AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons001_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236814 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0349 84 adenylate kinase (adk) #1 HI0350 141 permease, putative #2 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #3 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #4 HI0517 172 ribosomal protein L11 (rpL11) #5 HI0548 169 translation initiation factor 1 (infA) #6 HI0578 64 elongation factor Tu (tufA) #7 HI0579 83 elongation factor G (fusA) #8 HI0580 156 ribosomal protein S7 (rpS7) #9 HI0581 181 ribosomal protein S12 (rps12) #10 HI0632 300 elongation factor Tu (tufB) #11 HI0640 271 ribosomal protein L10 (rpL10) #12 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #13 HI0708 205 L-seryl-tRNA selenium transferase (selA) #14 HI0716 237 preprotein translocase SecE subunit (secE) #15 HI0776 190 ribosomal protein S10 (rpS10) #16 HI0781 25 ribosomal protein S19 (rpS19) #17 HI0788 280 ribosomal protein L14 (rpL14) #18 HI0792 36 ribosomal protein S8 (rpS8) #19 HI0798.1 28 ribosomal protein L36 (rpL36) #20 HI0799 139 ribosomal protein S13 (rpS13) #21 HI0801 27 ribosomal protein S4 (rpS4) #22 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #23 HI0803 40 ribosomal protein L17 (rplQ) #24 HI0817 170 conserved hypothetical protein #25 HI0864 230 GTP-binding protein #26 HI1282 300 conserved hypothetical protein #27 HI1644 233 pseudouridylate synthase I (truA) #28 HI1722 135 methionine aminopeptidase (map) #29 HI1727 155 argininosuccinate synthetase (argG) #30 HI1735 79 peptide chain release factor 3 (prfC) Motif 1 AAGTGCGGTAAAAATTATAAA 0 0 1 TGATAAAGCATAGTGCGGTCAAATTTTTTAT 0 26 0 AAAGTGCGGTTAATTTTAGTTG 1 129 0 GAAATCGCCGAAGTGCGGTCAAAATTCTCCG 2 172 1 TAAAGGTTTAAAGTGCGGTTAAAAATTTCGG 2 200 0 CTTACTTCTATAGTGGGGTGACAACTCAAAT 3 195 0 GTAAGGTTCAGAGTGCGGTCATTTTAACGGT 3 221 1 ATTATATAAAAAGTGCGGTTGTTTTTCAAGC 4 34 0 TTAATAAGAAAAGTGCGGTTATTATAGGGGT 5 19 1 GTTTCCTAAGAAGTGCGGTATAAAACAATCA 6 36 0 AAAAAAACAAAAGTGCGGTAAATTTTAATCT 9 20 1 CCGTGGTTGAAATTGCGGTCACTTTAGCGTA 13 143 1 TTAATCGCAAAAGTGCGGTTGTTTTCACCAG 14 12 1 ATAATTCCAAAAGTGCGGTAAATTTTAACTG 17 102 1 GGTTATGATATAGTGCGGTGAATTACACCCT 26 234 1 TGGCTTAATAAAGTGCGGTTATGGTAGCCCA 27 201 0 CAAAGAGGAAAAGTGCGGTTATACTCTATAG 29 75 1 ********* * MAP Score: 68.8606 Motif 2 GTGGATGTGCTTTCTATCAAAAACACGGTTAAA 3 105 0 TCGCCGTCTATTTCTATATAGAAGTAGATTTTT 9 111 1 CACTTTTGTTTTTTTATAAAAAACT 9 2 0 AGCGATGGCTTTTTTATTTACAAAGGTTTACAC 24 118 1 AAATTAGGATTTTTTATGCACAAAGCTAAATAA 29 10 1 CGTATTTTTCTTTTTATCAACAATTTCGGTTGC 14 155 0 CTCTATAGAATTTTTATTCACAAAAATCGATTA 29 98 1 TATAGCACGATTTCTAGGAAAAAACTGGATTGC 28 77 0 TTGTTTTTCTTTTTTAGGAAGAAGAATGCTAAA 1 23 1 CCTTTCTCTTTTTCTTTTGATAAAATCCGCCGC 17 179 1 AGTTTTGGGGTTTTTTTCTATAAGAAATTTAGT 26 84 1 AGATTTTTGCTTTTAATGCACAAAACACTAGAC 29 43 1 TAAATGTGAATTTTTTGTGATAAAGATCTCATT 27 88 0 TTTATCTCACTTTTTTGAAAAAACTTTACGAGA 28 111 0 GCAGTTTATTTTTCATTCGATAAATTTTTGAGA 17 53 1 TATTTTTACATTTCCATTTAAAACGGATTCAAT 14 116 1 CAAATTGAGTTTTTCATGAACAATATTATTTTT 5 84 1 GAAAAATAAATTTCATGAAAAAATAGCATGGCT 25 61 0 TTGCGCCATTTTTTATGTAACAATGCAATAAAA 25 176 1 ATCCTTTTACTTTAAATGAACAA 19 0 0 GATGAAGCCCTTTAAATTCAAAAACTTA 7 5 0 TGTTTAATGCTTTAATTGGATAAGATGCAATTT 25 207 0 AGTCCACATTTTTAATTGAACAAAGAAGAAACA 30 56 1 ******* * ** MAP Score: 22.7544 Motif 3 ACCGAAATTGTTGATAAAAAGAAAAATACGCAAGAA 14 158 1 GGCGGCGGATTTTATCAAAAGAAAAAGAGAAAGGCA 17 177 0 ACTCAACTGGTTCTTGGCAAGAAAAATGTTAA 20 6 0 GCCATTATTTATAATAAAAATGTCATTACA 24 4 1 AAATAATCGATTTTTGTGAATAAAAATTCTATAGAG 29 98 0 CGTTTTTAGCTTTCTACGAAAGAAAAAATAATATTG 5 104 0 TCAATTCTAATTATTAGTAAGGAAAATAT 29 136 1 AGCATTCTTCTTCCTAAAAAAGAAAAACAAATATTA 1 17 0 AGTTACTAAATTTCTTATAGAAAAAAACCCCAAAAC 26 85 0 TATTTGCAAATTCGTTTGAGCAAAAACCTAAAATCA 30 12 1 TCCCTCTATTTTAGTAATAGTAAAAAGATAGTTTAT 26 169 0 TGTTTCTTCTTTGTTCAATTAAAAATGTGGACTAT 30 54 0 CTCTCAAAAATTTATCGAATGAAAAATAAACTGCAG 17 51 0 AGTTTTTTATAAAAAAACAAAAGTGCGG 9 2 1 GGTTAAGATTTTTCTGAGAAGGATAAGATC 23 20 1 GCTTATCCTTTTACTTTAAATGAACAA 19 1 0 AACAATCAATTCCTAAAATAAATAAAGTTAGATGA 12 29 0 ** * ** ***** MAP Score: 18.7805 Motif 4 AATTATAAAAAATTTGACCGCACTATGCTTTATCA 0 22 1 AATACAACTAAAATTAACCGCACTTT 1 125 1 AGTGCGGTCAAAATTCTCCGAAATTTTTAACCGCA 2 183 1 CATTCATTTAAAATTTACCGCCTTAAAATTAGCAA 3 25 1 TTTATTGCTTAATTTAACCGTGTTTTTGATAGAAA 3 93 1 ACACAATGACAAATTCACCGTTATTTGTCGTTGTT 3 136 1 CGTTTTTCTTAACTTTTCCGCCTAAA 5 153 1 TGCGAATTTCTCCGTATTTTAATCTTCAG 8 137 0 AACTAGATTAAAATTTACCGCACTTTTGTTTTTTT 9 20 0 AAAACTATTAGAATTCGCCGTCTATTTCTATATAG 9 97 1 AATGTGGTTTAATTTACCCATCGATAACCGTGTCT 10 256 1 AATCCAGTTAAAATTTACCGCACTTTTGGAATTAT 17 102 0 TCTTTTGATAAAATCCGCCGCCTATCTGCCATTCT 17 191 1 ** ** **** ** MAP Score: 16.6013 Motif 5 CTTCCTAAAAAAGAAAAACAAATATTAGAGAATA 1 10 0 AATATTGTTCATGAAAAACTCAATTTGGCATAAC 5 77 0 CTTTCTACGAAAGAAAAAATAATATTGTTCATGA 5 97 0 GCCCAGAAGCAAGAAAAATTCTTATTCTGTTCAC 11 172 0 GCAAGGCGAAAAGAAAATGCTACAATCGCAGGTT 14 72 1 TGTTGATAAAAAGAAAAATACGCAAGAAGTGATC 14 166 1 AAATAAACTGCAGAAAAAATGAAATGCTCTCTTC 17 30 0 AATTTATCGAATGAAAAATAAACTGCAGAAAAAA 17 45 0 ATTTTATCAAAAGAAAAAGAGAAAGGCAATGATA 17 171 0 GGTTCTTGGCAAGAAAAATGTTAA 20 0 0 TTATCCTTCTCAGAAAAATCTTAACCTATGACCA 23 12 0 AATAAATTTCATGAAAAAATAGCATGGCTACGTT 25 56 0 TGACTAGAATAAGAAAAATAAATTTCATGAAAAA 25 72 0 CTAGTCATAGCAGAAAAAGAAAAATACATGTATA 25 99 1 TCAACGTATTATGAAAAACTAAAAGGAAATT 27 7 0 ******** * * MAP Score: 13.7131 Motif 6 GGGCGGAAGGGGGCTTAGGATATAAATCCCC 2 83 0 CTCGCAAAGCAGGGGAAGGCAAGAGGAACAA 2 128 1 AGTTTATATAAGGGTAAGGCTTCATCAACGA 7 36 0 TTAGCTTGGAAGGCTAAGGTAATAGCCATTA 10 64 0 ACCCTTGGTAAGGGTGAGGTCGGCGGTTCAA 10 157 1 GATTGATATAAGGATGAGGAATTATAAGACT 10 205 0 TGACTAACACAGGCGCAGGATTATAGAGAAA 11 55 0 TCCTAGTCTTAGGATTAGGTAAATTAATTCC 11 216 1 AATTTTTGAGAGGATGAGGATATTTTTATAA 17 75 1 TTTAGTAACTGGGCTTAGGTTCTTATGAACC 26 111 1 GCATAAAAAAAGGGTTAGGTTCATAAGAACC 26 128 0 AGTATTGTTTAGGATAAGGTTTCATAAGGTT 26 207 1 ***** ***** MAP Score: 11.2163 Motif 7 AAAAATCCCCTAATTTTTACAAAAATCCTTTAATTGAAA 1 72 1 AAAAGTGCGGTTGTTTTTCAAGCACTTCTTAAATCCGAT 4 18 0 TCCCCGATAATTTTTAGTGCAAGATTCATTGCACCACAC 4 102 0 TATTATAACCTTGTTTATTTAATATCAGTTTATATAAGG 7 54 0 AGTTTTTTATAAAAAAACAAAAGTGCGGTAA 9 2 1 GAATTTGGCTCTTTTTTCAACAATATTCTTTACAAGA 11 8 1 TATTAAGCGTTTCTTACTTCATCTAACTTTATTTATTTT 12 11 1 TCTTATGGCATTATTTTTACATTTCCATTTAAAACGGAT 14 105 1 GAGCATTTCATTTTTTCTGCAGTTTATTTTTCATTCGAT 17 35 1 TTTCTTTCTCCAACTATCCTATACGTC 21 7 0 AAGCGATGGCTTTTTTATTTACAAAGGTTTACACTAATT 24 117 1 CGTAGCCATGCTATTTTTTCATGAAATTTATTTTTCTTA 25 58 1 CATTGCGCCATTTTTTATGTAACAATGCAATAAAAATTG 25 174 1 GTTTTGGGGTTTTTTTCTATAAGAAATTTAGTAACTGGG 26 85 1 ACCTAACCCTTTTTTTATGCCTGAGATTTAATAAACTAT 26 139 1 AATTTCCTTTTAGTTTTTCATAATACGTTGATCAATTA 27 9 1 AAACTATCGCTTATTTTTGAATAAATTTTGGAGTGTTTT 27 137 1 AAATTAGGATTTTTTATGCACAAAGCTAAATAAAGATT 29 9 1 CAAAAATCGATTATTTATTCAATTCTAATTATTAGTAAG 29 118 1 TGTTTCTTCTTTGTTCAATTAAAAATGTGGACTAT 30 54 0 ** *** * ** * * MAP Score: 10.2804 Motif 8 AGGGGAATGATTAAAAATCCCCTAATTTTTACA 1 60 1 AGTTGTATTTTAGAAATTTCGCCTTTCAATTAA 1 101 0 GGGCTTAGGATATAAATCCCCCCTCAGTCTTCG 2 71 0 CAACATAAGATTTGAAATCGCCGAAGTGCGGTC 2 159 1 CGAAGTGCGGTCAAAATTCTCCGAAATTTTTAA 2 180 1 CTGCATTCATTTAAAATTTACCGCCTTAAAATT 3 22 1 TCCACACAATGACAAATTCACCGTTATTTGTCG 3 133 1 CTAAAAACGGCTATAATCCGCCCGTTTTTCTTA 5 131 1 TTTTTGTAAACCAGCGGTGTAAAATA 6 3 1 TAAAACTAGATTAAAATTTACCGCACTTTTGTT 9 25 0 CGTAAAACTATTAGAATTCGCCGTCTATTTCTA 9 94 1 GAGGTCGGCGGTTCAAATCCGCCTATCAGCACC 10 172 1 TAGCTTTTCTCTATAATCCTGCGCCTGTGTTAG 11 50 1 GGGAATGGGAGTTGAACCCACCCAAGAACGCTG 13 58 1 TCAACAGGATTTGAAATCCTGCCACCTCACCGG 13 97 1 AATAATCCAGTTAAAATTTACCGCACTTTTGGA 17 107 0 TTTTTCTTTTGATAAAATCCGCCGCCTATCTGC 17 187 1 AGGTCGTTGGTTCAAATCCAGCCCCCGCAACCA 26 26 1 CCTATATAGGGTGTAATTCACCGCACTATATCA 26 239 0 TTTCCTAAAATTTCAATCCCGCCATTATCTAAT 28 23 1 ** ***** *** MAP Score: 9.52281 Motif 9 AAGTGCGGTAAAAATTATAAAAAATTTGACCGCACT 0 9 1 TCTTCCTAAAAAAGAAAAACAAATATTAGAGAATA 1 8 0 GGGAATGATTAAAAATCCCCTAATTTTTACAAAAATC 1 62 1 AAATACAACTAAAATTAACCGCACTTT 1 124 1 AAGTGCGGTCAAAATTCTCCGAAATTTTTAACCGCAC 2 182 1 AAATCAATCTAAATCTTTGCTAATTTTAAGGCGGTAA 3 39 0 GAAGTGCTTGAAAAACAACCGCACTTTTTATATAATC 4 29 1 GCTTTCTACGAAAGAAAAAATAATATTGTTCATGAAA 5 95 0 AAACTAGATTAAAATTTACCGCACTTTTGTTTTTTTA 9 19 0 AATATTGTTGAAAAAAGAGCCAAATTC 11 0 0 TAATTTACGCTAAAGTGACCGCAATTTCAACCACGGA 13 142 0 AAAATCTGGTGAAAACAACCGCACTTTTGCGATTAAA 14 11 0 ATGATTACATTAAACGGCTCTCATATTGAGAGCTCGT 15 54 0 TAATCCAGTTAAAATTTACCGCACTTTTGGAATTATA 17 101 0 TTAGTCTTATTAAGATAAGCGCACATTATAACGTAGC 25 27 1 ATAAGTTCAGTAAAAGAACCCCAGTTTTGGGGTTTTT 26 62 1 CAATTTTTAGAAACTATCGCTTATTTTTGAATAAATT 27 127 1 CAAATGCATAAAAACACTCCAAAATTTATTCAAAAAT 27 149 0 TACTCCATTCAAGTGCAATCCAGTTTTTTCCTAGAAA 28 63 1 AAAATCAGGGAAAATAGTCCACATTTTTAATTGAACA 30 41 1 **** * ** *** MAP Score: 3.79207 Motif 10 TACTATAAATGGTGCTGATCCCTTGGCTCCACCCGTTTACGGGGG 2 18 1 ACTGAGGGGGGATTTATATCCTAAGCCCCCTTCCGCCCTTCGGGC 2 76 1 TTCGTAGAAAGCTAAAAACGGCTATAATCCGCCCGTTTTTCTTAA 5 120 1 GGAAGGCTAAGGTAATAGCCATTATACGATGCCCGCAAGTCCTAA 10 43 0 AATGATGCGGGTTCGATTCCCGCTGCCCGCTCCAGACGCTGATAT 10 93 1 GAGGTCGGCGGTTCAAATCCGCCTATCAGCACCAGTCTTATAATT 10 172 1 CAAGAACATAGCTTTTCTCTATAATCCTGCGCCTGTGTTAGTCAA 11 42 1 CCTCAACAGGATTTGAAATCCTGCCACCTCACCGGAGATGACGCC 13 95 1 CATTTCTAGCGTTAAAAGCTGTGACGCACCACCAGCCTCTTAATC 24 58 1 TAACCCGAAGGTCGTTGGTTCAAATCCAGCCCCCGCAACCAATAA 26 18 1 * * * ** * * ** * MAP Score: 2.92367 Motif 11 AAGTGCGGTAAAAATTATAAAAAATT 0 3 1 TAAAGCATAGTGCGGTCAAATTTTTTATAATTT 0 21 0 ATTTCTAAAATACAACTAAAATTAACCGCACTT 1 117 1 ATCGCCGAAGTGCGGTCAAAATTCTCCGAAATT 2 175 1 AGGTTTAAAGTGCGGTTAAAAATTTCGGAGAAT 2 195 0 GAAAGCTGCATTCATTTAAAATTTACCGCCTTA 3 17 1 CAATGAATCTTGCACTAAAAATTATCGGGGAGC 4 110 1 AAAAGCGCTTTGCGCTGCAAATTTTCTCAATGA 8 76 1 TTTTGAATCCGTTTAAAATAACGTTGAATT 13 185 0 TCATTTTTTCTGCAGTTTATTTTTCATTCGATA 17 42 1 TTATTTTTCATTCGATAAATTTTTGAGAGGATG 17 58 1 ATTCCAAAAGTGCGGTAAATTTTAACTGGATTA 17 105 1 AAAAATAAATTTCATGAAAAAATAGCATGGCTA 25 60 0 TATGTAACAATGCAATAAAAATTGCATCTTATC 25 189 1 TTCTAAAAATTGCAGTAATAAATGTGAATTTTT 27 106 0 TTCTTCTTTGTTCAATTAAAAATGTGGACTATT 30 53 0 * ** * ****** MAP Score: 2.9025 Motif 12 ATTTATGTCCTTGATATTCTGTTTGAGTATCCT 20 60 1 TTTAATTAATTTGATATTCTGATCTTGAAAAGC 20 101 0 GCAAGAAAAATTCTTATTCTGTTCACCATCTAC 11 165 0 CAAAACGTGATTAAGATACTGATAAAGCATAGT 0 43 0 GTGGCAGGATTTCAAATCCTGTTGAGGACGCCA 13 89 0 AACCAATAAATTTATTTGCTGATTGATATAAGG 10 223 0 ACATGTATTTTTCTTTTTCTGCTATGACTAGAA 25 97 0 TTAAATTAGATTAAGAGGCTGGTGGTGCGTCAC 24 78 0 ACCAGTTGAGTAGTTATACTGCTCAACTCATTT 20 31 1 GGATGAGGAATTATAAGACTGGTGCTGATAGGC 10 192 0 AAATTTATTTTTCTTATTCTAGTCATAGCAGAA 25 81 1 ATGGTTTAAATTGTTTTGCTAATTTAGACGTTT 8 32 0 ** **** *** * MAP Score: 1.84702 Motif 13 CCCCTAATGTTTAGCATTCTTCTTCCTAAAAAAG 1 31 0 CCCTATAATAACCGCACTTTTCTTATTAAATAGT 5 14 0 GAGTTTTTCATGAACAATATTATTTTTTCTTTCG 5 90 1 CCAAAACCCATCAGCAATATTTCTCATTGAGAAA 8 98 0 ATTAAAATTTACCGCACTTTTGTTTTTTTATAAA 9 15 0 GGCTCTTTTTTCAACAATATTCTTTACAAGAACA 11 16 1 GCAGGTTCTTATGGCATTATTTTTACATTTCCAT 14 99 1 TTAACATTTTTCTTGCCAAGAACC 20 0 1 AGATCTTGTAATGACATTTTTATTATAAATAATG 24 12 0 TTGAATAAATTTTGGAGTGTTTTTATGCATTTGC 27 153 1 ATAGAGTATAACCGCACTTTTCCTCTTTGTCTAG 29 70 0 ** *** * ** ** MAP Score: 1.10577