AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_fusions007_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236434 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0205 292 H. influenzae predicted coding region HI0205 #1 HI0206 22 5'-nucleotidase, putative #2 HI0207 284 shikimic acid kinase I (aroK) #3 HI0604 300 adenylate cyclase (cyaA) #4 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #5 HI0658 160 ABC transporter, ATP-binding protein #6 HI0660 269 H. influenzae predicted coding region HI0660 #7 HI0661 300 hemoglobin-binding protein #8 HI1587 300 DNA-binding protein H-NS (hns) #9 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif 1 AGCGCGTTAAATACGCGCTATTTTTAGCCTATTTT 2 16 0 AAATCAAGCTATTTTCGCTATTTTTGCGATCTAGA 6 133 1 AACCTATTTTATGGGTTCTATTTTTTTATCTAAAC 9 29 1 TATCGCAATAAATCACCCTATTTTTCAACCTCTAT 2 148 0 AGCGCGTATTTAACGCGCTATTTTTGTTATTAGTC 2 32 1 AGGCGCAATTATTATAAGTATTTTTTCAGAGTGGA 8 56 0 GATAGGTAAAATTTATAGTATTTTTCGAAAAATTG 3 191 1 TATTGCGATAATCTACCCCATTTTTTGGGAGATCT 2 173 1 TTTGAGGCTATTTTGCAATATTTTTTCTTTTCTCG 5 116 0 TTGTGTTTATTTTCTTTATATTTTTATTAAAGTTT 8 162 0 GAGTGGTAGGATAGTACCTAGTTTTATTGCGTAAA 3 129 0 ATAAGACGCAATAAAAACTATTTATAATATAACAA 5 30 0 AATTTATCCTATTTATCTACTTATTT 6 253 0 ATAAAAATCTATATTTTCTATTATTAGTGGATAGC 3 76 0 AATAAATTTTATTTTCTCTATTATTAAATAAATTT 8 242 1 AAATGGTCGAAACAGATATATTTTTTTGTGTTTAT 8 187 0 CGCCAAATTTTTAGTTTCTATTTATGATTACACAT 6 191 1 CTCACAATACTAAAAGTGTATTTTTGATCAAAATC 7 251 0 TATTAGTGGATAGCTTGATATTTTTCTTATCAACG 3 55 0 AGATCTTTCTATCTTCTGCATTTTTACGCAGTTTA 2 202 1 AATGTTGTGTGCTATGTTTAGATAAAAAA 9 50 0 AAATTGTGATTTATGTCACATTTTTTTGCATTTAT 3 220 1 AAATTTATTGTAAATATCTATTATTAAATAAATGG 8 216 0 TACAGCAAATAATGAGAATAGTTTTTATTTCTTGA 7 218 1 TATTTTTGTTATTAGTCCTAGGTTTGAAGACTTCA 2 50 1 ** ******** MAP Score: 30.2014 Motif 2 TTGCGTTGATAAGAAAAATATCAAGCTATCCACTAATAATAGAAA 3 52 1 AATAAGACGCAATAAAAACTATTTATAATATAACAAGTCAATATA 5 21 0 ACCGTAAAACAAACAAAATGCCAACAGATTTTATAAAAATTTTAT 8 117 1 ACCTATCTAAAATCAAAAGTGCGGTAAATTTTTACCGCACTTTTT 6 10 1 TTACTCCTAAAATAAAAAGAAGTACGCATAGAAAGAATTATGCGT 7 44 1 AATATGGAATAGTTAAAATTCTTAATCATCTATGAAGTCTTCAAA 2 72 0 CAAAATCAAGAAATAAAAACTATTCTCATTATTTGCTGTATTTAA 7 213 0 ATATATACAGAGAAAAAAGTAAGCTATATTCTCAAATCACTTTCG 0 55 0 CTGTATATATAGACAAAAAGCCTGCGAATTTTATACTTTTCAAGC 0 90 1 TTATATCGTAAAACAAAATAAATTGTGAATGATAATTAAAAGGAA 0 171 0 TATAAACTTTAATAAAAATATAAAGAAAATAAACACAAAAAAATA 8 159 1 TATACTTTTCAAGCAAAATTGCAAGTTTTGTATGCATAAAGTAGG 0 121 1 ATAATAGAGAAAATAAAATTTATTGTAAATATCTATTATTAAATA 8 221 0 TCGATTTTCTAGTCAAAAAAGCCACGTATAATAAGACGCAATAAA 5 50 0 ATTAAAAGTGAAATAAAATTCGATCATTTCTAATGAAAATAAACT 2 231 0 TAGGACTAATAACAAAAATAGCGCGTTAAATACGCGCTATTTTTA 2 25 0 TGTTCCGAGAAAAGAAAAAATATTGCAAAATAGCCTCAAATTAAG 5 111 1 CTACCAGAACAACAAAAATTGGCGAACAATTTACCACTTAGGGAG 3 256 0 GATTGTTGATAGGTAAAATTTATAGTATTTTTCGAAAAATTGTGA 3 184 1 GCTATTTACGCAATAAAACTAGGTACTATCCTACCACTCTTAGGT 3 125 1 GGCTTCAGCCCACCAAAATATCTTACGATTGTTTGATGGTGGGCT 7 104 1 TCGCAAAAATAGCGAAAATAGCTTGATTTTCAAGGAGATTTTGCA 6 117 0 AAAATAAACACAAAAAAATATATCTGTTTCGACCATTTATTTAAT 8 184 1 AGTATAAATGCAAAAAAATGTGACATAAATCACAATTTTTCGAAA 3 213 0 GATAACGAAGAAGAAAAAAGAAAGGAATAGTTGCCGAAATCAAAT 8 13 0 ACCTATCAACAATCAAAATGACTTTTTTACCTAAGAGTGGTAGGA 3 153 0 AAATAAACTGCGTAAAAATGCAGAAGATAGAAAGATCTCCCAAAA 2 195 0 ** **** ** * * MAP Score: 27.3672 Motif 3 GATCTCCCAAAAAATGGGGTAGATTATCGCAATAAAT 2 170 0 AATTTTTCGAAAAATACTATAAATTTTACCTATCAAC 3 188 0 AATAATAGAGAAAATAAAATTTATTGTAAATATCTAT 8 230 0 CTTAGGTAAAAAAGTCATTTTGATTGTTGATAGGTAA 3 163 1 TCTAAAATCAAAAGTGCGGTAAATTTTTACCGCACTT 6 15 1 TACAGAGAAAAAAGTAAGCTATATTCTCAAATCACTT 0 58 0 TATTTTTATTAAAGTTTATAAAATTTTTATAAAATCT 8 142 0 AAAGTGAAATAAAATTCGATCATTTCTAATGAAAATA 2 235 0 TAGAGGTTGAAAAATAGGGTGATTTATTGCGATAATC 2 149 1 TAAATGTGGGAAAATTTATTTAATAATAGAGAAAATA 8 251 0 TAGAACCCATAAAATAGGTTCTAGTTTCAAATAGAAA 9 12 0 CTAATAATAGAAAATATAGATTTTTATATCGGCAGAA 3 84 1 CTTTTCAAGCAAAATTGCAAGTTTTGTATGCATAAAG 0 125 1 TGAAAAGTATAAAATTCGCAGGCTTTTTGTCTATATA 0 95 0 TTGTATGCATAAAGTAGGTTGTATTCCTTTTAATTAT 0 148 1 CCACTCTGAAAAAATACTTATAATAATTGCGCCTCTA 8 57 1 AAAAATAGCGAAAATAGCTTGATTTTCAAGGAGATTT 6 121 0 AAATTTTTATAAAATCTGTTGGCATTTTGTTTGTTTT 8 122 0 ATTATATCGTAAAACAAAATAAATTGTGAATGATAAT 0 180 0 TATTTTTCGAAAAATTGTGATTTATGTCACATTTTTT 3 209 1 TGGAATAGTTAAAATTCTTAATCATCTATGAAGTCTT 2 76 0 TTATCAACGCAAAGTATTATAAAATACCTTACTCAAT 3 27 0 GATTACTCCTAAAATAAAAAGAAGTACGCATAGAAAG 7 42 1 TTACACATCAAAAATCAATAACTTATTGGTTATTGAA 6 218 1 AGACGCAATAAAAACTATTTATAATATAACAAGTCAA 5 25 0 GTTGATAAGAAAAATATCAAGCTATCCACTAATAATA 3 56 1 ***** * *** * MAP Score: 24.1688 Motif 4 AATATAGCTTACTTTTTTCTCTGTATATATAGACAAAAAGCCT 0 70 1 GTCTATTCCGATTTTATCGATTTTCTAGTCAAAAAAGCCACGT 5 68 0 AATTTATCCTATTTATCTACTTATTTCAATAAC 6 246 0 TATCATTCACAATTTATTTTGTTTTACGATATAATACGAGGCA 0 182 1 TGATAGGTAAAATTTATAGTATTTTTCGAAAAATTGTGATTTA 3 190 1 TTTACAATAAATTTTATTTTCTCTATTATTAAATAAATTTTCC 8 237 1 ACTAGAACCTATTTTATGGGTTCTATTTTTTTATCTAAACATA 9 24 1 AAATGATCGAATTTTATTTCACTTTTAATTTAATTAGATAAAG 2 247 1 TATTATAAATAGTTTTTATTGCGTCTTATTATACGTGGCTTTT 5 36 1 ATTTTGCAATATTTTTTCTTTTCTCGGAACAGTCTATTCCGAT 5 99 0 TATCTCGCCAAATTTTTAGTTTCTATTTATGATTACACATCAA 6 186 1 TTTTTATTAAAGTTTATAAAATTTTTATAAAATCTGTTGGCAT 8 134 0 AAACAGATATATTTTTTTGTGTTTATTTTCTTTATATTTTTAT 8 170 0 TTTATGTCACATTTTTTTGCATTTATACTCCCTAAGTGGTAAA 3 229 1 TGAGTAAGGTATTTTATAATACTTTGCGTTGATAAGAAAAATA 3 29 1 TAATGAGAATAGTTTTTATTTCTTGATTTTGATCAAAAATACA 7 227 1 ATTGTTCGCCAATTTTTGTTGTTCTGGTAGGGACACCAC 3 271 1 AAGTGCGGTAAATTTTTACCGCACTTTTTCTTAAGAAAGGATC 6 26 1 CTCTATAGGGAATTTATTTTCCACGAGAAAGCATCTAAATATG 2 111 0 AAGCCTGCGAATTTTATACTTTTCAAGCAAAATTGCAAGTTTT 0 107 1 TTCTATGCGTACTTCTTTTTATTTTAGGAGTAATCATTATGAT 7 34 0 ATTTTTACGCAGTTTATTTTCATTAGAAATGATCGAATTTTAT 2 221 1 * ***** * * * * MAP Score: 23.4157 Motif 5 AATAGGCTAAAAATAGCGCGTATTTAACGCGCTATTTTTGTTATTAG 2 18 1 CATAGGTCTTAATTTGAGGCTATTTTGCAATATTTTTTCTTTTCTCG 5 116 0 TGAAATGACTATCTCGCCAAATTTTTAGTTTCTATTTATGATTACAC 6 177 1 TATTGCGATAATCTACCCCATTTTTTGGGAGATCTTTCTATCTTCTG 2 173 1 CTAAAATCAAAAGTGCGGTAAATTTTTACCGCACTTTTTCTTAAGAA 6 16 1 AAAATAGCGAAAATAGCTTGATTTTCAAGGAGATTTTGCACAAATGC 6 110 0 ATATAAACCTCATTTAACTGATATTTTATCAAGCTAA 0 265 0 TTTTGTGTTTATTTTCTTTATATTTTTATTAAAGTTTATAAAATTTT 8 152 0 TTATTAAATAAATTTTCCCACATTTAATGTTATTTATTGAGGTTTAT 8 262 1 TTCTATTTGAAACTAGAACCTATTTTATGGGTTCTATTTTTTTATCT 9 13 1 GAAAAGTATAAAATTCGCAGGCTTTTTGTCTATATATACAGAGAAAA 0 84 0 AAAAATTGTGATTTATGTCACATTTTTTTGCATTTATACTCCCTAAG 3 218 1 AATAATAGATATTTACAATAAATTTTATTTTCTCTATTATTAAATAA 8 226 1 TTTTCTTAAGAAAGGATCTATCTTTTACTCTCTCTTTCAAAGCCAAT 6 51 1 AAACACAAAAAAATATATCTGTTTCGACCATTTATTTAATAATAGAT 8 189 1 AAACAAACAAAATGCCAACAGATTTTATAAAAATTTTATAAACTTTA 8 123 1 AGATCTTTCTATCTTCTGCATTTTTACGCAGTTTATTTTCATTAGAA 2 202 1 ACAGAGAAAAAAGTAAGCTATATTCTCAAATCACTTTCGAATTTGAG 0 47 0 TTTTCATTAGAAATGATCGAATTTTATTTCACTTTTAATTTAATTAG 2 237 1 TTGATAGGTAAAATTTATAGTATTTTTCGAAAAATTGTGATTTATGT 3 189 1 TTTATTTGATTTCGGCAACTATTCCTTTCTTTTTTCTTCTTCGTT 8 8 1 TACAGCAAATAATGAGAATAGTTTTTATTTCTTGATTTTGATCAAAA 7 218 1 TAACTATTCCATATTTAGATGCTTTCTCGTGGAAAATAAATTCCCTA 2 102 1 ** * *** * *** MAP Score: 22.1026 Motif 6 AAATCACCCTATTTTTCAACCTCTATAGGGAATTTATTTTCCAC 2 130 0 TTTACAATAAATTTTATTTTCTCTATTATTAAATAAATTTTCCC 8 237 1 AATCTACCCCATTTTTTGGGAGATCTTTCTATCTTCTGCATTTT 2 182 1 ATGCCAACAGATTTTATAAAAATTTTATAAACTTTAATAAAAAT 8 134 1 CAGATATATTTTTTTGTGTTTATTTTCTTTATATTTTTATTAAA 8 166 0 TATAGCTTACTTTTTTCTCTGTATATATAGACAAAAAGCCTGCG 0 72 1 GTGCGGTAAATTTTTACCGCACTTTTTCTTAAGAAAGGATCTAT 6 28 1 ATCTTCTGCATTTTTACGCAGTTTATTTTCATTAGAAATGATCG 2 212 1 AAAACTTGCAATTTTGCTTGAAAAGTATAAAATTCGCAGGCTTT 0 106 0 ATGTCACATTTTTTTGCATTTATACTCCCTAAGTGGTAAATTGT 3 232 1 GTCTATTCCGATTTTATCGATTTTCTAGTCAAAAAAGCCACGTA 5 67 0 AAAAATCTATATTTTCTATTATTAGTGGATAGCTTGATATTTTT 3 65 0 TATTAAATAAATTTTCCCACATTTAATGTTATTTATTGAGGTTT 8 263 1 ATTTTCGCTATTTTTGCGATCTAGATCGAAAGATTGAAATGACT 6 143 1 TGCGTACTTCTTTTTATTTTAGGAGTAATCATTATGATGATAGA 7 28 0 TTATAAATAGTTTTTATTGCGTCTTATTATACGTGGCTTTTTTG 5 38 1 ATTTGAGGCTATTTTGCAATATTTTTTCTTTTCTCGGAACAGTC 5 108 0 AATTTATCCTATTTATCTACTTATTTCAATAACCAA 6 243 0 ATTATAAGTATTTTTTCAGAGTGGATAACGAAGAAGAAAAAAGA 8 37 0 AATACTATAAATTTTACCTATCAACAATCAAAATGACTTTTTTA 3 169 0 AAATGATCGAATTTTATTTCACTTTTAATTTAATTAGATAAAGA 2 247 1 ACTAGAACCTATTTTATGGGTTCTATTTTTTTATCTAAACATAG 9 24 1 AAAATATAGATTTTTATATCGGCAGAATTAAGCTATTTACGCAA 3 94 1 TATAAACCTCATTTAACTGATATTTTATCAAGCTAAAATACCGC 0 257 0 GAGAATAGTTTTTATTTCTTGATTTTGATCAAAAATACACTTTT 7 231 1 TTCACAATTTATTTTGTTTTACGATATAATACGAGGCATCCAGC 0 187 1 ***** * * * * * MAP Score: 19.9578 Motif 7 TTAGCTTGATAAAATATCAGTTAAATGAGGTTTATAT 0 265 1 AATTGAAAAATAGGCTAAAAATAGCGCGTATTTA 2 5 1 ATAAATTCCCTATAGAGGTTGAAAAATAGGGTGATTTAT 2 137 1 TAAAATTTATAGTATTTTTCGAAAAATTGTGATTTATGT 3 197 1 TGGTGTCCCTACCAGAACAACAAAAATTGGCGAACAATT 3 270 0 CCGAGAAAAGAAAAAATATTGCAAAATAGCCTCAAATTA 5 115 1 TGTAATCATAAATAGAAACTAAAAATTTGGCGAGATAGT 6 184 0 TATCATCATAATGATTACTCCTAAAATAAAAAGAAGTAC 7 30 1 CCACTCTGAAAAAATACTTATAATAATTGCGCCTCTACT 8 57 1 TTATATTTTTATTAAAGTTTATAAAATTTTTATAAAATC 8 143 0 ATATAAAGAAAATAAACACAAAAAAATATATCTGTTTCG 8 176 1 ATCTGTTTCGACCATTTATTTAATAATAGATATTTACAA 8 205 1 TTTATTTAATAATAGAGAAAATAAAATTTATTGTAAATA 8 235 0 AATAAATAACATTAAATGTGGGAAAATTTATTTAATAAT 8 261 0 TAGATAAAAAAATAGAACCCATAAAATAGGTTCTAGTTT 9 22 0 * * * ******* MAP Score: 8.44289 Motif 8 ATTGTGAATGATAATTAAAAGGAATACAACCTACTTTAT 0 156 0 CCTCGTATTATATCGTAAAACAAAATAAATTGTGAATGA 0 184 0 AGATGCTTTCTCGTGGAAAATAAATTCCCTATAGAGGTT 2 118 1 AATTAAATTAAAAGTGAAATAAAATTCGATCATTTCTAA 2 243 0 TCACTTTTAATTTAATTAGATAAAGAACA 2 265 1 CAAGCTATCCACTAATAATAGAAAATATAGATTTTTATA 3 73 1 CAATTTTTCGAAAAATACTATAAATTTTACCTATCAACA 3 187 0 ATACGTGGCTTTTTTGACTAGAAAATCGATAAAATCGGA 5 66 1 AATAGACTGTTCCGAGAAAAGAAAAAATATTGCAAAATA 5 104 1 TTGATGTGTAATCATAAATAGAAACTAAAAATTTGGCGA 6 190 0 TGGTTATTGAAATAAGTAGATAAATAGGATAAATT 6 244 1 CATAATGATTACTCCTAAAATAAAAAGAAGTACGCATAG 7 36 1 AGAGTGGATAACGAAGAAGAAAAAAGAAAGGAATAGTTG 8 25 0 TTGGGGAGATTACCGTAAAACAAACAAAATGCCAACAGA 8 106 1 AAATGCCAACAGATTTTATAAAAATTTTATAAACTTTAA 8 132 1 AAATTTTATAAACTTTAATAAAAATATAAAGAAAATAAA 8 153 1 TAATAAAAATATAAAGAAAATAAACACAAAAAAATATAT 8 168 1 TTAATAATAGATATTTACAATAAATTTTATTTTCTCTAT 8 224 1 * *** * *** * * MAP Score: 5.74849 Motif 9 TATAGCTTACTTTTTTCTCTGTATATATAGACAAAAAG 0 72 1 AATAGCGCGTATTTAACGCGCTATTTTTGTTATTAGTC 2 29 1 TCTACCCCATTTTTTGGGAGATCTTTCTATCTTCTGCA 2 184 1 ATCTTCTGCATTTTTACGCAGTTTATTTTCATTAGAAA 2 212 1 AATGATCGAATTTTATTTCACTTTTAATTTAATTAGAT 2 248 1 AAAATTGTGATTTATGTCACATTTTTTTGCATTTATAC 3 219 1 GACTTGTTATATTATAAATAGTTTTTATTGCGTCTTAT 5 27 1 TGCGGTAAATTTTTACCGCACTTTTTCTTAAGAAAGGA 6 29 1 TCTCGCCAAATTTTTAGTTTCTATTTATGATTACACAT 6 188 1 TATTTTTTTGTGTTTATTTTCTTTATATTTTTATTAAA 8 166 0 TACAATAAATTTTATTTTCTCTATTATTAAATAAATTT 8 239 1 ACTAGAACCTATTTTATGGGTTCTATTTTTTTATCTAA 9 24 1 ***** * *** * MAP Score: 0.77211