AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons025_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944238330 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0030 51 lipoprotein, putative #1 HI0033 53 conserved hypothetical protein #2 HI0034 124 conserved hypothetical protein #3 HI0035 205 conserved hypothetical protein #4 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #5 HI0081 141 conserved hypothetical protein #6 HI0271 78 conserved hypothetical protein #7 HI0272 23 orotate phosphoribosyltransferase (pyrE) #8 HI0273 300 ribonuclease PH (rph) #9 HI0274 300 glutamyl-tRNA synthetase (gltX) #10 HI0454 54 conserved hypothetical protein #11 HI0457 69 conserved hypothetical protein #12 HI0458 70 stationary phase survival protein SurA, putative #13 HI0459 131 pyrimidine operon regulatory protein (pyrR) #14 HI0549 169 dimethyladenosine transferase (ksgA) #15 HI1354 300 glutaminyl-tRNA synthetase (glnS) #16 HI1603 207 conserved hypothetical protein #17 HI1604 24 phosphate permease, putative #18 HI1605 65 conserved hypothetical protein #19 HI1607 62 hemM protein (hemM) #20 HI1664 27 conserved hypothetical protein #21 HI1665 53 H. influenzae predicted coding region HI1665 #22 HI1667 73 conserved hypothetical protein #23 HI1668 21 tail specific protease (prc) #24 HI1669 38 conserved hypothetical protein #25 HI1670 183 H. influenzae predicted coding region HI1670 Motif 1 ATTTTAGTAAAGTGCGGTAAAAAATAAC 1 8 1 CCTTATCTAAAAAGTGCGGTTATTTTTTAC 1 26 0 TTAGACATAAAAAGCGCGGTTAATTTCGCG 2 26 1 ATCCGAGATAAAAGTGCGGTGAAAAATAAC 3 19 1 CCTTTTACAAAAAGTGCGGTTATTTTTCAC 3 37 0 AAGTGCTATAAAAGTGCGGTTTGTTTTTAT 4 30 0 AATCGAGGTAAAAGTGCTATAAAAGTGCGG 4 41 0 CTGTTAAGTCAAAGTGCGGTTATTTTTATA 6 50 0 TTTAATAAGAAAAGTGCGGTTATTATAGGG 14 141 0 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 15 123 0 ATCTCAATAAAAAGTGCGGTTAATTTTAAC 18 13 1 CATCACAACAAAAGTGCGGTTAAAATTAAC 18 31 0 AAAAGTGCGGTTAATTTTACA 20 16 0 TTTCTCAAACAAAGTGCGGTCAAAACCATT 22 16 0 AGAAAAGCAACAAGTGCGGTGATTTTAATA 22 41 1 AATTTTGTAAAAAGTGCGATAAACTAGGCA 25 128 1 ********** MAP Score: 82.7201 Motif 2 TCTAAAAAGTGCGGTTATTTTTTACCGCACTT 1 19 0 CATAAAAAGCGCGGTTAATTTCGCGCTTATTT 2 31 1 GGTTAATTTCGCGCTTATTTTTTGCGTGGATT 2 43 1 TACAAAAAGTGCGGTTATTTTTCACCGCACTT 3 30 0 TATAAAAGTGCGGTTTGTTTTTATTTCATTTT 4 22 0 CGATAATTAGGGGATTTTTTATAGAATTTAGA 5 108 1 AAGTCAAAGTGCGGTTATTTTTATAATGTTAT 6 43 0 CTAGAATAGTGCGCTTTTTTATTACATCGTTC 8 256 1 TGAGCTAATCGCCCTTAATGTTGTGGGTTGGC 9 126 1 AGCATAAAATCCGCTTTTTTATTTAGAAGTCA 9 225 1 GCAATTAAGCCCCTTTATTTTTGATACTTTG 11 9 0 GGTTATTATAGGGGTTGTTTTAGCTTTGTAAA 14 122 0 TAATTTCGTGGCGGTTTTTTATGGCAAGTTTT 15 165 1 TATAGAATAGCCGAATATTTTTTTATTTTAAC 15 270 1 CGCATATTACCCGATTTTTGTTGATAGTTAAA 16 147 0 AATAAAAAGTGCGGTTAATTTTAACCGCACTT 18 18 1 AAAAGTGCGGTTAATTTTACATTTGTT 20 9 0 TAAAGGAAAAGCCATTGATTTTCGTATTGCGG 21 29 1 GTGCGGTTGATTTTTCACAAATTT 24 2 1 GTGAAGTCTTGGCGTTATTTTTGTGTGAAATT 25 70 1 *** ** ***** MAP Score: 37.9807 Motif 3 ATTTTAGTAAAGTGCGGTAAAAAATAA 1 7 1 GTGCGGTAAAAAATAACCGCACTTTTTAGA 1 21 1 AATTTAGACATAAAAAGCGCGGTTAATTTC 2 23 1 TCCACGCAAAAAATAAGCGCGAAATTAACC 2 43 0 CATCCGAGATAAAAGTGCGGTGAAAAATAA 3 18 1 GTGCGGTGAAAAATAACCGCACTTTTTGTA 3 32 1 AAAGTGCTATAAAAGTGCGGTTTGTTTTTA 4 31 0 AAATTCTATAAAAAATCCCCTAATTATCGC 5 107 0 AACATTATAAAAATAACCGCACTTTGACTT 6 45 1 ATATCCCCATAAAAGACAGCGACATGATAA 8 68 0 TTATTTTTGTTAAAATTCGCTAAGATATTG 8 213 0 ACGATGTAATAAAAAAGCGCACTATTCTAG 8 256 0 AAAATAAGCATAAAATCCGCTTTTTTATTT 9 219 1 AAAATACGCCTAAAAAGCGACGGCATTTGC 13 66 0 TAAAAACGGCTATAATCCGCCCGTTTTTCT 14 27 0 ACAACCCCTATAATAACCGCACTTTTCTTA 14 136 1 TACATCACATTAAAAAGCGGTATCGCCGTG 15 26 1 TATAAATGCACAAAGTGCGGTAAGTTTTTT 15 124 0 AACTTGCCATAAAAAACCGCCACGAAATTA 15 165 0 TAACTATCAACAAAAATCGGGTAATATGCG 16 149 1 AAAAATCGGGTAATATGCGCACGAATTTTT 16 160 1 GATCTCAATAAAAAGTGCGGTTAATTTTAA 18 12 1 ACATCACAACAAAAGTGCGGTTAAAATTAA 18 32 0 AAAAGTGCGGTTAATTTTAC 20 17 0 TTTTCTCAAACAAAGTGCGGTCAAAACCAT 22 17 0 GAGAAAAGCAACAAGTGCGGTGATTTTAAT 22 40 1 GTTAATTTTGTAAAAAGTGCGATAAACTAG 25 125 1 ********** MAP Score: 35.1466 Motif 4 CTTTCTTTAAGAAAGAAAAAATGAAA 0 6 0 AGCTTTCTACGAAAGAAAAAATAATATTGT 14 56 1 CTCGTAAAATGAAATAAAAACAAACCGCAC 4 17 1 TAAATAAAAATTGACTCGGA 23 0 1 GTTTGACTTCTAAATAAAAAAGCGGATTTT 9 230 0 TAAGAAAGAGAAAATAAAAAACAACAAAAG 11 43 0 TTCTCTCGTTAAAATAAAAAAATATTCGGC 15 279 0 AATTTTAACAAAAATAAAAACTAAAGCGTG 8 226 1 TTTTCTTTCTTAAAGAAAGAATAAATGAAA 0 17 1 TTTTGATTTATAAAGAAAGACCACAAGC 25 8 0 AGGCATTAATAAAATAAAGATTTGCCTAGT 25 150 0 AAAAAAATTTGTAAGAAAAAAGGTTTATCT 16 110 0 GGCGGAAAAGTTAAGAAAAACGGGCGGATT 14 14 1 GCTCAATTTCGCAAGAAAAAATGTGACGAA 3 97 1 ATACTAGATTTAAATAAAAGATTGTAAAAA 15 193 0 TTCGAACGATGTAATAAAAAAGCGCACTAT 8 261 0 TAAACAAAATTTAATAAAAAGGTATTGACT 9 180 0 TTGATCTCAATAAAAAGTGCGGTTAA 18 6 1 AGTATAACGAACAAGAAAAATGGTGCAAAT 13 42 1 AAGCTATAAGAAAGAGAAAATAAAA 11 54 0 AATCTAAGGGAAAATAAAGGTTCATCTCCT 15 238 0 CAAAGTATCAAAAATAAAGGGGCTTAATTG 11 10 1 GTACTATTTAATAAGAAAAGTGCGGTTATT 14 147 0 GTTATCACATTAAAGGAAAAGCCATTGATT 21 19 1 TGCGGTGATTTTAATAAAGGTTTAGGAA 22 55 1 TTCTCACTTAGCAATAAAGGTGCGGAATTC 2 100 0 AAAGAAAGAATAAATGAAAAGCGTTAATAT 0 28 1 AGCCTTAGGCATAAGGAAAAATAATT 10 38 1 ********** MAP Score: 34.0173 Motif 5 AAGTGCGGTAAAAAATAACCGCACTTTTTAGATAAGGA 1 19 1 ATTTAGACATAAAAAGCGCGGTTAATTTCGCGCTTATT 2 24 1 AAGTGCGGTGAAAAATAACCGCACTTTTTGTAAAAGGG 3 30 1 AAATGAAATAAAAACAAACCGCACTTTTATAGCACTTT 4 23 1 ATTGTGGAATAATACAACCCTTAATTTTTTAGAGGGAA 4 68 1 TAAATTCTATAAAAAATCCCCTAATTATCGCTAATCAG 5 100 0 ATAACATTATAAAAATAACCGCACTTTGACTTAACAGA 6 43 1 TAAAAATAAGCATAAAATCCGCTTTTTTATTTAGAAGT 9 217 1 AAACATTCAAAAAACTTACCGCACTTTGTGCATTTATA 15 116 1 GCAAGAACAGGAGATGAACCTTTATTTTCCCTTAGATT 15 230 1 TTAAAATAAAAAAATATTCGGCTATTCTATACAAATCT 15 263 0 TACTTAGTCGAAGATAAACCTTTTTTCTTACAAATTTT 16 99 1 TGATCTCAATAAAAAGTGCGGTTAATTTTAACCGCACT 18 11 1 TGAGAAAAGCAACAAGTGCGGTGATTTTAATAAAGGTT 22 39 1 ** * **** ** * MAP Score: 16.6344 Motif 6 TATTCTTTCTTTAAGAAAGAAAAAATGAAA 0 5 0 ACCGCACTTTTTGTAAAAGGGTCAAAAATTTTCGG 3 47 1 CTATGCTCAATTTCGCAAGAAAAAATGTGACGAAC 3 93 1 TTAAATTTCATTTTTAAGGGGTCAAT 3 189 1 AACCCTTAATTTTTTAGAGGGAAAACAAA 4 83 1 TTAGCGAATTTTAACAAAAATAAAAACTAAAGCGT 8 220 1 ACTTGTTTGACTTCTAAATAAAAAAGCGGATTTTA 9 229 0 AAGCTATAAGAAAGAGAAAATAAAAAACAA 11 49 0 TCAATAACGTTGGTTAGAGTAACAATTCTATTGAA 12 29 0 AGTATTTCAATGCACAAAGTATAAAGAAAATACGC 13 87 0 TTTTTTCTTTCGTAGAAAGCTAAAAACGGCTATAA 14 42 0 CTAACAATGATTTACAAAGCTAAAACAACCCCTAT 14 112 1 ATCGTGGCGATGTATAAATGCACAAAGTGCGGTAA 15 131 0 TTTCTCTCGTTAAAATAAAAAAATATTCGGCT 15 278 0 AGCGAGAAAATTTGAAAGGTAAAAAA 16 1 0 AATTTTCTCGCTTTTAAAGCGAAAAGTGTATTGAG 16 24 1 ACCCGATTTTTGTTGATAGTTAAAATTTTTCAAAA 16 136 0 TTTGTTGTGATGTTTAAGGGGAAAAA 18 49 1 GCACTTTGTTTGAGAAAAGCAACAAGTGCGGTGAT 22 29 1 GTGGTCTTTCTTTATAAATCAAAAACGTGCCATTC 25 14 1 ATCGCACTTTTTACAAAATTAACAACGGATCCCGT 25 113 0 ** **** **** MAP Score: 14.1755 Motif 7 CATTTATTCTTTCTTTAAGAAAGAAAAAATG 0 13 0 ATAACCGCACTTTTTGTAAAAGGGTCAAAAA 3 44 1 ATTAGGGGATTTTTTATAGAATTTAGATAAA 5 113 1 TTAGTTTTTATTTTTGTTAAAATTCGCTAAG 8 219 0 ATAGTGCGCTTTTTTATTACATCGTTCGAAA 8 261 1 AGTCAATACCTTTTTATTAAATTTTGTTTAA 9 180 1 CTTGTTTGACTTCTAAATAAAAAAGCGGATT 9 232 0 AACGACTAATATTTTATTGAAGATAGGTTAT 9 275 1 CCAAATTGAGTTTTTCATGAACAATATTATT 14 75 0 AACCGCACTTTTCTTATTAAATAGTACTT 14 150 1 AGATAAACCTTTTTTCTTACAAATTTTTTTG 16 110 1 TTTCTTACAAATTTTTTTGAAAAATTTTAAC 16 122 1 AAGTGCGGTGATTTTAATAAAGGTTTAGGAA 22 52 1 GTGCGGTTGATTTTTCACAAATTTCTGTTGG 24 10 1 CTTGTGGTCTTTCTTTATAAATCAAAAACGT 25 11 1 TCCGTTGTTAATTTTGTAAAAAGTGCGATAA 25 119 1 ***** ***** MAP Score: 5.45051