AlignACE 3.0 10/20/99 AlignACE2 -i CT/CT_operons001_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944241543 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 lepA 185 GTPase #1 truB 37 tRNA Pseudouridine Synthase #2 nusA 117 Transcription antitermination factor #3 rs1 244 S1 Ribosomal Protein #4 adk 206 adenylate kinase #5 rpoC 24 RNA Polymerase Beta' #6 rpoB 300 RNA Polymerase Beta #7 rl7 31 L7/L12 Ribosomal Protein #8 rl10 21 L10 Ribosomal Protein #9 rl1 22 L1 Ribosomal Protein #10 rl11 105 L11 Ribosomal Protein #11 secE 142 Preprotein translocase subunit #12 tufA 300 Elongation Factor Tu #13 infA 300 Initiation Factor IF-1 #14 fusA 41 Elongation Factor G #15 rs7 49 S7 Ribosomal Protein #16 rs12 259 S12 Ribosomal Protein #17 CT460 300 SWIB (YM74) complex protein #18 yaeI 57 phosphohydrolase #19 rs11 21 S11 Ribosomal Protein #20 rs13 55 S13 Ribosomal Protein #21 secY 22 Translocase #22 rl18 21 L18 Ribosomal Protein #23 rl6 27 L6 Ribosomal Protein #24 rl16 32 L16 Ribosomal Protein #25 rl2 23 L2 Ribosomal Protein #26 rl3 300 L3 Ribosomal Protein #27 mutL 294 DNA Mismatch Repair #28 rs4 300 S4 Ribosomal Protein #29 rl36 300 L36 Ribosomal Protein #30 rs14 23 S14 Ribosomal Protein #31 pnp 28 Polyribonucleotide Nucleotidyltransferase #32 rs15 156 S15 Ribosomal Protein #33 map 57 Methionine Aminopeptidase #34 CT853 194 hypothetical protein Motif 1 GTAAGGGAAAAAAAGCAAAAAAAATAATGCTAA 2 77 0 TCCTAAAAAAACCTAAAAAACATTCTATCT 13 280 0 TCCCACACCAAAAATCGCAAAAACAAAGCCTGA 26 65 0 TCTTATTTAAAAAATCTCAAAAAAGGTCGATTT 28 110 0 TCGCAAAAACAAAGCCTGAAAAATCGTTCTAGG 26 51 0 AGCACAACTAAAAACCATAAAAGTTTTCTTACA 29 138 0 AACGAGGGGGAAAAACGAAAAAGTTAAATTATA 10 48 0 TAAAAACTACAAAGTCAAAAAGAGTAGTGTAAA 3 206 0 GGGGATTTTTAAAGACAAAAGAAAAGCCCCGTC 0 56 0 GATATCCTTGAAAATCTCAAGGATTGACAGTCC 3 18 1 CAACTTGTCAAAAAACAGAAGGAAAAGTATCTT 13 131 0 TTATTCCCGCAAAAACTCAAGAGAGAATGTCAA 13 98 1 GATAATTCCTAAAAAAATAAAAATAACAAATTA 27 13 1 TATTAAAAGCAAAATATTAAAAACGTTTTTATT 27 92 0 TCTGTTTCGAAAAAAAATAAAAACTCGTGTACA 4 128 1 CGCGCTTGACAAAATACAAAAGAGCATTCTAGT 28 199 0 ACTGAATAGTAAAGTCTTAAAATCATAGCGGAG 27 264 1 GATATCGCCAAAAGTCTTAAAGTCTTAGGAGAG 6 272 1 TAAAGAAGGAAGAGAAGAATAAC 25 1 1 CTGTTAGTTCAAAAACTTGAAAACAAGACTTGT 16 13 0 **** * ***** MAP Score: 21.9353 Motif 2 TAATTAATAAAAAAAGAGTTAAATCCTTGC 16 69 0 CTCTTTGAAAAAGAAGAGTTTAAAGTTGGA 17 16 0 TTTTTTAAATAAGAAGAGTTTTTTTAGCAC 28 129 1 TCTCTTTATTAAAAAAAGTTTCACTAGTTT 3 123 0 AGAAGATGATAAGAAAAGTTTAGGGCTCTT 17 263 0 TAACTTACGCAAAAAGAATTAATTATGTTT 27 125 0 AGGTAACTGAAAGAAGAATTCGCTT 11 127 1 TGCACAGAGAAAAAAAACTTCTTACTCTAG 32 130 1 ACCTCCTGTTAAAAAAAATTGCAAGGCAAC 27 177 0 GCTTCCTTGGAAGAAAACTTATAACGCT 26 8 0 AGATCACTGTAAGAAAACTTTTATGGTTTT 29 131 1 GTTCTTATAAAAAAAGCCTTTCCTAATTAA 4 68 1 AAAAAAACCTAAAAAACATTCTATCTCTTG 13 276 0 CAATTTTATTAAAAAACATTTCCTCCAAAA 16 129 0 AAGAAATAAAAAGAAACCTTTTTCAGTATC 28 59 1 CTACAAAGTCAAAAAGAGTAGTGTAAATAT 3 203 0 AGTTAAGGCATAAAAGAGTTGCGAAGGAAG 17 236 1 AATCTAGATCTAGAAGAGTTTATAAAAAAG 0 93 0 GAAAAAAAGCAAAAAAAATAATGCTAACGG 2 74 0 TTCTGTTTCGAAAAAAAATAAAAACTCGTG 4 127 1 AGCAAAATATTAAAAACGTTTTTATTAATT 27 88 0 TCGTCAAAATAAAAAACATAGCCAAGTCTT 17 199 0 CGATAATTCCTAAAAAAATAAAAATAACAA 27 12 1 GTAAACAAATTAAAAAAATATTTGTTATTC 13 74 1 ********** MAP Score: 19.0858 Motif 3 CTCTTGACATAGAGAAGAGCT 33 1 0 GCTCTTTGAAAAAGAAGAGTTTAAAGTTGG 17 17 0 AAGAGTTGCGAAGGAAGAGCCCTAAACTTT 17 249 1 AGCAAACATAAGAGCAGAGCTCTAGGGCTC 2 40 1 TAAAGAAGGAAGAGAAGAATAAC 25 5 1 GAATGCGTAGAGAGCAGAGATCACTGTAAG 29 114 1 TTGGGCTCTTAAAAAAGAGACTGATTCTTA 29 268 0 AAGTCTTCAGCAAGAAGAGAGGTAAAAGCG 17 176 0 ATAATTAATAAAAAAAGAGTTAAATCCTTG 16 70 0 TTTAAAGACAAAAGAAAAGCCCCGTCCGAG 0 52 0 AATCTTCGTTAGTGAAGAGCAAACATAAGA 2 23 1 CAGCTAGGACAAAACAGAGCCTATCCAATG 6 187 0 CCCTAAACCTAAAGAAAAGAAATACGAAGA 15 17 1 GAGGTTGAATCGAGAAGAGTAC 16 247 1 GAGCCTATCCAATGCAGAGACGCTAGATAC 6 171 0 ACAGAATTGCAAACAAGAGCCTTCCCGGAT 29 58 0 TTGTCTATCTAGAGAAAAGTAATCTAGATC 0 113 0 TTATATCTTGAAAGAAGGGATCTTTCAGTC 34 149 0 AACTTTTTTTAATAAAGAGATGCATCTTAT 3 133 1 AGGGTAAAGTAGAGTCGAACT 22 5 1 ACTACAAAGTCAAAAAGAGTAGTGTAAATA 3 204 0 ATTTTTTAAATAAGAAGAGTTTTTTTAGCA 28 128 1 CAAAAAACAGAAGGAAAAGTATCTTTTGAC 13 126 0 GAAGATTATTAGTAAAGAGA 2 0 0 AAAAATCGCAAAAACAAAGCCTGAAAAATC 26 59 0 GAGGAATACTAAGGTAGAGTAGGGTTGAAT 10 85 1 ********** MAP Score: 15.2443 Motif 4 TAGTGAAACTTTTTTTAATAAAGAGATGCATCTT 3 127 1 CTATAACAATTTTATTAAAAAACATTTCCTCCAA 16 131 0 TTTTTTGAGATTTTTTAAATAAGAAGAGTTTTTT 28 119 1 CGAGGCGATGTTTTTTAAGGAATAAAATAAGGAC 28 271 1 TAACTAGCTGTTTGTTTAGAAAGATACTGAAAAA 28 77 0 TGTTTTCAAGTTTTTGAACTAACAGTATTCGAAG 16 21 1 AAAAAAAGCCTTTCCTAATTAAAATCTTTTATCG 4 76 1 TCTTATCATCTTCTTTAACTAGGAGTCATCC 17 279 1 GCCTTGCAATTTTTTTTAACAGGAGGTACCGTTA 27 180 1 TAGGAAAGGCTTTTTTTATAAGAACCTTTCGTTC 4 59 0 ATTTTTTTAATTTGTTTACAAGCAAAAACCCAAT 13 59 0 ATGTTTGCTCTTCACTAACGAAGATTATTAGTAA 2 15 0 AAAAAAGGTTTTCTTGAATTAAGAATTAGTTTGA 32 30 1 TAACATGTCCTTTTCGAAGCAAAAACTCGGTTAA 0 156 1 TAGGGAAGGCTTGTTTTAAGAAAATCTTTTGGAG 16 103 1 TGAGGGGTTTTTGATTTAGAAAAAATCAAACTAA 32 55 0 TCAAAGAGTTTTGATGAAGAAATAAAAAGAAACC 28 43 1 TTTCTAAAAATTCTCTAAAAAGAAGCCCCGTTCT 0 16 1 TTTTTATTTTTTTTCGAAACAGAAGTCGTATAAA 4 117 0 TAAAAACGTTTTTATTAATTAACTTGTTAAATCA 27 74 0 TCACCTTGATTCCATTAAGAAAAAACCATTGCAA 6 105 0 TCTCTTTACTAATAATCTTCGTTA 2 0 1 GATTTAACTCTTTTTTTATTAATTATTTTTAGGG 16 74 1 GTTATTTTTATTTTTTTAGGAATTATCGCG 27 6 0 GGAAAATAGCTCTTTGAAAAAGAAGAGTTTAAAG 17 21 0 *** **** ** * MAP Score: 13.9809 Motif 5 TCTTATGGGTAAGGGAAAAAAAGCAAAAAAA 2 87 0 AGAGATCACAGAGAGACTAAATAGGGAAATG 6 242 1 CTCTCAAAACGAGGGGGAAAAACGAAAAAGT 10 57 0 TGATGTGTTGGCGAGGCTGAAAAGCCTTGCC 11 16 1 GTCTGCGGCTGAGGGATTGAGAAAACTAGTT 12 93 1 CTTAGCACAAAAGAGGAAGCAACCTAATTAG 12 163 0 TGCTGGGATCAAGAGATAGAATGTTTTTTAG 13 267 1 ATTCGTGTGTGAGAGGCAAAAAAGTTCG 14 23 1 AAGAAATACGAAGAGGTTGAGTTTAT 15 33 1 CTGTTTGTAAGAGAGGTTGAATCGAGAAGAG 16 235 1 TCAGCAAGAAGAGAGGTAAAAGCGAATTAGA 17 169 0 GAGACAGCACGAGAGAAAGCGTGAAGTCCAA 27 231 0 ACTATTCAGTGAGAGACAGCACGAGAGAAAG 27 243 0 CTGAGAGGCAGTATACGAGATGG 28 2 1 TGTTGAAACAAAGAGGTTGAG 34 0 0 CTAATAATCAACGAGAAAGAGTAACATTTTT 34 51 0 ****** **** MAP Score: 7.76057 Motif 6 TGACAGTCCTTTCCATGGGGATGTTTAGATGGAATAT 3 42 1 TAAAAGATTTTAATTAGGAAAGGCTTTTTTTATAAGA 4 70 0 CTAGCGTCTCTGCATTGGATAGGCTCTGTTTTGTCCT 6 175 1 ATTAAGTGATGTGTTGGCGAGGCTGAAAAGCCTTGC 11 9 1 AAGCTACACACCCAAAGGCAAGGCTTTTCAGCCTCGC 11 26 0 TTATTAATTATTTTTAGGGAAGGCTTGTTTTAAGAAA 16 89 1 AAGAAAATCTTTTGGAGGAAATGTTTTTTAATAAAAT 16 120 1 TAATTTTTAGGAGAGAGTGTT 19 3 1 ACAAAGGCGGCGAATGGGCAATGGTATATGACCTGCG 26 134 0 GTCTTAAAATCATAGCGGAGATGCTTT 27 277 1 TCGCTAACTTTCATCGGGAGACGTTGTTGAACGCGAG 28 237 0 CGATGAAAGTTAGCGAGGCGATGTTTTTTAAGGAATA 28 258 1 TAATCCTCCTTTATCCGGGAAGGCTCTTGTTTGCAAT 29 46 1 ACTTCTTGTCCGGTAGGAGGAGGCTGTTTTGCTAGGG 29 193 1 TCTAAGTATTTTATGTGGTGAGGGTGTAGTAAGAATC 29 239 1 * ** ****** * MAP Score: 7.73223 Motif 7 TCTCGGACGGGGCTTTTCTTTTGTCTTTAAAA 0 51 1 TGGAGTTCAGAAGGATTGTCTTTTTG 1 4 0 AGAAACTAGTGAAACTTTTTTTAATAAAGAGA 3 121 1 TTAATTAGGAAAGGCTTTTTTTATAAGAACCT 4 66 0 ATTGCAACAGAAATATTCTGTTTGCGATGCCA 6 80 0 CGAGGCTGAAAAGCCTTGCCTTTGGGTGTGTA 11 27 1 CGGGAATAACAAATATTTTTTTAATTTGTTTA 13 75 0 TTGGGTGCCCAAGCCTGTTTTTTTGTTTGAAT 13 236 1 TCAAGAGATAGAATGTTTTTTAGGTTTTTTTA 13 275 1 GATACAAGTCTTGTTTTCAAGTTTTTG 16 5 1 CTTGCTGATAAAATGTTTTCTTCGAATACTGT 16 42 0 ATTTTTAGGGAAGGCTTGTTTTAAGAAAATCT 16 98 1 ATTTCCTCCAAAAGATTTTCTTAAAACAAGCC 16 110 0 TCTTTTGGAGGAAATGTTTTTTAATAAAATTG 16 127 1 TCCAACTTTAAACTCTTCTTTTTCAAAGAGCT 17 16 1 ATCTTAGGTCAAAAATTGTTATTTT 20 3 0 ACGATTTTTCAGGCTTTGTTTTTGCGATTTTT 26 57 1 ATCCACACAAGAGATTTTTCTTGACGCTAAGA 26 100 0 AAAATATTAAAAACGTTTTTATTAATTAACTT 27 83 0 GATACTGAAAAAGGTTTCTTTTTATTTCTTCA 28 57 0 TTTAAATAAGAAGAGTTTTTTTAGCACTGAGA 28 132 1 TAAAAACCATAAAAGTTTTCTTACAGTGATCT 29 131 0 TAATTCAAGAAAACCTTTTTTATCGGGTTATA 32 19 0 GCTAGAGTAAGAAGTTTTTTTTCTCTGTGCAG 32 129 0 GAGAAAGAGTAACATTTTTTTTGACTAACGAA 34 38 0 *** ******* MAP Score: 2.30369 Motif 8 TTCTAAAAATTCTCTAAAAAGAAGCCCCGTT 0 17 1 CTAGAAGAGTTTATAAAAAAGGCGAGGGGAT 0 83 0 AAGGGAAAAAAAGCAAAAAAAATAATGCTAA 2 77 0 TGCATCTCTTTATTAAAAAAAGTTTCACTAG 3 126 0 AAAACTACAAAGTCAAAAAGAGTAGTGTAAA 3 206 0 CGAAAGGTTCTTATAAAAAAAGCCTTTCCTA 4 62 1 GACTTCTGTTTCGAAAAAAAATAAAAACTCG 4 124 1 GTGTTTGGCATCGCAAACAGAATATTTCTGT 6 75 1 TGTTAACATTCTAAAAAATAAGGGTGAC 7 7 1 GGGTTTTTGCTTGTAAACAAATTAAAAAAAT 13 62 1 TCAAACAACTTGTCAAAAAACAGAAGGAAAA 13 138 0 CCCAGCATTCAAACAAAAAAACAGGCTTGGG 13 243 0 TCCTAAAAAAACCTAAAAAAC 13 289 0 CGTGTGTGAGAGGCAAAAAAGTTCG 14 26 1 TAAAAATAATTAATAAAAAAAGAGTTAAATC 16 74 0 CAAAAGATTTTCTTAAAACAAGCCTTCCCTA 16 103 0 ATAACAATTTTATTAAAAAACATTTCCTCCA 16 132 0 AAATAACCCCTTGCAAACAAAGATATTCTTA 16 192 1 ACACCAAAAATCGCAAAAACAAAGCCTGAAA 26 63 0 CGCGATAATTCCTAAAAAAATAAAAATAAC 27 9 1 CGGTACCTCCTGTTAAAAAAAATTGCAAGGC 27 180 0 TTTGATGAAGAAATAAAAAGAAACCTTTTTC 28 52 1 TTCAGTATCTTTCTAAACAAACAGCTAGTTA 28 80 1 ATTTAAAAAATCTCAAAAAAGGTCGATTTAA 28 108 0 AAACTCTTCTTATTTAAAAAATCTCAAAAAA 28 119 0 AGATTCTCAGTGCTAAAAAAACTCTTCTTAT 28 137 0 CTTATTTTATTCCTTAAAAAACATCGCCTCG 28 271 0 ATACACAGAATTGCAAACAAGAGCCTTCCCG 29 61 0 TTACTTGGGCTCTTAAAAAAGAGACTGATTC 29 271 0 GGAGTTGTCCTAAAAACGAAATGGGGTA 31 10 0 CGAGTTCGTTAGTCAAAAAAAATGTTACTCT 34 34 1 ** ******** MAP Score: 1.02746