AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons003_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236980 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0016 167 GTP-binding membrane protein (lepA) #1 HI0229 298 polynucleotide phosphorylase (pnp) #2 HI0273 300 ribonuclease PH (rph) #3 HI0431 35 conserved hypothetical protein #4 HI0432 66 conserved hypothetical protein #5 HI0433 75 orfG protein #6 HI0439 98 competence protein A (comA) #7 HI0568 95 transcription accessory protein (tex) #8 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #9 HI0964 300 virulence factor (mviN) #10 HI1002 130 thiophene and furan oxidation protein (thdF) #11 HI1219 279 cytidylate kinase 1 (cmkA) #12 HI1220 75 ribosomal protein S1 (rpS1) #13 HI1221 122 integration host factor, beta-subunit (himD) #14 HI1288 300 ribosome binding factor A (rbfA) #15 HI1311 148 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #16 HI1312 33 phenylalanyl-tRNA synthetase, beta subunit (pheT) #17 HI1328 135 ribosomal protein S15 (rpS15) #18 HI1331 163 transcription elongation factor (greA) #19 HI1368 103 zinc protease, putative #20 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #21 HI1475 227 H. influenzae predicted coding region HI1475 #22 HI1646 300 cytidylate kinase 2 (cmkB) Motif 1 CTTCTTTATTATAAAAAAACGAAGATAGAATAC 7 65 0 CAAGAAAAAATGGAATAGCGAATAC 15 2 1 CTTCGTTTATACAAAAAACTGAAATTAAGCACG 22 83 0 TCTCTATAAAATAAAAAACCGAGTAATGATAAT 15 105 0 TGTTCGTCTAAAAAAAAATAGCAACCATAACAA 18 17 0 GAACGATGTAATAAAAAAGCGCACTATTCTAGC 2 255 0 AAAGCACTGGAAAAAAAAGCGCGATAAGCGTAT 5 13 1 TTTATTTTATAGAGAAAAGAGAAGCAGGGGAAA 15 123 1 CAATTTAATAATAGAAAAAAGAGCTACTTTAGC 22 139 1 TATTTTACCTAGAAAAAAGAAAACTCTACGCTA 19 80 0 AAGAATTTAAACAAAAAAGAAAACGCCCGTTTA 21 26 0 GCTTATCAAAAATAAAAATGGAATAACGTATTC 15 29 0 CAAAACAAAGAAAACAAAAGAAATAGGAA 21 208 0 ATTGATAGACAAAATAAAGGGCATCAATATGCC 9 27 1 ATTCTTAGGGAAAGAAAACTAAGAAAAAATCAG 21 97 0 TTTCAGTTTGAATGAAAAAAGAAACCCCGAAGT 0 10 1 AATAAAAATAAAAGAAAGTTTTT 7 0 1 TTTTAACAAAAATAAAAACTAAAGCGTGCTAGA 2 228 1 TAATGAAAAGTGCGGTAACTTTAA 17 1 1 ATATTCCGTGAAAAAAAACTGATAAAATCCGCC 9 176 0 TTAAGATCAAATAATAAAGAAAGCACATTCCGT 10 34 0 TCTTTCCCTAAGAATAAAAAAAGGGGCAATGCA 21 115 1 AGATCTATTGATAATAAATTACACAAATATATT 13 68 0 * ****** *** MAP Score: 27.1697 Motif 2 CGGGGTTTTGTTTTATCTAAAAAGTTTGAAAAT 0 47 1 TAAGGCATTGTTTTTAATATAAATTTTAAGGAA 1 269 1 TATTTTACCTAGAAAAAAGAAAACT 19 88 0 AGATAGAGTTTTTTTAGTAGAAACAGGGATAAG 10 86 1 TTAATTTCAGTTTTTTGTATAAACGAAGTGTAG 22 88 1 TCAGGTGTCATTTTATCGAAAAACAGTATTAAG 14 203 1 CGGTTTTTTATTTTATAGAGAAAAGAGAAGCAG 15 117 1 GTGCGGTTATTTTTATGGAGAAAAA 4 51 1 AATTTAATGATTTTTGAGAAAAACAATCTTTT 0 145 1 CACATCCTTATTTTAAGTAAGAAAATATCATTA 20 42 0 GAACAATCAATTTTTAGGAGGAAAATACTGTCG 1 58 1 GTTGCTATTTTTTTTTAGACGAACAATAATAAG 18 25 1 TTAGTTTTTATTTTTGTTAAAATTCGCTAAGAT 2 217 0 AATGTGTGATTTTTATCGACAATCTTGGTCGTC 14 88 1 CTATCTTCGTTTTTTTATAATAAAGAAGTACGA 7 70 1 GTGGTTTTTGTTTTATTTAGTAAAAGGAAAAAC 18 139 1 CGGGGTTTCTTTTTTCATTCAAACTGAAA 0 6 0 GGGCGTTTTCTTTTTTGTTTAAATTCTTAGTTT 21 31 1 TTAATATAAATTTTAAGGAAAACATT 1 282 1 ATTTCTTACATTTTTATTACTATTTGTGTTTAG 11 127 1 AAAGTAGCTCTTTTTTCTATTATTAAATTGGAC 22 136 0 CGCATTATTCTTTTACTTTTTAAGGACTTGGTA 15 73 1 TTCAAGTTTATTTTTGATAATACTGCAGTAAGA 18 91 1 ***** ** *** MAP Score: 23.1623 Motif 3 TGCGGTCAAATTTTCAAACTTTTTAGATAAAACAAAACCC 0 49 0 GCCAGTTAAATTTAATGATTTTTGAGAAAAACAATCTTTT 0 137 1 GCATTGCCCCTTTTTTTATTCTTAGGGAAAGAAAACTAAG 21 107 0 TTTACTGTGGTTTTTGTTTTATTTAGTAAAAGGAAAAACA 18 133 1 AAATTTTGTTTTTACGCTATATTCCGTGAAAAAAAACTGA 9 187 0 TGTGGTTAGATTTTCTGAAATTTAAGAAAAAGCTTGAAAG 22 246 1 AAAAACAAAATTTCTATACAATTAGGCAAAAATTTTAGGG 9 214 1 AATAAGAGAATTTCGGCATTATAGCGAGAAG 8 1 0 ATGTGATTATTTTATGGATTTATATGCAAAGCATATACCT 11 37 1 TTCTCCAAATTTTGCGCATTATAGTGAGAATTTGGTAATC 11 227 0 GTTATTCCATTTTTATTTTTGATAAGCCAATGATTTTTCG 15 35 1 ATTACTCGGTTTTTTATTTTATAGAGAAAAGAGAAGCAGG 15 111 1 TAGATCTTAATTTAAGTAATATTAAGGAAGTATAGACG 13 94 1 GTTGTTATCCTTTTAATTCAAATCCGAGAAA 16 1 0 TTAGTTTTTATTTTTGTTAAAATTCGCTAAGATATTGATT 2 210 0 ATGCGCAAAATTTGGAGAATGAAAGGATAATTTGTATGGG 11 248 1 TATTTTACCTAGAAAAAAGAAAACTCTACGCTA 19 80 0 CAATGGAAAATTTGTGTTGATTTCGGTGAGACACAACCGA 9 78 1 CCCTTTCAACTTAATACTGTTTTTCGATAAAATGACACCT 14 205 0 *** * * ** * ** MAP Score: 20.1765 Motif 4 TGAAAATTTGACCGCACTTTTCCCTTTCAT 0 73 1 CCTAGCGATTTCCGCGCTTTTCAGGTACAA 0 104 1 CGAAAAAATGACCGCACTTTGGGCGTTTAA 1 206 0 GCACTATTCTAGCACGCTTTAGTTTTTATT 2 238 0 GTAATAAAAAAGCGCACTATTCTAGCACGC 2 251 0 ATTTATAATGACCGCACTTTTGAAAGTGCG 4 26 1 CATAAAAATAACCGCACTTTCAAAAGTGCG 4 38 0 TAATACGCTTATCGCGCTTTTTTTTCCAGT 5 18 0 GATTAAAGTTACCGCACTTTTCATTA 17 6 0 ********** MAP Score: 19.6353 Motif 5 TCCTAAAATTTCTGTTGATTGATAGACAAA 9 4 1 GCGTAAAAACAAAATTTCTATACAATTAGGCAAAAA 9 210 1 TTACGTCCGTAAAATTTCGCCAAATTCCTATTTCTT 21 184 1 AAAATATCCTCAGAGTTAGATTAAAA 11 0 1 TTGTCAATGGAAAATTTGTGTTGATTTCGGTGAGAC 9 74 1 CAAGTTTGAAAAAATGTGTATATATTAAAAGGCATA 22 39 1 AAAAAGTTTGAAAATTTGACCGCACTTTTCCCTTTC 0 65 1 TGGGCGTTTAAAAATTTCTTTTGATAGCCGCACGCT 1 181 0 TTTAAGTAAGAAAATATCATTATACACATATTTATA 20 28 0 ACGCTAAGTAAAAATAAGCGTAGAGTAGGGCTAGTG 19 50 0 ACTTCCGATAAAAATCACTTTACAGAGGGCATAATT 14 147 0 ACAAAAGTATAAAAAATCGGCATATTGATGCCCTTT 9 42 0 GTTTTTCGATAAAATGACACCTGATAATTTGTTTGA 14 191 0 CAGGATTACCAAATTCTCACTATAATGCGCAAAATT 11 224 1 TCCCATACAAATTATCCTTTCATTCTCCAAATTT 11 255 0 AATAGTTATTAAAAAAACCTTGAAATGTTTTTAAAA 22 199 1 TGGCTTATCAAAAATAAAAATGGAATAACGTATTCG 15 28 0 AGTATTATCAAAAATAAACTTGAAATGAGAAAATAA 18 79 0 AAATCTTTCGAAAAAATGACCGCACTTTGGGCGTTT 1 208 0 TGTTTTCCTTAAAATTTATATTAAAAACAATGCCTT 1 270 0 GTAAAATTCTAAAATCTTACTGCAGTATTATCAAAA 18 102 0 TAAATTTCAGAAAATCTAACCACATAGAAAAAGGTT 22 234 0 CATTTTATCGAAAAACAGTATTAAGTTGAAAGGGAT 14 211 1 ATAAATAATCTTCTTAATTTAAGTTAAT 12 57 0 ***** ** * * * MAP Score: 19.2231 Motif 6 GTTTTATCTAAAAAGTTTGAAAATTTGACCGCACTTTT 0 56 1 TGTTTTTCTCAAAAATCATTAAATTTAACTGGCGGATT 0 132 0 CATCCTGTATAATGCACGGGCTTTATTTTCTACATTAG 1 145 1 TTAAACGCCCAAAGTGCGGTCATTTTTTCGAAAGATTT 1 206 1 AGCGTGCTAGAATAGTGCGCTTTTTTATTACATCGTTC 2 250 1 CGCACTTTCAAAAGTGCGGTCATTATAAATCTTCTTTT 4 18 0 CGCACTTTTGAAAGTGCGGTTATTTTTATGGAGAAAAA 4 38 1 AATATTCATTAACGAAGCGAGAATTTTACG 6 2 0 AAAGGGCATCAATATGCCGATTTTTTATACTTTTGTCA 9 42 1 AGAACTAACAACAATGCTAGATTTTAAAAGTCGTTTA 9 273 0 AAAGGCACGGAATGTGCTTTCTTTATTATTTGATCTTA 10 28 1 CTATCTCTACAAAATGCAGAATATATTAAGATCAAATA 10 54 0 AGTTAGATTAAAAGATGTGATTATTTTATGGATTTATA 11 23 1 TTTCCAGTAGAATGAGGCGCTTTTATAAATAAGGAATA 14 269 1 TTTACTTTTTAAGGACTTGGTATTATCATTACTCGGTT 15 84 1 TAATGAAAAGTGCGGTAACTTTAATCTTTATCTT 17 6 1 ACGCCATTTAAACGGGCGTTTTCTTTTTTGTTTAAATT 21 18 1 TAAATCAACCAAAGATCTGATTTTTTCTTAGTTTTCTT 21 81 1 ACAAGTTTGAAAAAATGTGTATATATTAAAAGGCATAA 22 38 1 AGAACGTCAGAAGGATTGTCCAATTTAATAATAGAAAA 22 119 1 TCTTTCAGCTAAAGTAGCTCTTTTTTCTATTATTAAAT 22 141 0 AAATGTTTTTAAAAACCTTTTTCTATGTGGTTAGATTT 22 221 1 ** * * * * *** * MAP Score: 13.4839 Motif 7 TTTCAGTTTGAATGAAAAAAGAAACCCCGA 0 4 1 ATTTTCAAACTTTTTAGATAAAACAAAACCCCGAAT 0 44 0 AAATTTAATGATTTTTGAGAAAAACAATCTTTT 0 144 1 CATTACATTATATTTCATATAAAAGAACCTAATTTC 1 17 1 AAAAGAACCTAATTTCAGAGAGAACAATCAATTTTT 1 37 1 GCAAAAGAAATCTTTCGAAAAAATGACCGCACTTTG 1 215 0 TTTCCTTAAAATTTATATTAAAAACAATGCCTTATT 1 267 0 AAGTGCGGTTATTTTTATGGAGAAAAA 4 49 1 GGATGGCTCAAATATAATTCAAAAAACTTTCTTTTA 7 18 0 CGTACTTCTTTATTATAAAAAAACGAAGATAGAATA 7 66 0 TTTCACGGAATATAGCGTAAAAACAAAATTTCTATA 9 196 1 TTAGGCAAAAATTTTAGGGTAGAGAAGAATATTTTG 9 235 1 TAGAGAAGAATATTTTGAGTAAACGACTTTTAAAAT 9 254 1 ATGCAGAATATATTAAGATCAAATAATAAAGAAAGC 10 43 0 GGCTTATCCCTGTTTCTACTAAAAAAACTCTATCTC 10 85 0 TATTTTATGGATTTATATGCAAAGCATATACCTATT 11 44 1 GATGTTATTAACTTAAATTAAGAAGATTATTTAT 12 51 1 CTTAATACTGTTTTTCGATAAAATGACACCTGATAA 14 200 0 TACTCGGTTTTTTATTTTATAGAGAAAAGAGAAGCA 15 113 1 TTTCTCGGATTTGAATTAAAAGGATAACAACAA 16 8 1 TATGGTTGCTATTTTTTTTTAGACGAACAATAATAA 18 21 1 TCAAAAATAAACTTGAAATGAGAAAATAATTTACTC 18 72 0 TATTTTACCTAGAAAAAAGAAAACTC 19 87 0 GCACATCCTTATTTTAAGTAAGAAAATATCATTATA 20 40 0 AAAACTAAGAATTTAAACAAAAAAGAAAACGCCCGT 21 29 0 CTTTTTTTATTCTTAGGGAAAGAAAACTAAGAAAAA 21 102 0 TTAATTTCAGTTTTTTGTATAAACGAAGTGTAGAAC 22 88 1 GGATTGTCCAATTTAATAATAGAAAAAAGAGCTACT 22 131 1 AAAAAGAGCTACTTTAGCTGAAAGAATTTCGTCCTT 22 154 1 * *** * *** ** MAP Score: 12.0843 Motif 8 GAAAAGTGCGGTCAAATTTTCAAACTTTTTAGATAAAACAAA 0 53 0 CAATCCGCCAGTTAAATTTAATGATTTTTGAGAAAAACAATC 0 131 1 CAGCCACATAGTCAAATTTTATCATGTCGCTGTCTTTTATGG 2 50 1 TTTCTATGTGGTTAGATTTTCTGAAATTTAAGAAAAAGCTTG 22 240 1 TAATACTGCAGTAAGATTTTAGAATTTTACTGTGGTTTTTGT 18 108 1 TTTTGTCAATGGAAAATTTGTGTTGATTTCGGTGAGACACAA 9 72 1 ACTTACGTCCGTAAAATTTCGCCAAATTCCTATTTCTTTTGT 21 182 1 GAANCAAAATGTTAAATTTTATGAGATATTGATCACATTTTC 11 84 0 TCATTTTTTCGAAAGATTTCTTTTGCTAGTCGCAATCTGGGA 1 225 1 ACTATAATGCGCAAAATTTGGAGAATGAAAGGATAATTTGTA 11 242 1 TATCCTCAGAGTTAGATTAAAAGATGTGATTATTTTATGGAT 11 14 1 TAACAACAATGCTAGATTTTAAAAGTCGTTTACTCAAAATAT 9 263 0 * ****** * * * MAP Score: 8.23283 Motif 9 CCCGAATAACTTCGGGGTTTCTTTTTTCATTCAAA 0 16 0 CCCGAAGTTATTCGGGGTTTTGTTTTATCTAAAAA 0 35 1 GTAAAGCACCTTGCTGTTTTATTATCAATAATCAA 2 181 1 TCTAGCACGCTTTAGTTTTTATTTTTGTTAAAATT 2 226 0 AAAACCAGTATTCTATCTTCGTTTTTTTATAATAA 7 58 1 GTGGCGGATTTTATCAGTTTTTTTTCACGGAATAT 9 174 1 TTTATTACTATTTGTGTTTAGTTATAGCATTAATA 11 139 1 GAATACGTTATTCCATTTTTATTTTTGATAAGCCA 15 29 1 ATTTTTCGCATTATTCTTTTACTTTTTAAGGACTT 15 67 1 GTATTATCATTACTCGGTTTTTTATTTTATAGAGA 15 103 1 TTTGTTATGGTTGCTATTTTTTTTTAGACGAACAA 18 16 1 TATTTTCTCATTTCAAGTTTATTTTTGATAATACT 18 80 1 AGAATTTTACTGTGGTTTTTGTTTTATTTAGTAAA 18 128 1 TTTACTTAGCGTAGAGTTTTCTTTTTTCTAGGTAA 19 74 1 GCCATTTAAACGGGCGTTTTCTTTTTTGTTTAAAT 21 20 1 ATTCTTAGTTTTTCTGGTTCATTTTGACTAAATCA 21 53 1 ATCTGATTTTTTCTTAGTTTTCTTTCCCTAAGAAT 21 95 1 GCCAAATTCCTATTTCTTTTGTTTTCTTTGTTTTG 21 202 1 CGTGCTTAATTTCAGTTTTTTGTATAAACGAAGTG 22 83 1 ** **** **** MAP Score: 6.86119 Motif 10 GATTGTTTTTCTCAAAAATCATTAAATTTA 0 143 0 GTATTTTCCTCCTAAAAATTGATTGTTCTC 1 56 0 AATGTTTTCCTTAAAATTTATATTAAAAA 1 279 0 CGTAAAATTCTCGCTTCGTT 6 0 1 TCCTAAAATTTCTGTTGATTG 9 1 1 TCTTCTCTACCCTAAAATTTTTGCCTAATT 9 233 0 ATCAATATCTCATAAAATTTAACATTTTGN 11 93 1 CACTATAATGCGCAAAATTTGGAGAATGAA 11 241 1 GAATTTAGCACGCAAAAATCCCTTTCAACT 14 234 0 CAAAAACCACAGTAAAATTCTAAAATCTTA 18 119 0 CACTTACGTCCGTAAAATTTCGCCAAATTC 21 181 1 CGTAAAATTTCGCCAAATTCCTATTTCTTT 21 191 1 ********** MAP Score: 6.66482 Motif 11 AATGATTTTTGAGAAAAACAATCTTTT 0 150 1 CAAATATAATTCAAAAAACTTTCTTTTATTTTTATT 7 9 0 GAGCCATCCCGCTAAAACCAGTATTCTATCTTCGTTT 7 45 1 GGAATATAGCGTAAAAACAAAATTTCTATACAATTAG 9 202 1 ATTTTTGCGTGCTAAATTCAATGATTTCCAGTAGAAT 14 245 1 AAAAACCACAGTAAAATTCTAAAATCTTACTGCAGTA 18 111 0 TTCTTTTTTGTTTAAATTCTTAGTTTTTCTGGTTCAT 21 38 1 AGAAAACTAAGAAAAAATCAGATCTTTGGTTGATTTA 21 81 0 GCAATGCACCGCCAAAGCCCCTGTTTTCAATAATTCC 21 140 1 GTAAAATTTCGCCAAATTCCTATTTCTTTTGTTTTCT 21 192 1 AATTCTTTCAGCTAAAGTAGCTCTTTTTTCTATTATT 22 145 0 TTGAAATGTTTTTAAAAACCTTTTTCTATGTGGTTAG 22 218 1 * *** * * **** MAP Score: 4.33607 Motif 12 GTTTGAATGAAAAAAGAAACCCCGAAGTTATTCGGG 0 15 1 TTTTGTTTTATCTAAAAAGTTTGAAAATTTGACCGC 0 52 1 AAAGCACTGGAAAAAAAAGCGCGATAAGCGTATTAT 5 13 1 TTTTTTTATAATAAAGAAGTACGACA 7 79 1 GAACAGGCAAAAAGAAAGGCACGGAATGTGCTTTCT 10 14 1 ATAACTCCTAACAAATAAGGCTGGACATCAGCCCAG 13 28 0 TTGGCTTATCAAAAATAAAAATGGAATAACGTATTC 15 29 0 TTTATAGAGAAAAGAGAAGCAGGGGAAACT 15 128 1 TAATGAAAAGTGCGGTAACTTTAATCT 17 1 1 TTAGACGAACAATAATAAGCCCCGAATGAAATTGAG 18 39 1 CAGTATTATCAAAAATAAACTTGAAATGAGAAAATA 18 80 0 TTTTACTAAATAAAACAAAAACCACAGTAAAATTCT 18 128 0 ATATTTATATAATGATAAACTATGTAC 20 1 0 AAAGAAAACTAAGAAAAAATCAGATCTTTGGTTGAT 21 84 0 TTTCCCTAAGAATAAAAAAAGGGGCAATGCACCGCC 21 117 1 GAAAAGTCTTTAGAACAAGTTTGAAAAAATGTGTAT 22 24 1 CAATAGTTATTAAAAAAACCTTGAAATGTTTTTAAA 22 198 1 TCTGAAATTTAAGAAAAAGCTTGAAAGGGAGTTTAC 22 259 1 ** ** *** ** * MAP Score: 2.44725