AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons021_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944238053 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 GTGAAAAATGACCGCACTTTTTGTTGATTA 0 50 0 GTCATTTTTCACCGCACTTTTTACCTGTTA 0 68 1 TGCTGATTATACCGAAATTTAGGCGTTTTT 0 249 0 CGGTATAATCAGCACAATTTTTTAAGAAAA 0 265 1 ATACTTTTCAAGCAAAATTGCAAGTTTTGT 4 160 0 GTCTAAACTAAGCACAATTTTCAATAAAAA 5 20 0 GTGCCATTATAGCGAGATTTGCCAAAATAA 6 44 1 CCAATTTTCCACCGCACTTTAACCATAAAT 6 172 0 TTCATTTTCAACCGCACTTTACACACCAAA 9 19 1 CTAAAAAATAACCGCACTTTGGTGTGTAAA 9 36 0 AGTTCGGGAAACCGAACTTGAGTAACAATT 12 97 0 TGTTCTAATACGCGCAATTTTCTAGTCAAT 14 24 0 ********** MAP Score: 24.1136 Motif 2 TTATGGTTAAAGTGCGGTGGAAAATTGGAGCGTTT 6 174 1 TGGTGTGTAAAGTGCGGTTGAAAATGAAGAAGTTT 9 12 0 ACAGGTAAAAAGTGCGGTGAAAAATGACCGCACTT 0 61 0 ACCATAAATGAATGGGTAGAAAAATCACTTGATCT 6 146 0 CGTTTAACCAAATCGGTTTAATAATATACAGGAAG 12 49 1 TAATACCTGAAATTGGCTAAATAATCATTCTTTTT 0 149 1 AACAAAATAAATTGTGAATGATAATTAAAAGGAAT 4 107 1 AAAACTTGCAATTTTGCTTGAAAAGTATAAAATTC 4 162 1 TTGACCTTTTTATTGACTAGAAAATTGCGCGTATT 14 13 1 AAAGGGTGTTATTCTACTAAAAAATAGGTTATTTG 8 14 0 AATCTTGTCCATTATAGACGAAAATTTTATAA 12 278 1 GTTTTTCATCATTTCAAATGAAAATGACTTTTTGA 0 220 0 AATAGCTAAGAGTGGGCAGAATAATACCTGAAATT 0 128 1 TAAAATCGGGATGAAAAAAACGCCACTC 12 3 1 AACAATCCTGTTTTTCTTAAAAAATTGTGCTGATT 0 271 0 CAAATTTATCCTAAAAAATAACCGCACTT 9 47 0 GTTTTTTCCTTCTGGCTTAAAAAATTGGCTTATTC 11 11 1 ACTAAGCACAATTTTCAATAAAAATCGAATCTTT 5 9 0 TATAGCGGTATTTTAGCTTGATAAAATATCAGTTA 4 24 0 CTTTTGATGATTTAACCTAGAAAAAACAACGCCAT 7 11 0 CCGATTTCCTTTTAAACAAGATAATTTGCTCTCCT 14 99 1 TTCAGTTACATCTAGGATCAATAAAGGATCAAACA 1 11 1 TTTGTCTATATATACAGAGAAAAAAGTAAGCTATA 4 205 1 * * * * ****** MAP Score: 21.8096 Motif 3 CTTTTTGAGTAGGCGATTTCATAAAGAAAGTA 0 196 0 CTACTCAAAAAGTCATTTTCATTTGAAATGAT 0 216 1 ACCGAAATTTAGGCGTTTTTCATCATTTCAAA 0 237 0 ATCAGTTAAATGAGGTTTATAT 4 0 0 ACAAAAAGCCTGCGAATTTTATACTTTTCAAG 4 178 0 CTTTCGAATTTGAGAATATTCTTTTAGTAATT 4 251 1 TGCTTAGTTTAGACGATTTTTTGCTAGA 5 36 1 ATCATAAAACAGTGGTTTTTATAGGTTTTCAG 6 84 1 AATCAGATCAAGTGATTTTTCTACCCATTCAT 6 142 1 AATGGCGTTGTTTTTTCTAGGTTA 7 2 1 CACACCAAAGTGCGGTTATTTTTTAGGATAAA 9 40 1 TTATAGAATAAGCCAATTTTTTAAGCCAGAAG 11 19 0 TCTTGAGCGGTTATTTTATAGAATAAG 11 39 0 TCTCATTGAGTGGCGTTTTTTTCATCCCGATT 12 13 0 AAAGGACAAGTGACGTTTTTTTATTTGAGGTA 12 224 1 TTTTTGACCTTTTTATTGACTAGAAA 14 4 1 ** ******* * MAP Score: 16.5006 Motif 4 TTGTTCGTTAATCAACAAAAAGTGCGGTCATT 0 42 1 AGACAAAAAAATAAAAAAAATGTTCAATAAGA 14 133 0 TCTAGGTTAAATCATCAAAAGGTCGCCATT 7 25 1 AGTATAGGACATAAGGAAAAAGAATGATTATT 0 168 0 ATTGTGAATGATAATTAAAAGGAATACAACCT 4 117 1 CTAGTTGAAAATCATAAAACAGTGGTTTTTAT 6 74 1 CAATTTTCTAGTCAATAAAAAGGTCAAAAA 14 8 0 TAAAATCGGGATGAAAAAAACGCCACTCAATG 12 10 1 AACTGTTTTCATAACCAAAAAGGACGTCGCGA 13 13 1 TTGATAAAATATCAGTTAAATGAGGTTTATAT 4 10 0 ATTTATAGCTAAAAATAAAACGCACTCAATAT 10 13 0 ATTTAGCAAAATCAAATAACAGGTAAAAAGTG 0 82 0 TGGTTGTATTGTAAGGAAAAGGGTAGGAAAGG 12 197 1 CTCTGTATATATAGACAAAAAGCCTGCGAATT 4 192 0 GGCTTATTCTATAAAATAACCGCTCAAGA 11 37 1 CTTCCTGTATATTATTAAACCGATTTGGTTAA 12 52 0 TAATACCTCAAATAAAAAAACGTCACTTGTCC 12 227 0 AATTTATCCTAAAAAATAACCGCACTTTGGTG 9 42 0 ***** **** * MAP Score: 15.5128 Motif 5 ATTTGAGCAGCTATTTGATTTAGCAAAATCAAATAACAGGTAAAAA 0 85 0 TACTCAAAAAGTCATTTTCATTTGAAATGATGAAAAACGCCTAAAT 0 217 1 TTTTGCTTTTTGATTTAGTTCTCAAACTAAGATAG 3 9 1 GCTGGATGCCTCGTATTATATCGTAAAACAAAATAAATTGTGAATG 4 81 1 AAAATAAATTGTGAATGATAATTAAAAGGAATACAACCTACTTTAT 4 110 1 ATACAAAACTTGCAATTTTGCTTGAAAAGTATAAAATTCGCAGGCT 4 158 1 TTTTTTCTCTGTATATATAGACAAAAAGCCTGCGAATTTTATACTT 4 184 0 TTTGAGAATATTCTTTTAGTAATTAAACATTTAGAGGAAGGTT 4 259 1 AATGGCGTTGTTTTTTCTAGGTTAAATCATCAAAAGGTCGCCATT 7 9 1 GTTGATACCTTACAAAAAATAAACAAATAAAATCTA 10 59 0 TTAAGTATGGTTGTATTGTAAGGAAAAGGGTAGGAAAGGACAAGTG 12 190 1 TCAAATTAGTTTTTCTAATACCTCAAATAAAAAAACGTCACTTGTC 12 228 0 AATAAATCTTGTCCATTATAGACGAAAATTTTATAA 12 274 1 ATACGCGCAATTTTCTAGTCAATAAAAAGGTCAAAAA 14 1 0 AGAAAATTGCGCGTATTAGAACATAAATTTATAGAATTTGCTACTT 14 31 1 AGATAACGTGGTCTGTAAGACAAAAAAATAAAAAAAATGTTCAATA 14 136 0 ** * *** * * ** MAP Score: 14.143 Motif 6 AGCAAAATCAAATAACAGGTAAAAAGTGCGGTG 0 77 0 TGCTAAATCAAATAGCTGCTCAAATAGCTAAGA 0 106 1 TGAAATGATGAAAAACGCCTAAATTTCGGTATA 0 239 1 AAATTTCGGTATAATCAGCACAATTTTTTAAGA 0 259 1 ATCTAGGATCAATAAAGGATCAAACA 1 20 1 AGCTTGATAAAATATCAGTTAAATGAGGTTTAT 4 12 0 ATTATATCGTAAAACAAAATAAATTGTGAATGA 4 95 1 AATGATAATTAAAAGGAATACAACCTACTTTAT 4 123 1 AAAATCGTCTAAACTAAGCACAATTTTCAATAA 5 23 0 AGTTTTTCTGAAAACCTATAAAAACCACTGTTT 6 90 0 ACAGATCGCNAAAATCAGATCAAGTGATTTTTC 6 130 1 AGCTAAAAATAAAACGCACTCAATATAGC 10 6 0 GATACCTTACAAAAAATAAACAAATAAAATCTA 10 59 0 TATTCTATAAAATAACCGCTCAAGA 11 41 1 GGGATGAAAAAAACGCCACTCAATGAGAGCAGC 12 17 1 TTTCTAGTCAATAAAAAGGTCAAAAA 14 3 0 AAAAAAATAAAAAAAATGTTCAATAAGAGGAGA 14 128 0 **** * * **** MAP Score: 13.554 Motif 7 ATTTTTCTACCCATTCATTTATGGTTAAAGTGCGGTGGAAAA 6 156 1 GGCTAACAATCCTGTTTTTCTTAAAAAATTGTGCTGATTAT 0 269 0 ACCGCTATACGCGTAAATTTGACCTAAAACAGCTGGATGCCT 4 50 1 ACCGCACTTTTTGTTGATTAACGAACAAAAGGATTTTCCCTT 0 28 0 TTTTTGACCTTTTTATTGACTAGAAAATTGCGCGTATTAG 14 8 1 CCTGCGAATTTTATACTTTTCAAGCAAAATTGCAAGTTTTGT 4 160 0 TCCTTATGTCCTATACTTTCTTTATGAAATCGCCTACTCAAA 0 183 1 TCATTTTCAACCGCACTTTACACACCAAAGTGCGGTTATTTT 9 20 1 TCTAAACTAAGCACAATTTTCAATAAAAATCGAATCTTT 5 7 0 CTATCTTAGTTTGAGAACTAAATCAAAAAGCAAAA 3 10 0 TAGGCGTTTTTCATCATTTCAAATGAAAATGACTTTTTGAGT 0 218 0 AATGGCGTTGTTTTTTCTAGGTTAAATCATCAAAAGGTC 7 7 1 CAGCTGGATGCCTCGTATTATATCGTAAAACAAAATAAATTG 4 79 1 TTTTTGTACTGCTCCGATTTCCTTTTAAACAAGATAATTTGC 14 86 1 TCGCGACGTCCTTTTTGGTTATGAAAACAGTTCAC 13 5 0 CATTAAGTATGGTTGTATTGTAAGGAAAAGGGTAGGAAAGGA 12 188 1 TTACTTTTTTCTCTGTATATATAGACAAAAAGCCTGCGAATT 4 192 0 GAAATAAATCTTGTCCATTATAGACGAAAATTTTATAA 12 272 1 ATTGAGTGCGTTTTATTTTTAGCTATAAATATCGTATAATCC 10 15 1 GATGAAAAACGCCTAAATTTCGGTATAATCAGCACAATTTTT 0 245 1 GATGTTGTGTTTGCATATAGTTCGGGAAACCGAACTTGAGTA 12 103 0 ACAAAATAAATTGTGAATGATAATTAAAAGGAATACAACCTA 4 108 1 ** * *** *** * MAP Score: 12.7222 Motif 8 TTTTGTTCGTTAATCAACAAAAAGTGCGGTC 0 40 1 TGATTTAGCAAAATCAAATAACAGGTAAAAA 0 85 0 TGATTTTGCTAAATCAAATAGCTGCTCAAAT 0 100 1 GTATAGGACATAAGGAAAAAGAATGATTATT 0 168 0 TCATCATTTCAAATGAAAATGACTTTTTGAG 0 219 0 TTTTCATTTGAAATGATGAAAAACGCCTAAA 0 231 1 TAGGATCAATAAAGGATCAAACA 1 23 1 TTTGAGAACTAAATCAAAAAGCAAAA 3 5 0 TTTTGCTTGAAAAGTATAAAATTCGCAGGCT 4 173 1 AACTAGTTGAAAATCATAAAACAGTGGTTTT 6 72 1 TTTCTAGGTTAAATCATCAAAAGGTCGCCAT 7 23 1 GTGCGGTTGAAAATGAAGAAGTTTTA 9 5 0 ACCTTACAAAAAATAAACAAATAAAATCTAT 10 58 0 CTAATACCTCAAATAAAAAAACGTCACTTGT 12 229 0 TAAGACAAAAAAATAAAAAAAATGTTCAATA 14 136 0 **** ****** MAP Score: 12.6504 Motif 9 TCAAAAAGTCATTTTCATTTGAAATGATGAAAAA 0 220 1 AATCAGCACAATTTTTTAAGAAAAACAGGATTGT 0 271 1 AGCTTGATAAAATATCAGTTAAATGAGGTTTATA 4 11 0 TATACGCGTAAATTTGACCTAAAACAGCTGGATG 4 55 1 GATGCCTCGTATTATATCGTAAAACAAAATAAAT 4 85 1 AACAAAATAAATTGTGAATGATAATTAAAAGGAA 4 107 1 AAAACTTGCAATTTTGCTTGAAAAGTATAAAATT 4 162 1 AAAGATTCGATTTTTATTGAAAATTGTGCTTAG 5 9 1 TGTATCGCAAAGTTTTTCTGAAAACCTATAAAAA 6 99 0 CAAATAACCTATTTTTTAGTAGAATAACACCCTT 8 14 1 AGATAATTCTCCATAAAAGGGTGTTATT 8 36 0 CAAATTTATCCTAAAAAATAACCGCA 9 50 0 AGTGCGTTTTATTTTTAGCTATAAATATCGTATA 10 19 1 AAAAAATTGGCTTATTCTATAAAATAACCGCTCA 11 29 1 TAGAAAAACTAATTTGAAATAAATCTTGTCCATT 12 257 1 AATCTTGTCCATTATAGACGAAAATTTTATAA 12 278 1 ***** ***** MAP Score: 5.85149 Motif 10 CACTTTTTGTTGATTAACGAACAAAAGGATTTTCCCTT 0 28 0 TGTTATTTGATTTTGCTAAATCAAATAGCTGCTCAAAT 0 93 1 TATGTCCTATACTTTCTTTATGAAATCGCCTACTCAAA 0 187 1 GCGTTTTTCATCATTTCAAATGAAAATGACTTTTTGAG 0 219 0 TAATCAGCACAATTTTTTAAGAAAAACAGGATTGTTAG 0 270 1 AAATAAATTGTGAATGATAATTAAAAGGAATACAACCT 4 111 1 TTTTTGTCTATATATACAGAGAAAAAAGTAAGCTATAT 4 203 1 AATTTGAGAATATTCTTTTAGTAATTAAACATTTAGAG 4 257 1 AAAAGGGTGTTATTCTACTAAAAAATAGGTTATTTGAC 8 12 0 AGTGCGGTTATTTTTTAGGATAAATTTG 9 48 1 TTATACGATATTTATAGCTAAAAATAAAACGCACTCAA 10 16 0 TAAAATCGGGATGAAAAAAACGCCACTCA 12 1 1 GGTTTAATAATATACAGGAAGTAAATGAGTAACAAATT 12 63 1 TAAGTATGGTTGTATTGTAAGGAAAAGGGTAGGAAAGG 12 191 1 CGCGACGTCCTTTTTGGTTATGAAAACAGTTCAC 13 6 0 TTTGACCTTTTTATTGACTAGAAAATTGCGCGTATTAG 14 12 1 * *** * **** * MAP Score: 0.269174