AlignACE 3.0 10/20/99 AlignACE2 -i CT/CT_sum_all027_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944245161 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 CT406 300 hypothetical protein #1 CT409 101 Amino acid permease #2 pcnB_1 214 PolyA Polymerase #3 gltX 271 Glutamyl-tRNA Synthetase #4 euo 300 CHLPS Euo Protein #5 CT645 100 hypothetical protein #6 clpP_2 166 CLP Protease #7 tig 300 Trigger Factor-peptidyl prolyl isomerase #8 rsbV_2 153 Sigma Regulatory Factor Motif 1 CCCAAGCTACCTCTTTCTTTCATTTCTGAA 0 226 1 TCTCTTCTTCCTCTATTTTTCCCCTTTTTA 7 35 1 AAATGTTACCTTCTCTTTTTAAGGATTTTG 4 93 1 TTCCACTCTATTCTCTCTTCCTAGTGTAGC 4 143 0 CCTATATTATCTCTTTTTTCCTTTTTGTTT 1 43 0 TAGATGGGGTCTTTCTTTTCTAGGGTCAAG 6 91 1 TAGCGTTTTTCTTTATCTTTTTAAAATGAA 5 11 1 CAAAAAATTCTTTCTTTCAAGGATCTC 1 7 1 AAGGAAACTTTTCTATCTTTATGAAATGAA 3 234 0 CGGAGGGGGGCTTTTTTTTTGTTGAAAAAG 3 69 1 AGTCCAATTTTTCTTTTTTTACCACCTCTT 7 76 1 AGCTTTATGACTCTCTCTCCTT 2 2 0 AAAAAGATGTTTTTATTTTTTAAAATGAGC 5 45 0 AGTCTCTACCTTTTATCTTCCAATAAGGGT 8 79 0 CATCACCCGCTTCTCTTTCCCGGATAACTT 7 265 1 GGGTTTCTCACTTTTTTTCTATTTAAAAAA 8 53 0 CTCTTTTTTCCTTTTTGTTTGGTAGAGAGA 1 33 0 AAATGATGAATTCTATGTTTAAGTGTCTCT 6 38 0 CAAAAATAGCATTTATTTTTAACAAACCGC 4 38 1 AGATGAGAGGATTTATTTTTAAGTGGACGA 4 261 1 ATTTGTGGTGATTTTTTTTCAAAAGTCGCC 0 168 0 ********** MAP Score: 18.6185 Motif 2 TTTTTAAAATGAAGAGCGCTCATTTTAAAA 5 28 1 GTTCTCTCCAGGAAAGCTCTTCCTATAATA 2 132 0 TTTGATCGCAGGAAAACGCTTGACCCAAGA 6 11 1 AAAAGATAAAGAAAAACGCTAA 5 2 0 AGAATAGAGTGGAAAGGGCTTGTCCGACTT 4 159 1 ATTCTTGACGGAAGAAGTCTCTACCTTTTA 8 94 0 GCTTTCCTGGAGAGAACTCTAAAAGCCTTC 2 145 1 TTAAAAAACTCTGTTTATAATT 5 88 0 AAAGGATTGCGAAAAACTCCCCAGATTATC 7 156 1 GTGCCCTTACAGAGAAGGCTCTATCT 3 6 0 AAAAACTTTGGAAAAAGGTTTTTTGAGAAG 7 109 0 TTTTGTTGAAAAAGAGCTCCGAAAAACTCG 3 85 1 AGGTTTTACAAAAAAACTTTGGAAAAAGGT 7 120 0 TTGTAAAAAACTTTACAAAACTTT 4 4 1 AAAGAGCTCCGAAAAACTCGTTATTTTAGT 3 95 1 ACCTCTTCTTAGAAAGGTTTTCTCTACGGG 0 63 0 GCACAGCAGGGGAGAGCTTGGGCCTCCTCC 3 32 1 ACCTTTCTAAGAAGAGGTTCTTTTCAACAC 0 75 1 CCCGCGAGAAGAAGAGCATTCTAGATAATC 7 179 0 TCATAAAGATAGAAAAGTTTCCTTTCCTGG 3 240 1 TCTTTTTCAAGAAAAACATTAATTATAAAC 5 68 1 TAGAGGAAGAAGAGAGGGTCAAAATTTTCA 7 20 0 ********** MAP Score: 16.7277 Motif 3 AAACCTTTCTAAGAAGAGGTTCTTTTCAACACAA 0 73 1 CAGAAATGAAAGAAAGAGGTAGCTTGGGGGATCT 0 220 0 CACCCGCGAGAAGAAGAGCATTCTAGATAATCTG 7 177 0 AAAATAGAGGAAGAAGAGAGGGTCAAAATTTTCA 7 20 0 TTTCTATTATAGGAAGAGCTTTCCTGGAGAGAAC 2 128 1 TCGCTACACTAGGAAGAGAGAATAGAGTGGAAAG 4 141 1 CAAAATCCTTAAAAAGAGAAGGTAACATTTTCCC 4 89 0 ACAAAAAGGAAAAAAGAGATAATATAGGGTAATT 1 45 1 GATCCTTGAAAGAAAGAATTTTTTG 1 1 0 GGAAGATAAAAGGTAGAGACTTCTTCCGTCAAGA 8 88 1 AGATAGAGCCTTCTCTGTAAGGGC 3 0 1 AGAAGAATCTAAAAAGAATTGCTTTTTTAAATAG 8 31 1 AAGACAGGCCAAGATGAGAGGATTTATTTTTAAG 4 250 1 TTTATTTTTTAAAATGAGCGCTCTTCATTTTAAA 5 30 0 GTTGATGATCAAAAAGACGTGCCTTATATATGGT 2 32 1 ACCCTAGAAAAGAAAGACCCCATCTAATTCAAAA 6 83 0 CATTAATTATAAACAGAGTTTTTTAA 5 84 1 AAGGAGAGAGAGTCATAAAGCTGT 2 0 1 GTTTTTCTTGAAAAAGATGTTTTTATTTTTTAAA 5 51 0 CATTTCATAAAGATAGAAAAGTTTCCTTTCCTGG 3 236 1 AAAGTCGCCAAGAATGAATCTCTCTGGTATCGTT 3 131 1 AAATAGAAAAAAAGTGAGAAACCCTTATTGGAAG 8 59 1 ******** ** MAP Score: 16.6262 Motif 4 GACCGCCCGTAGAGAAAACCTTTCTAAGAAGAGGTTCT 0 58 1 TTTGTTTGGTAGAGAGATCCTTGAAAGAAAGAATTTTT 1 12 0 CTATAATAGAAAAAATTACGTTTACAAGGGCAAAATCA 2 102 0 TATTATAGGAAGAGCTTTCCTGGAGAGAACTCTAAAAG 2 132 1 GAGAACTCTAAAAGCCTTCTTGCTCAAGGACAAAATCC 2 156 1 AGATAGAGCCTTCTCTGTAAGGGCACAGCAGG 3 4 1 TAAAGATAGAAAAGTTTCCTTTCCTGGGTTAGTAGCGA 3 243 1 AAAACTTTACAAAACTTTGTTTCAAAAATAGCATTTAT 4 16 1 CACTAGGAAGAGAGAATAGAGTGGAAAGGGCTTGTCCG 4 147 1 CCAGTCTCTTAGAGCTATGCTTATTGAATCTCTAAGTC 4 184 0 CATAGCTCTAAGAGACTGGGTTAGAAGGTCACAGAGCC 4 203 1 AGAAGGTCACAGAGCCATTATTCACAAGACAGGCCAAG 4 225 1 GGCCAAGATGAGAGGATTTATTTTTAAGTGGACGAGGG 4 256 1 TTTAAAATGAAGAGCGCTCATTTTAAAAAATAAAAACA 5 30 1 TTTAAAAAATAAAAACATCTTTTTCAAGAAAAACATTA 5 51 1 AACTTTGGAAAAAGGTTTTTTGAGAAGGTGAAGAGGTG 7 98 0 TATCCGGGAAAGAGAAGCGGGTGATGAGGCTTGAACTC 7 253 0 AGAATACCCATTGGTAAGTTATCCGGGA 7 282 0 TCTATTTAAAAAAGCAATTCTTTTTAGATTCTTCTAGA 8 28 0 **** * ** *** MAP Score: 15.0171 Motif 5 AAGGCAAACAGCGGTTACTTATAATCAAAAAATAATTAT 0 12 1 TTTCTAAGAAGAGGTTCTTTTCAACACAAGACACAGGAT 0 78 1 AGATACCACGGTTTTTATTTTAATGGATAAAATCCTGTG 0 109 0 CAAAAAATTCTTTCTTTCAAGGATCTCTCTACCAA 1 6 1 ATTTTCAAGGAATTTTAGTTTTAATCATATATTTT 1 76 1 GAGTTTTTCGGAGCTCTTTTTCAACAAAAAAAAAGCCCC 3 75 0 CCCGGGACGGGGTGTTCATTTCATAAAGATAGAAAAGTT 3 220 1 AAACTTTACAAAACTTTGTTTCAAAAATAGCATTTATTT 4 17 1 TTCAAAAATAGCATTTATTTTTAACAAACCGCTTGATTA 4 36 1 CAAGATGAGAGGATTTATTTTTAAGTGGACGAGGGAGGA 4 259 1 TAAAATGAGCGCTCTTCATTTTAAAAAGATAAAGAAAAA 5 16 0 AAAATGAAGAGCGCTCATTTTAAAAAATAAAAACATCTT 5 33 1 AAAAAATAAAAACATCTTTTTCAAGAAAAACATTAATTA 5 54 1 TTTCAAGAAAAACATTAATTATAAACAGAGTTTTTTAA 5 72 1 ATCTAAAAAGAATTGCTTTTTTAAATAGAAAAAAAGTGA 8 37 1 * ** *** ** * * MAP Score: 13.7769 Motif 6 TAAGAAGAGGTTCTTTTCAACACAAGACACAG 0 82 1 TTGTGGTGATTTTTTTTCAAAAGTCGCCTAAT 0 164 0 AATCAAGAATTGTGTTACTAGATCCCCCAAGC 0 201 1 CAAAAAATTCTTTCTTTCAAGGATCTCTCTAC 1 10 1 AAATCACCTATATGTTTCTAAAAATTTTCAAG 2 76 0 TTTTCGGAGCTCTTTTTCAACAAAAAAAAAGC 3 78 0 TTCAAAGCCCTATGTTCCTAAACGATACCAGA 3 153 0 TTTACAAAACTTTGTTTCAAAAATAGCATTTA 4 21 1 AAAAATAGCATTTATTTTTAACAAACCGCTTG 4 39 1 AATGTTACCTTCTCTTTTTAAGGATTTTGCAA 4 94 1 GATGAGAGGATTTATTTTTAAGTGGACGAGGG 4 262 1 CGTTTTTCTTTATCTTTTTAAAATGAAGAGCG 5 14 1 AAGATGTTTTTATTTTTTAAAATGAGCGCTCT 5 40 0 AATAAAAACATCTTTTTCAAGAAAAACATTAA 5 58 1 AAAGACCCCATCTAATTCAAAATACACCTACG 6 73 0 GATGGGGTCTTTCTTTTCTAGGGTCAAGAGTA 6 93 1 GTCCAATTTTTCTTTTTTTACCACCTCTTCAC 7 77 1 TTTTCCAAAGTTTTTTTGTAAAACCTACAAGC 7 124 1 TAAAAAGAATTGCTTTTTTAAATAGAAAAAAA 8 40 1 * * ******** MAP Score: 12.8437 Motif 7 CTTTCTAAGAAGAGGTTCTTTTCAACACAAGACACAG 0 77 1 TGCAGATATTAGGCGACTTTTGAAAAAAAATCACCAC 0 157 1 ATTTTCAAGGAATTTTAGTTTTAATCATATATTTT 1 76 1 AAACTTTACAAAACTTTGTTTCAAAAATAGCATTTAT 4 17 1 TTTCAAAAATAGCATTTATTTTTAACAAACCGCTTGA 4 35 1 CCAAGATGAGAGGATTTATTTTTAAGTGGACGAGGGA 4 258 1 TAAAATGAAGAGCGCTCATTTTAAAAAATAAAAACAT 5 32 1 TAAAAAATAAAAACATCTTTTTCAAGAAAAACATTAA 5 53 1 TTTCAAGAAAAACATTAATTATAAACAGAGTTTTTTA 5 72 1 TTTGATGCGTAGGTGTATTTTGAATTAGATGGGGTCT 6 66 1 ACCTTTTTCCAAAGTTTTTTTGTAAAACCTACAAGCA 7 120 1 GAATCTAAAAAGAATTGCTTTTTTAAATAGAAAAAAA 8 35 1 ** * **** ** * MAP Score: 5.3856 Motif 8 TTGTTTGGTAGAGAGATCCTTGAAAGAAAG 1 19 0 AAGGAGAGAGAGTCATAAAGCTG 2 3 1 TTCTATTATAGGAAGAGCTTTCCTGGAGAG 2 129 1 AGATAGAGCCTTCTCTGTAAG 3 1 1 GGCACAGCAGGGGAGAGCTTGGGCCTCCTC 3 31 1 TTTTTGTTGAAAAAGAGCTCCGAAAAACTC 3 84 1 TAAACGATACCAGAGAGATTCATTCTTGGC 3 137 0 CGTTTAGGAACATAGGGCTTTGAACGGTCC 3 161 1 GAATAGAGTGGAAAGGGCTTGTCCGACTTA 4 160 1 GCTTGTCCGACTTAGAGATTCAATAAGCAT 4 176 1 AAGCATAGCTCTAAGAGACTGGGTTAGAAG 4 200 1 GTAGCTCAGTGGTAGAGCGCCACGTTGCCA 7 210 1 GAAGATAAAAGGTAGAGACTTCTTCCGTCA 8 89 1 ********** MAP Score: 0.700421