AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons018_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237882 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0244 300 tRNA-guanine transglycosylase (tgt) #1 HI0245 123 queuosine biosynthesis protein (queA) #2 HI0249 153 excinuclease ABC, subunit A (uvrA) #3 HI0301 300 hemolysin, putative #4 HI0313 62 Holliday junction DNA helicase (ruvA) #5 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #6 HI0315 159 conserved hypothetical protein #7 HI0442 116 conserved hypothetical protein #8 HI0443 61 recombination protein (recR) #9 HI0457 69 conserved hypothetical protein #10 HI0458 70 stationary phase survival protein SurA, putative #11 HI0459 131 pyrimidine operon regulatory protein (pyrR) #12 HI1230 147 adenine phosphoribosyltransferase (apt) #13 HI1590 60 conserved hypothetical protein #14 HI1593 34 H. influenzae predicted coding region HI1593 #15 HI1596 58 leucine responsive regulatory protein (lrp) #16 HI1597 84 DNA repair protein (radA) #17 HI1598 300 conserved hypothetical protein Motif 1 TGACCAGCATAATTGCTGGTTATTTTATCTTCCCCG 1 21 1 AAAAGTATGAAATAAATGTAAATTTTGCGATCATTA 2 117 0 CCCTCTCCGTAAAAATTGTGTATTTTTAACCGCACT 3 156 1 GATTTTTTCTAAAATATGATAATTTTTCGCCGTCAA 3 251 1 AAGTAAGATGAAAATATGAATATTTTCATCTTACTC 17 15 0 GTTTAAACCCAATGTGCGGTTATTTTTTATTGATTT 3 196 1 TTTATCTAAAAAAGTGCGGTTATTTTGCCTGAAATT 2 25 1 AATTCTGTAGAATAGTTGTTCCTTTTT 15 41 1 ATTGTGATTAAAATATTGCGACTTTTAAATAAAAAA 17 175 0 AAAATGGTGCAAATGCCGTCGCTTTTTAGGCGTATT 11 58 1 TTCAAACTAGACTTACCGCCTATTTTATTTAACCTA 1 88 1 CAACGAATAAACAGTTCGAAGATTTTTTAAACAAAA 0 266 0 TTTTTTAGATAAAAAATGAGGTTTTTTT 2 2 0 ATGATATCACAAAGCCTGTATTTTTTAACAGGCTTT 0 231 1 TTTCATTTTCAGTAGGCGATGATTTTT 15 1 0 TTTCATCGGATAATATTGATAATTTTAAATAACAAA 17 116 0 AAGCCAGATTAAAATGTGAATATTTACTAATCTAAA 17 82 0 GACATTTCACAATTATTGCTAATTTAGATTAGTAAA 17 60 1 CCCCGTTGGGAGTGGATGTAGCTTTTCCCAAAAGAG 6 43 0 TCATATAAACAAAATAAGAATATTTTGTTGTCTAGA 3 114 1 AATGCCAATCTAAAAACGTTTCTTTTTTTACCGCAC 12 106 1 TGATGCAATAAATGGGTAATTTAATTACCCAT 5 6 1 ATACAATAGAAATAAATCAAGATTTTTGTGGTGTTT 17 250 0 TTTATTTTATTCTATGCGTTAATTTTTTTATCATTC 4 27 1 ATTTTGCGATCATTATCGCATATTTTAATATCTGTG 2 96 0 *** ** ***** MAP Score: 33.3521 Motif 2 GTTTAAACCTAAAGTGCGGTTAAAAATACACAATTT 3 168 0 AAGTATAAAGAAAATACGCCTAAAAAGCGACGGCAT 11 70 0 ATAATGCTCAAAAGTGCGGTAAAAAAAGAAACGTTT 12 119 0 ATCTTTTAAAAAATTTCAGGCAAAATAACCGCACTT 2 36 0 CGAAAAGAGGAAAATCAATAAAAAATAACCGCACAT 3 207 0 TTGTAAATTCAAACTTAAATAAAAATCCCCAATTGG 12 31 1 TCGCCTACTGAAAATGAAAGGAAAATTCTGTAGAAT 15 18 1 TTTAAACAAAAAAGCCTGTTAAAAAATACAGGCTTT 0 241 0 TTTAAATAACAAAGCCAGATTAAAATGTGAATATTT 17 93 0 AACAAAATTTAGGTTAAATAAAATAGGCGG 1 103 0 TTTAAGCTATAAAGTGCGGTGAAATTTAGTGGCGTT 7 22 0 ACTAAGGATAAAAATATGACTAAATTTATGATTAAG 0 100 0 AATTTCTATAAAAAATGGGTAATTAA 5 30 0 TATCTGTGCAAATATCCAGTTAAAATATATAGATCT 2 68 0 TTACGAGATCAATTCACAATCAAAAATCCATTATTC 3 48 1 TTTATGATAGAATGCCAATCTAAAAACGTTTCTTTT 12 96 1 CAATAAGATCAAAACAGAAGGAAATAAA 6 141 1 AAATAACTCAAAAGTATGAAATAAATGTAAATTTTG 2 126 0 ATAATTGTGAAATGTCAATTAAAATAAGTAAGATGA 17 40 0 AAGCTATAAGAAAGAGAAAATAAAAAACAACAAAAG 9 43 0 GCCTCTGCTCAAAGAGCATTGAAAATATGATATCAC 0 205 1 TTTAAATAAAAAAATAATCCGAAAAACATAAACAGA 17 152 0 ATAGCTATTTAATATGTAAAGTAAAACACCACAAAA 17 227 1 *** * * ***** MAP Score: 24.7626 Motif 3 AAATCCCCAATTGGGGATTTTTATTTAAGTTTGAAT 12 37 0 AAATCCCCAATTGGGGATTTTTATTTTCCTCTCTTT 12 53 1 CGTCGCTTTTTAGGCGTATTTTCTTTATACTTTGTG 11 74 1 GTATTTTTTAACAGGCTTTTTTGTTTAAAAAATCTT 0 248 1 ATCTTCCCCGAGGGGAGATTTTTTCTTGAGATCATT 1 47 1 TCTTTTCGCGTTTTGCGATTTTTTCTAAAATATGAT 3 235 1 AACTAGACTTACCGCCTATTTTATTTAACCTAAATT 1 92 1 GTTTATGTTTTTCGGATTATTTTTTTATTTAAAAGT 17 155 1 CTGGATGTTCGTCCAGTTTTATTTTATTCTATGC 4 8 1 GACAACAAAATATTCTTATTTTGTTTATATGACGAA 3 110 0 AAACCCAATGTGCGGTTATTTTTTATTGATTTTCCT 3 200 1 AAATAGCTATAAATGAATTTTTATTTATTGTGATTA 17 201 0 TCTAAAAAAGTGCGGTTATTTTGCCTGAAATTTTTT 2 29 1 TCAAGATTTTTGTGGTGTTTTACTTTACATATTAAA 17 234 0 CAGCATAATTGCTGGTTATTTTATCTTCCCCGAGGG 1 25 1 CACATTTTAATCTGGCTTTGTTATTTAAAATTATCA 17 100 1 AGCGACGGCATTTGCACCATTTTTCTTGTTCGTTAT 11 45 0 AAGGGGCAATTAAGCCCCTTTATTTTTGATACTTTG 9 10 0 AAAAAAACCTCATTTTTTATCTAAAAAAGTGC 2 6 1 TAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTTTC 9 34 1 AACTTGTGAATAATGGATTTTTGATTGTGAATTGAT 3 55 0 AACACCACAAAAATCTTGATTTATTTCTATTGTATT 17 251 1 * ** **** *** MAP Score: 23.3436 Motif 4 CATACTAAGGATAAAAATATGACTAAATTTATGATTA 0 102 0 GATTTTTTAAACAAAAAAGCCTGTTAAAAAATACAGG 0 245 0 TTAATCCCAAATGACCAGCATAATTGCTGGTT 1 5 1 TTTAGGTTAAATAAAATAGGCGGTAAGTCTAGTTTGA 1 89 0 AACAAAATTTAGGTTAAATAAAATAGG 1 106 0 CATTTTTTATCTAAAAAAGTGCGGTTATTTTGCCTGA 2 20 1 TAGATCTTTTAAAAAATTTCAGGCAAAATAACCGCAC 2 38 0 TTGCACAGATATTAAAATATGCGATAATGATCGCAAA 2 93 1 GAATTGATCTCGTAAAAAGAGGGCAAAGATCCTTATC 3 26 0 TCCGAATGATAAAAAAATTAACGCATAGAATAAAATA 4 29 0 GATCAATAAGATCAAAACAGAAGGAAATAAA 6 138 1 CACTTTATAGCTTAAAAGTGCGGTAAGATTTTCTAAG 7 42 1 AGAAAGAGAAAATAAAAAACAACAAAAGGGGCAATTA 9 34 0 CTCATCCAAAAAAGAGTCAATAACGTTGGTTA 10 48 0 TATAACGAACAAGAAAAATGGTGCAAATGCCGTCGCT 11 44 1 ACAAAGTATAAAGAAAATACGCCTAAAAAGCGACGGC 11 72 0 TCATAAAAAAATAGAAAGAGAGGAAAATAAAAATCCC 12 66 0 AAATAATGCTCAAAAGTGCGGTAAAAAAAGAAACG 12 122 0 TTTTGTTAGCAAAGAAACTTGAGTAAAA 14 1 0 TCATCGCCTACTGAAAATGAAAGGAAAATTCTGTAGA 15 15 1 CTTTTAAATAAAAAAATAATCCGAAAAACATAAACAG 17 153 0 TAATATGTAAAGTAAAACACCACAAAAATCTTGATTT 17 236 1 * **** * * *** MAP Score: 21.4481 Motif 5 ACTTAATCATAAATTTAGTCATATTTTTATCCTTAGT 0 99 1 TATGATATCACAAAGCCTGTATTTTTTAACAGGCTTT 0 230 1 TTTTTAGATAAAAAATGAGGTTTTTTT 2 0 0 TTTTATCTAAAAAAGTGCGGTTATTTTGCCTGAAATT 2 24 1 TATCCAGTTAAAATATATAGATCTTTTAAAAAATTTC 2 55 0 ATAATGATCGCAAAATTTACATTTATTTCATACTTTT 2 116 1 TTATATGACGAAAAGTATCTATGTTGTGGATAACTTG 3 85 0 CTAGACAACAAAATATTCTTATTTTGTTTATATGACG 3 112 0 CCTCTCCGTAAAAATTGTGTATTTTTAACCGCACTTT 3 157 1 GGTTTAAACCCAATGTGCGGTTATTTTTTATTGATTT 3 195 1 ATTGACGGCGAAAAATTATCATATTTTAGAAAAAATC 3 251 0 TAAAAATCCCCAATTGGGGATTTTTATTTTCCTCTCT 12 50 1 TGCCAATCTAAAAACGTTTCTTTTTTTACCGCACTTT 12 108 1 CTATTCTACAGAATTTTCCTTTCATTTTCAGTAGGCG 15 19 0 ATGAAAATATGAATATTTTCATCTTACTCAGCAT 17 7 0 AGCCAGATTAAAATGTGAATATTTACTAATCTAAATT 17 80 0 TTTGTTATTTAAAATTATCAATATTATCCGATGAAAT 17 116 1 TTATCCGATGAAATCTGTTTATGTTTTTCGGATTATT 17 139 1 TTTTTTATTTAAAAGTCGCAATATTTTAATCACAATA 17 175 1 AGCTATAAATGAATTTTTATTTATTGTGATTAAAATA 17 196 0 AAAACACCACAAAAATCTTGATTTATTTCTATTGTAT 17 249 1 **** * ** ** * MAP Score: 16.8255 Motif 6 TACGAGATCAATTCACAATCAAAAATCCATTATTCACAAGTTA 3 49 1 AAAGAGGAAAATCAATAAAAAATAACCGCACATTGGGTTTAAA 3 197 0 AAAAATTATCATATTTTAGAAAAAATCGCAAAACGCGAAAAGA 3 235 0 ATTAACGCATAGAATAAAATAAAACTGGACGAACATCCAG 4 7 0 AGCTATAAGAAAGAGAAAATAAAAAACAACAAAAGGGGCAATT 9 35 0 GGATAGTATAACGAACAAGAAAAATGGTGCAAATGCCGTCGCT 11 38 1 TCAATGCACAAAGTATAAAGAAAATACGCCTAAAAAGCGACGG 11 73 0 TTGTAAATTCAAACTTAAATAAAAATCCCCAATTGGGGATTTT 12 31 1 AAATAGAAAGAGAGGAAAATAAAAATCCCCAATTGGGGATTTT 12 52 0 CGCCTACTGAAAATGAAAGGAAAATTCTGTAGAATAGTTGTTC 15 19 1 TGCGACTTTTAAATAAAAAAATAATCCGAAAAACATAAACAGA 17 152 0 TATTTTAATCACAATAAATAAAAATTCATTTATAGCTATTTAA 17 196 1 AGCTATTTAATATGTAAAGTAAAACACCACAAAAATCTTGATT 17 229 1 * ** **** * ** MAP Score: 14.2285 Motif 7 AATAACAGGCAAAGTAGAATAATGATGACCA 0 68 1 ACTAAGGATAAAAATATGACTAAATTTATGA 0 105 0 AAGAGCATTGAAAATATGATATCACAAAGCC 0 216 1 AAATTTAGGTTAAATAAAATAGGCGGTAAGT 1 98 0 AAATAACTCAAAAGTATGAAATAAATGTAAA 2 131 0 TCATATAAACAAAATAAGAATATTTTGTTGT 3 114 1 AGTGCGGTTAAAAATACACAATTTTTACGGA 3 161 0 GATTTTTTCTAAAATATGATAATTTTTCGCC 3 251 1 CGCATAGAATAAAATAAAACTGGACGAACAT 4 14 0 TGATGCAATAAATGGGTAATTTAATTACC 5 8 1 CAAAGTATCAAAAATAAAGGGG 9 1 1 TAAGAAAGAGAAAATAAAAAACAACAAAAGG 9 42 0 AAGTATAAAGAAAATACGCCTAAAAAGCGAC 11 75 0 TTCAATGCACAAAGTATAAAGAAAATACGCC 11 86 0 AATTCAAACTTAAATAAAAATCCCCAATTGG 12 36 1 GAAAGAGAGGAAAATAAAAATCCCCAATTGG 12 59 0 CTATCATAAAAAAATAGAAAGAGAGGAAAAT 12 75 0 AAGTAAGATGAAAATATGAATATTTTCATCT 17 20 0 AATGTCAATTAAAATAAGTAAGATGAAAATA 17 35 0 TTACTAATCTAAATTAGCAATAATTGTGAAA 17 64 0 AAGCCAGATTAAAATGTGAATATTTACTAAT 17 87 0 TTGATAATTTTAAATAACAAAGCCAGATTAA 17 106 0 TTGCGACTTTTAAATAAAAAAATAATCCGAA 17 165 0 TTAATCACAATAAATAAAAATTCATTTATAG 17 200 1 TTTAATATGTAAAGTAAAACACCACAAAAAT 17 234 1 ATTAACTGGTTAAATATACAATACAATAGAA 17 275 0 ****** **** MAP Score: 11.6886 Motif 8 TTAATCCCAAATGACCAGCATAATTGC 1 4 1 AGAAAAAATCTCCCCTCGGGGAAGATAAAATAA 1 40 0 TCTAGAATTTTCCCCTCTCCGTAAAAATTGTGT 3 144 1 ATGTAGCTTTTCCCAAAAGAGAACCGCTATCAC 6 31 0 CTACATCCACTCCCAACGGGGTAACACTTTTAC 6 58 1 ATCCCACAGTTCCCAAAAGCCCATTTTTTCGCT 7 90 1 AAATAAAAATCCCCAATTGGGGATTTTTATTTA 12 46 0 CATCAAACTACCCCAACGGAGTAGCACTGAGAT 16 25 0 AGTTTGATGTTCCCCAAAGGGGAACCACTATAA 16 49 1 ****** *** * MAP Score: 10.9852 Motif 9 ATCACAAAGCCTGTATTTTTTAACAGGCTTT 0 236 1 TATTTTTTAACAGGCTTTTTTGTTTAAAAAA 0 249 1 TAAACAGTTCGAAGATTTTTTAAACAAAAAA 0 264 0 AGCATAATTGCTGGTTATTTTATCTTCCCCG 1 26 1 TTCCCCGAGGGGAGATTTTTTCTTGAGATCA 1 50 1 ACTAGACTTACCGCCTATTTTATTTAACCTA 1 93 1 GATAAAAAATGAGGTTTTTTT 2 0 0 GCAAAATAACCGCACTTTTTTAGATAAAAAA 2 22 0 TTATTTTGCCTGAAATTTTTTAAAAGATCTA 2 44 1 TTTAAAAGATCTATATATTTTAACTGGATAT 2 62 1 TATATTTTAACTGGATATTTGCACAGATATT 2 75 1 GCGATCATTATCGCATATTTTAATATCTGTG 2 96 0 AGGATCTTTGCCCTCTTTTTACGAGATCAAT 3 30 1 AACCCAATGTGCGGTTATTTTTTATTGATTT 3 201 1 TTTCGCGTTTTGCGATTTTTTCTAAAATATG 3 238 1 ATTCTATGCGTTAATTTTTTTATCATTCGGA 4 35 1 AATTTAATTACCCATTTTTTATAGAAATT 5 27 1 GCAATTAAGCCCCTTTATTTTTGATACTTTG 9 10 0 CAACGTTATTGACTCTTTTTTGGATGAG 10 52 1 TGCAAATGCCGTCGCTTTTTAGGCGTATTTT 11 65 1 ATCCCCAATTGGGGATTTTTATTTAAGTTTG 12 40 0 ATCCCCAATTGGGGATTTTTATTTTCCTCTC 12 55 1 TCCTCTCTTTCTATTTTTTTATGATAGAATG 12 79 1 CAAGTGATTATTTTAAATAAGGGC 13 3 1 AAATACGCCCTTCAATTTTTTGAGAAATAAA 13 38 1 TTATGTTTTTCGGATTATTTTTTTATTTAAA 17 157 1 ATTTAAAAGTCGCAATATTTTAATCACAATA 17 181 1 * ********* MAP Score: 2.83043