AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons021_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944238015 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0106 300 signal recognition particle protein (ffh) #1 HI0201 36 ribosomal protein L19 (rpL19) #2 HI0202 37 tRNA (guanine-N1)-methyltransferase (trmD) #3 HI0203 35 conserved hypothetical protein #4 HI0204 292 ribosomal protein S16 (rpS16) #5 HI0768 54 cell division protein (ftsY) #6 HI0938 200 H. influenzae predicted coding region HI0938 #7 HI0942 45 exodeoxyribonuclease V, gamma chain (recC) #8 HI0943 54 conserved hypothetical protein #9 HI1060 66 lipid-A-disaccharide synthetase (lpxB) #10 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #11 HI1064 56 conserved hypothetical protein #12 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #13 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #14 HI1259 193 periplasmic serine protease Motif 1 TAATCAACAAAAAGTGCGGTCATTTTTCAC 0 50 1 TAACAGGTAAAAAGTGCGGTGAAAAATGAC 0 68 0 AAAAACGCCTAAATTTCGGTATAATCAGCA 0 249 1 TTTTCTTAAAAAATTGTGCTGATTATACCG 0 265 0 ACAAAACTTGCAATTTTGCTTGAAAAGTAT 4 160 1 TTTTTATTGAAAATTGTGCTTAGTTTAGAC 5 20 1 TTATTTTGGCAAATCTCGCTATAATGGCAC 6 44 0 ATTTATGGTTAAAGTGCGGTGGAAAATTGG 6 172 1 TTTGGTGTGTAAAGTGCGGTTGAAAATGAA 9 19 0 TTTACACACCAAAGTGCGGTTATTTTTTAG 9 36 1 AATTGTTACTCAAGTTCGGTTTCCCGAACT 12 97 1 ATTGACTAGAAAATTGCGCGTATTAGAACA 14 24 1 ********** MAP Score: 24.1136 Motif 2 ATTTCGGTATAATCAGCACAATTTTTTAAGAAAAAC 0 261 1 TATTTTATAGAATAAGCCAATTTTTTAAGCCAGAAG 11 19 0 AAAAGTATAAAATTCGCAGGCTTTTTGTCTATATAT 4 182 1 TGATTTGAGAATATAGCTTACTTTTTTCTCTGTATA 4 215 0 TTTATGTTCTAATACGCGCAATTTTCTAGTCAATAA 14 22 0 AAAACGCTCCAATTTTCCACCGCACT 6 184 0 GAAATGATGAAAAACGCCTAAATTTCGGTATAATCA 0 240 1 TCGTCAAATAACCTATTTTTTAGTAGAATAA 8 5 1 AAATTGGCTAAATAATCATTCTTTTTCCTTATGTCC 0 158 1 CTCTCCTCTTATTGAACATTTTTTTTATTTTTTTGT 14 127 1 TTNGCGATCTGTATCGCAAAGTTTTTCTGAAAACCT 6 106 0 TCTCGCTATAATGGCACGGAATTTTTCTGTTCTTTA 6 25 0 CACAAACGTAATGTAGTAGGCTTTTT 2 21 1 CGCTGCTCTCATTGAGTGGCGTTTTTTTCATCCCGA 12 15 0 AATCGTCTAAACTAAGCACAATTTTCAATAAAAATC 5 18 0 GGCTAACAATCCTGTTTTTCTTAAAAAATT 0 280 0 TTTACACACCAAAGTGCGGTTATTTTTTAGGATAAA 9 36 1 TAATCAACAAAAAGTGCGGTCATTTTTCACCGCACT 0 50 1 AATGGCGTTGTTTTTTCTAGGTTAAAT 7 1 1 TATAAACCTCATTTAACTGATATTTTATCAAGCTAA 4 11 1 GGTAGGAAAGGACAAGTGACGTTTTTTTATTTGAGG 12 218 1 TAAAACTTCTTCATTTTCAACCGCACTT 9 2 1 GACCGTTTTTGTACTGCTCCGATTTCCTTTTAAACA 14 81 1 ** *** ***** MAP Score: 23.2681 Motif 3 TAACAGGTAAAAAGTGCGGTGAAAAATGACCGCACTTTTTGTTGATTA 0 50 0 GTTTTTCTTAAAAAATTGTGCTGATTATACCGAAATTTAGGCGTTTTT 0 249 0 CTCAAATTCGAAAGTGATTTGAGAATATAGCTTACTTTTTTCTCTGTA 4 217 0 ACCTTCCTCTAAATGTTTAATTACTAAAAGAATATTCTCAAATTCGAA 4 253 0 GATTTTTATTGAAAATTGTGCTTAGTTTAGACGATTTTTTGCTAGA 5 18 1 TTATTTTGGCAAATCTCGCTATAATGGCACGGAATTTTTCTGTTCTTT 6 26 0 AAAACGCTCCAATTTTCCACCGCACTTTAACCATAAAT 6 172 0 TAAAACTTCTTCATTTTCAACCGCACTTTACACACCAAA 9 1 1 TTTACACACCAAAGTGCGGTTATTTTTTAGGATAAATTTG 9 36 1 CGGGATGAAAAAAACGCCACTCAATGAGAGCAGCGTTTAACCAAATCG 12 16 1 ATTGTAAGGAAAAGGGTAGGAAAGGACAAGTGACGTTTTTTTATTTGA 12 204 1 AATTTGAAATAAATCTTGTCCATTATAGACGAAAATTTTATAA 12 267 1 TATTGACTAGAAAATTGCGCGTATTAGAACATAAATTTATAGAATTTG 14 23 1 AAAAATAAAAAAAATGTTCAATAAGAGGAGAGCAAATTATCTTGTTTA 14 111 0 *** * ** * *** MAP Score: 19.5558 Motif 4 CAAAAAGTCATTTTCATTTGAAATGATGAAAAACGC 0 221 1 TTATAAAATTTTCGTCTATAATGGACAAGATTTA 12 276 0 ACAATCCTGTTTTTCTTAAAAAATTGTGCTGATTAT 0 269 0 AAAGATTCGATTTTTATTGAAAATTGTGCTTAGTTT 5 10 1 CAAATTTATCCTAAAAAATAACCGCACTTTG 9 45 0 GTGAACTGTTTTCATAACCAAAAAGGACGTCGCG 13 8 1 GATCAAGTGATTTTTCTACCCATTCATTTATGGTTA 6 147 1 AAAAATTGGCTTATTCTATAAAATAACCGCTCAAGA 11 30 1 ATTTGTTTATTTTTTGTAAGGTATCAAC 10 67 1 AATTTTATACTTTTCAAGCAAAATTGCAAGTTTTGT 4 160 0 TTCCTTTTAATTATCATTCACAATTTATTTTGTTTT 4 105 0 AGTGGCGTTTTTTTCATCCCGATTTTA 12 1 0 TTTCCTACCCTTTTCCTTACAATACAACCATACTTA 12 191 0 AAATAACCTATTTTTTAGTAGAATAACACCCTTTTA 8 15 1 GGAGAGCAAATTATCTTGTTTAAAAGGAAATCGGAG 14 97 0 TTTCAACTAGTTATTTTGGCAAATCTCGCTATAATG 6 48 0 TGGCACGGAATTTTTCTGTTCTTTAAAAGCTGGTGG 6 14 0 AAAACAGTGGTTTTTATAGGTTTTCAGAAAAACTTT 6 89 1 ATAGCTTACTTTTTTCTCTGTATATATAGACAAAAA 4 203 0 TGAGTGCGTTTTATTTTTAGCTATAAATATCGTATA 10 17 1 TATTGAACATTTTTTTTATTTTTTTGTCTTACAGAC 14 136 1 ATGACCGCACTTTTTGTTGATTAACGAACAAAAGGA 0 37 0 ATACGCGCAATTTTCTAGTCAATAAAAAGGTCAAAA 14 11 0 AACTGATATTTTATCAAGCTAAAATACCGCTATACG 4 25 1 TATCTGAAATTTATTTTGGAGTATTT 14 177 1 ATGGCGTTGTTTTTTCTAGGTTAAATCATCAAAAGG 7 11 1 TTCCTGTATATTATTAAACCGATTTGGTTAAACGCT 12 47 0 ***** * *** * MAP Score: 18.3569 Motif 5 AACAAAAAGTGCGGTCATTTTTCACCGCACT 0 55 1 GCTTAGTTTAGACGATTTTTTGCTAGA 5 37 1 AATGGCGTTGTTTTTTCTAGGTTA 7 3 1 AATGGCGACCTTTTGATGATTTAA 7 31 0 ACACCAAAGTGCGGTTATTTTTTAGGATAAA 9 41 1 TATAGAATAAGCCAATTTTTTAAGCCAGAAG 11 19 0 TCTTGAGCGGTTATTTTATAGAATAAG 11 39 0 CTCATTGAGTGGCGTTTTTTTCATCCCGATT 12 13 0 AAGGACAAGTGACGTTTTTTTATTTGAGGTA 12 225 1 TCGCGACGTCCTTTTTGGTTATGAA 13 20 0 ****** **** MAP Score: 16.3351 Motif 6 GCAATTTTGCTTGAAAAGTATAAAATTCGCAGGCTTTTTG 4 169 1 CCACCAGCTTTTAAAGAACAGAAAAATTCCGTGCCATTAT 6 14 1 TTTGACCTTTTTATTGACTAGAAAATTGCGCGTATTAGAA 14 12 1 TGTTTTTTCCTTCTGGCTTAAAAAATTGGCTTATTCTATA 11 10 1 TACAACCTACTTTATGCATACAAAACTTGCAATTTTGCTT 4 141 1 AAATAACCTATTTTTTAGTAGAATAACACCCTTTTATGGA 8 15 1 GTGAACTGTTTTCATAACCAAAAAGGACGTCGCGA 13 9 1 TAACTGATATTTTATCAAGCTAAAATACCGCTATACGCGT 4 24 1 TTTTGATGATTTAACCTAGAAAAAACAACGCCATT 7 5 0 TATACGATATTTATAGCTAAAAATAAAACGCACTCAATAT 10 13 0 TAAAATCGGGATGAAAAAAACGCCACTCAATGAG 12 4 1 CTTTTGTTCGTTAATCAACAAAAAGTGCGGTCATTTTTCA 0 39 1 TTATTTGATTTTGCTAAATCAAATAGCTGCTCAAATAGCT 0 95 1 CAAATTTATCCTAAAAAATAACCGCACTTTGGTGT 9 41 0 AAAAATTGGCTTATTCTATAAAATAACCGCTCAAGA 11 30 1 GTCATTTTCATTTGAAATGATGAAAAACGCCTAAATTTCG 0 227 1 AGTTTTTCTAATACCTCAAATAAAAAAACGTCACTTGTCC 12 227 0 AAATAACTAGTTGAAAATCATAAAACAGTGGTTTTTATAG 6 68 1 ATTTATTTTGTTTTACGATATAATACGAGGCATCCAGCTG 4 79 0 TTGTCTATATATACAGAGAAAAAAGTAAGCTATATTCTCA 4 206 1 TCCGATTTCCTTTTAAACAAGATAATTTGCTCTCCTCTTA 14 98 1 ** * * **** ** MAP Score: 15.8129 Motif 7 TCATTGAGTGGCGTTTTTTTCATCCCGATTTTA 12 10 0 AGGACAAGTGACGTTTTTTTATTTGAGGTATTA 12 226 1 CTCTTATTGAACATTTTTTTTATTTTTTTGTCT 14 132 1 CTTAGTTTAGACGATTTTTTGCTAGA 5 38 1 AAATGACCGCACTTTTTGTTGATTAACGAACAA 0 42 0 CGTCAAATAACCTATTTTTTAGTAGAATAACAC 8 11 1 AACTTGAGTAACAATTTGTTACTCATTTACTTC 12 80 0 TATAATCAGCACAATTTTTTAAGAAAAACAGGA 0 268 1 ATAGAATAAGCCAATTTTTTAAGCCAGAAGGAA 11 16 0 ACTTGTAAGACCGTTTTTGTACTGCTCCGATTT 14 73 1 TCGCGACGTCCTTTTTGGTTATGAAAACAGTT 13 13 0 TATATTGAGTGCGTTTTATTTTTAGCTATAAAT 10 12 1 AAATTCGCAGGCTTTTTGTCTATATATACAGAG 4 191 1 TCTAATACGCGCAATTTTCTAGTCAATAAAAAG 14 18 0 ATTATCATTCACAATTTATTTTGTTTTACGATA 4 99 0 AATGGCGACCTTTTGATGATTTAACCTAGA 7 25 0 AATATAGCTTACTTTTTTCTCTGTATATATAGA 4 209 0 TACAAAACTTGCAATTTTGCTTGAAAAGTATAA 4 159 1 CAAGGGAAAATCCTTTTGTTCGTTAATCAACAA 0 27 1 ** ******* * MAP Score: 14.9373 Motif 8 AAAATGACCGCACTTTTTGTTGATTAACGAACAAAAGGATT 0 35 0 CCTTATGTCCTATACTTTCTTTATGAAATCGCCTACTCAAA 0 184 1 AGGCGTTTTTCATCATTTCAAATGAAAATGACTTTTTGAGT 0 218 0 GTATAATCAGCACAATTTTTTAAGAAAAACAGGATTGTTAG 0 267 1 TTTTGCTTTTTGATTTAGTTCTCAAACTAAGATAG 3 8 1 CCGCTATACGCGTAAATTTGACCTAAAACAGCTGGATGCCT 4 51 1 AGCTGGATGCCTCGTATTATATCGTAAAACAAAATAAATTG 4 80 1 ATACAAAACTTGCAATTTTGCTTGAAAAGTATAAAATTCGC 4 158 1 AAAGATTCGATTTTTATTGAAAATTGTGCTTAGTTT 5 5 1 TTTTTCTACCCATTCATTTATGGTTAAAGTGCGGTGGAAAA 6 157 1 AATGGCGTTGTTTTTTCTAGGTTAAATCATCAAAAGGTC 7 8 1 AAAAAATAACCGCACTTTGGTGTGTAAAGTGCGGTTGAAAA 9 23 0 TCGGATTATACGATATTTATAGCTAAAAATAAAACGCACTC 10 18 0 TGTTTTTTCCTTCTGGCTTAAAAAATTGGCTTATT 11 4 1 TCGCGACGTCCTTTTTGGTTATGAAAACAGTTCAC 13 6 0 TTTTTGACCTTTTTATTGACTAGAAAATTGCGCGTATTAG 14 9 1 TTTTGTACTGCTCCGATTTCCTTTTAAACAAGATAATTTGC 14 87 1 * * *** * *** * MAP Score: 14.3396 Motif 9 AAAAGTGCGGTCATTTTTCACCGCACTTTTTACCTG 0 59 1 TTTGAGTAGGCGATTTCATAAAGAAAGTATAGGACA 0 189 0 ACTCAAAAAGTCATTTTCATTTGAAATGATGAAAAA 0 218 1 ATAATCAGCACAATTTTTTAAGAAAAACAGGATTGT 0 269 1 GTATTCCTTTTAATTATCATTCACAATTTATTTTGT 4 108 0 ACAAAACTTGCAATTTTGCTTGAAAAGTATAAAATT 4 160 1 AAACTAAGCACAATTTTCAATAAAAATCGAATCTTT 5 10 0 AAAACGCTCCAATTTTCCACCGCACTTTAACCATA 6 175 0 GTCAAATAACCTATTTTTTAGTAGAATAACACCCTT 8 12 1 TAAAACTTCTTCATTTTCAACCGCACTTTACACACC 9 10 1 CAAAGTGCGGTTATTTTTTAGGATAAATTTG 9 45 1 TGAGTGCGTTTTATTTTTAGCTATAAATATCGTATA 10 17 1 TCTTGAGCGGTTATTTTATAGAATAAGCCAATTTTT 11 30 0 TAAATCTTGTCCATTATAGACGAAAATTTTATAA 12 276 1 TGTACTGCTCCGATTTCCTTTTAAACAAGATAATTT 14 90 1 * ***** * * ** MAP Score: 13.5991 Motif 10 TGTTTTTTCCTTCTGGCTTAAA 11 0 1 GGACAAGTGACGTTTTTTTATTTGAGGTATTA 12 227 1 TTATTGAACATTTTTTTTATTTTTTTGTCTTA 14 135 1 TTTTGCTTTTTGATTTAGTTCTCAA 3 3 1 ATGACCGCACTTTTTGTTGATTAACGAACAAA 0 41 0 TAAAAACCACTGTTTTATGATTTTCAACTAGT 6 73 0 TAAATAATCATTCTTTTTCCTTATGTCCTATA 0 166 1 AGGGAAAATCCTTTTGTTCGTTAATCAACAAA 0 29 1 ATATTGAGTGCGTTTTATTTTTAGCTATAAAT 10 13 1 TGTTTGATCCTTTATTGATCCT 1 24 0 ACTTTTTACCTGTTATTTGATTTTGCTAAATC 0 83 1 GCACGGAATTTTTCTGTTCTTTAAAAGCTGGT 6 16 0 AATGGCGACCTTTTGATGATTTAACCTAGAA 7 24 0 ATCCGATAGATTTTATTTGTTTATTTTTTGTA 10 53 1 TCGCGACGTCCTTTTTGGTTATGAAAACAG 13 15 0 GTAGGTTGTATTCCTTTTAATTATCATTCACA 4 119 0 CATTGAGTGGCGTTTTTTTCATCCCGATTTTA 12 10 0 TCATTCACAATTTATTTTGTTTTACGATATAA 4 96 0 ******** ** MAP Score: 13.4925 Motif 11 ATCAACAAAAAGTGCGGTCATTTTTCACCGCACTT 0 52 1 GAAATGATGAAAAACGCCTAAATTTCGGTATAATC 0 240 1 ATTTCGGTATAATCAGCACAATTTTTTAAGAAAAA 0 261 1 AAAAAGCCTACTACATTACGTTTGTGC 2 20 0 TTATGCATACAAAACTTGCAATTTTGCTTGAAAAG 4 152 1 ATATAGACAAAAAGCCTGCGAATTTTATACTTTTC 4 181 0 ATTTGAGAATATAGCTTACTTTTTTCTCTGTATAT 4 214 0 AATCGTCTAAACTAAGCACAATTTTCAATAAAAAT 5 19 0 GAACAGAAAAATTCCGTGCCATTATAGCGAGATTT 6 29 1 AAAACGCTCCAATTTTCCACCGCAC 6 185 0 GCTATATTGAGTGCGTTTTATTTTTAGCTATAAA 10 9 1 ATGATTGGTAATTCCTTACTAGTTAATGAGTTTCA 12 156 0 TTTATGTTCTAATACGCGCAATTTTCTAGTCAATA 14 23 0 * * *** * * *** MAP Score: 1.64219