 CCTGGTAGGGCGCGGGCCTTGAGAG 24 1 1 GAATGGGATTCTGGCGCCGGGACGGGGATTTGAA 24 59 0 GGCTAGGCTACCGGGGCACCGAGAAATGGAAAAG 25 31 0 GTAGCCTAGCCTGGTGGGGCGGGGGACTTGTAAT 25 54 1 ACGGCCCCTCTTGGAGCCCCGGGCGGGATTTGAA 25 102 0 CCTGCGGGCTTTGGGAGCCCGTGACCCGGGTTCA 25 153 1 AAAAAGTCTGGTGGGGCCGCCGGGATTTGAACCC 25 180 0 GTGGCTCAGCCTGGTAGAGCGGCCGCTTGGTAAG 26 66 1 CGCTTGGTAAGCGGCAGGTCCCGGGTTCAAAGCC 26 89 1 CTTTATTAGAATGGAGCCCCGGCCGGGCTTTGAA 26 114 0 AAAGCTTAAGCCGGGAGTTGGTGAAGTTCATCCT 26 190 1 GGGTTTCCCGCCGGAGGGAGCCGATGTCCGAAAA 27 203 1 CTTAATAAACCTGGGAGGTCGCGAG 29 1 0 **** ** ** ** MAP Score: 6.00707 Motif 10 AGTGGTAATCGCGTTTGAGGGGGATGGTATAT 2 1 1 AATTATAGATGTGAATAGATTACCAGAGGGCTCCAATTCCG 18 86 0 TATCGACGTTGGGGATCCTGGGCTAGACAGCATTCCAGAGT 22 72 0 AAACGCCCACGGGCTCTCAAGGCCCGCGCCCTACCAGG 24 7 0 TTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCCC 24 28 1 CCAAATGAATGGGATTCTGGCGCCGGGACGGGGATTTGAAC 24 58 0 TCTCGGTGCCCCGGTAGCCTAGCCTGGTGGGGCGGGGGACT 25 41 1 CCCGCGACCTGGGGATTACAAGTCCCCCGCCCCACCAGGCT 25 61 0 GGAGCCCCGGGCGGGATTTGAACCCGCGACCTGGGGATTAC 25 83 0 CCCGGGTCACGGGCTCCCAAAGCCCGCAGGATAGACCAAGC 25 142 0 GCCCGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAGACT 25 169 1 GATCGAGATAGTTGCAAAAAAGTCTGGTGGGGCCGCCGGGA 25 189 0 CTGAGGAATTCTCGGCTAATGCCCCGGTGGCTCAGCCTGGT 26 40 1 GTGGCTCAGCCTGGTAGAGCGGCCGCTTGGTAAGCGGCAGG 26 66 1 CGGCAGGTCCCGGGTTCAAAGCCCGGCCGGGGCTCCATTCT 26 100 1 CCGAGCAAATGAGGCTTCCTCCTCTGTGGCGGGTTTCCCGC 27 173 1 * ** *** * *** MAP Score: 1.65425