AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_fusions003_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236280 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0096 300 H. influenzae predicted coding region HI0096 #1 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #2 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #3 HI0129 300 H. influenzae predicted coding region HI0129 #4 HI0354 300 ABC transporter, ATP-binding protein #5 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #6 HI1188 300 DNA helicase II (uvrD) #7 HI1347 268 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #8 HI1692 173 molybdenum ABC transporter, permease protein (modB) #9 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif 1 GGAACAATTATTCCGCCTTATTTATTTGATCTGAC 0 39 0 TGTTCCGCCTTTTCCTATTATTTCTTCAATGCTTT 0 68 1 TCGCTTTCCATTTCAGCTTGTTTATACAGTTTTTT 0 140 1 TCGTTTAATGTACCGTTTTGTTTTTCATCTAAATA 1 30 1 AGCCGTAGCGGCTTCTTTGTGCTGACCATT 1 252 0 TCCGTTATGTTTGCCGTTTCTGTATGTCATTTTGC 2 180 1 TCCATAATGCATTCTGCTTATTTTTGGATTATTTT 3 190 1 ATGCACTTGATTACGGTTTGTTTGAAAGTACTTCA 3 257 1 AGAAACCTAATTGCTTGTTTTTTCTACCAAACAAG 4 98 1 TTTCATTCCATTTCTTATCCTTTCTTTTTTATTAC 4 247 1 CGGTGAATTTTTACCGCACTTTTATTATCTACGAG 5 57 1 TGCGGTTAAATTTCTCGTTATTTTTATGAACGGCA 7 117 1 CCCTGCAGTCTTGCAGGTTTTATTTCTACTCAGTA 7 232 1 AGGGCGGATATTTCTGCCCTTTTGTTATTATAGAG 8 32 1 TTCATTTTGCTTACCCAATTTTTTTCATTTTTCAA 8 138 1 ** * * ** *** * MAP Score: 13.6688 Motif 2 CTATTATTTCTTCAATGCTTTTTTCAATTCAAG 0 82 1 TTCCGCAGAATTGACCGCACTTTGTGTTGAAAC 0 232 1 TAAGGAGCTTTTCAATGCAATTTAAACATTTCA 1 155 1 GTTCCCCTTTGGGACAGCTTTTTACTCCCCAAT 3 65 1 GAATGCATTATGGAAAGTTTTTTTGCGTTCATA 3 171 0 GAATGGAACAAGAAAAGCATTTTTAAATTTCTC 4 61 0 GCGGTAAAAATTCACCGCACTCTTCAAAGAAAT 5 41 0 GCGGTGAATTTTTACCGCACTTTTATTATCTAC 5 56 1 ATAATAGCATAGGAATGTTGTTTAATGACTTAA 6 12 0 ACCATATGCTTTGAAAGCTATTTTTATACTATT 6 126 0 AACGAGAAATTTAACCGCACTTTCGATGAATTT 7 103 0 GTTATTTTTATGAACGGCAGTTTTTTACTTTCT 7 133 1 TCTCCTACGATTAAACGTTATTTACTTGATTAT 9 108 0 ** ** *** *** MAP Score: 12.8924 Motif 3 TTGATCTGACATTTTAATAGTTATCATTTTTATCTATAA 0 8 0 TTGCTACCCTTGCGGCACACTTGCTTTTTCTGCTAATAGTT 1 191 1 TAATCGGGCTTCCGTTATGTTTGCCGTTTCTGTATGTCATT 2 170 1 CCATAATGCATTCTGCTTATTTTTGGATTATTTTATCCTTG 3 191 1 TCGGATAGAAACCTAATTGCTTGTTTTTTCTACCAAACAAG 4 92 1 TTCATTCCATTTCTTATCCTTTCTTTTTTATTACGCACTCC 4 248 1 AATTCAAGAGTATTATATTTTTTACCGATTAAT 5 2 1 TCATTCCTAAAATGCAAGGTTTCTCATTTTTCCAAAAATAC 6 56 0 ATTGTTATATATCAAGATGTTTTCTATTTTTCTCGTTAAAC 7 41 0 TATTTTTATGAACGGCAGTTTTTTACTTTCTAAGGCATTAA 7 135 1 TCATTTTGCTTACCCAATTTTTTTCATTTTTCAATCTGACG 8 139 1 CTAAGTGGTAAGCCTAAGCGTTATATATTTTACTAAATAAT 9 30 1 TTATATATTTTACTAAATAATTTTTCTTTTGCTATATGATT 9 50 1 ATTTTTCTTTTGCTATATGATTGTTATTTATTTCAATATAT 9 69 1 * * * ** * *** * MAP Score: 12.6161 Motif 4 AATTGAAAAAAGCATTGAAGAAATAATAGGA 0 80 0 GTGAATTACTTGAATTGAAAAAAGCATTGAA 0 92 0 AAATGGAAAGCGAATTGAAACAGTTACGTCG 0 122 0 AGTGATGATGCGCTCTCAACAAGCAGAAACC 0 178 0 CAATTCAGGCTGAACTGAATAATTTGCACTC 1 120 1 CTGAATAATTTGCACTCAACATAAGGAGCTT 1 134 1 ATGTTTAAATTGCATTGAAAAGCTCCTTATG 1 153 0 TTCAAATACACGCACGCAATATTTGGA 2 6 0 TTTCAGTTCACGCACGCAAGCGGTTAATTTT 2 69 0 CTTGCGTGCGTGAACTGAAAAGTTCACATTC 2 80 1 TTCTGTCGCACGCAAAATGACATACAG 2 199 0 CGAGGTTGTATGAACGCAAAAAAACTTTCCA 3 163 1 GGTTTCTATCCGAATGGAACAAGAAAAGCAT 4 74 0 ********* * MAP Score: 12.1552 Motif 5 ACATTTTAATAGTTATCATTTTTATCTATAA 0 5 0 AATTATTCCGCCTTATTTATTTGATCTGACATTTTA 0 33 0 TGTTTCAATTCGCTTTCCATTTCAGCTTGTTTATAC 0 131 1 TTTAATGTACCGTTTTGTTTTTCATCTAAATATCAA 1 33 1 TTTTTCATCTAAATATCAATTTAAATTGAGAACTAT 1 50 1 AAATTGAGAACTATTTGCATTTAAATAAAATTAGGC 1 72 1 CATTCTGGCTCACTTTACTTATCATCTTAATCGGGC 2 143 1 TTTTGGATTATTTTATCCTTGTTAGCGTTTGCACTT 3 211 1 GCCAAAAAATCCATTTTCTTTTCATTCCATTTCTTA 4 228 1 CCATTTCTTATCCTTTCTTTTTTATTACGCACTCCC 4 254 1 AATTCAAGAGTATTATATTTTTTACCGATTAATTTC 5 10 1 AACATTCCTATGCTATTATTGTCATCATGGGTATTT 6 26 1 AACGAATTAAAAGTTTGTTTATAAATAGTATAAAAA 6 103 1 CTCCTTTTAAAAATATCTTTTTTAGTTTAACGAGAA 7 17 1 TTAAATTTCTCGTTATTTTTATGAACGGCAGTTTTT 7 122 1 GGCATTAAGTCCTTTTCATTATTAACAATTCACTAT 7 168 1 TAAGCCTAAGCGTTATATATTTTACTAAATAATTTT 9 38 1 TTTTCTTTTGCTATATGATTGTTATTTATTTCAATA 9 71 1 * *** **** * * MAP Score: 10.8014 Motif 6 TCAACACAAAGTGCGGTCAATTCTGCGGAAGTTT 0 228 0 TTAATCTCTCAAGCGGTTTATTATCCAGATACGA 0 265 1 CAAATATTGCGTGCGTGTATTTGAAAAAATTCAC 2 12 1 TTGTAAACGCGTGCGTGAATTTTTTCAAATACAC 2 26 0 TCACGCACGCAAGCGGTTAATTTTGTTAGAGAAT 2 59 0 TCTTTGAAGAGTGCGGTGAATTTTTACCGCACTT 5 44 1 TTCATCGAAAGTGCGGTTAAATTTCTCGTTATTT 7 106 1 ACTATATCATAGGCGTCTATTTTTATATGTCGCC 7 199 1 TAGTCATGAAGGGCGGATATTTCTGCCCTTTTGT 8 23 1 * **** **** * MAP Score: 10.4635 Motif 7 ATCTCTCAAGCGGTTTATTATCCAGATACGAAATTTGT 0 268 1 ATGTACCGTTTTGTTTTTCATCTAAATATCAATTTAAA 1 37 1 TGCGGCACACTTGCTTTTTCTGCTAATAGTTTTGCTGA 1 201 1 AGTATACCCACGGCTAATTATCGTAATAGTAGTTCCCC 3 34 1 ATAATGCATTCTGCTTATTTTTGGATTATTTTATCCTT 3 193 1 ATTGTCATCATGGGTATTTTTGGAAAAATGAGAAACCT 6 43 1 AAAAGTAGGGTAGAACATTTTAAGAATAATATTAAGCG 6 192 0 ATTCTCGCTCCTTTTAAAAATATCTTTTTTAG 7 4 1 GAATTTTACTTCGTTAATTTTATAAATATTGTTATATA 7 71 0 CTCTTTAAATCCCTTGTTTATGGGAATATCCCACATTG 8 82 0 GTAAGCAAAATGAATCCTTATCTAAATAGCCTCTCTTT 8 114 0 TGCTATATGATTGTTATTTATTTCAATATATAATCAAG 9 79 1 * * * ** * **** MAP Score: 9.80114 Motif 8 GTTTCAACACAAAGTGCGGTCAATTCTGCG 0 235 0 GATGATAAGTAAAGTGAGCCAGAATGGCGG 2 139 0 ACCCTAGGCGAAAGTCAGGTTTTCTTTACT 3 132 1 ATTTCTTTGAAGAGTGCGGTGAATTTTTAC 5 41 1 GTAGATAATAAAAGTGCGGTAAAAATTCAC 5 59 0 GCATTTTAGGAATGAGAGGTAAACGAATTA 6 82 1 AAATTCATCGAAAGTGCGGTTAAATTTCTC 7 103 1 CAAGGGATTTAAAGAGAGGCTATTTAGATA 8 104 1 ********** MAP Score: 9.53112 Motif 9 AAATGTCAGATCAAATAAATAAGGCGGAATAATT 0 35 1 TTTTTTCAATTCAAGTAATTCACGACGTAACTGT 0 100 1 TATTTGCATTTAAATAAAATTAGGCATAGAATAG 1 83 1 TGCGTGTATTTGAAAAAATTCACGCACGCGTTTA 2 23 1 ATAACAATATTTATAAAATTAACGAAGTAAAATT 7 74 1 AAACTGCCGTTCATAAAAATAACGAGAAATTTAA 7 122 0 GATTGAAAAATGAAAAAAATTGGGTAAGCAAAAT 8 141 0 AATTATTTAGTAAAATATATAACGCTTAGGCTTA 9 38 0 GATTATATATTGAAATAAATAACAATCATATAGC 9 80 0 CAATATATAATCAAGTAAATAACGTTTAATCGTA 9 102 1 * ** **** *** MAP Score: 7.9891 Motif 10 GTGAATTACTTGAATTGAAAAAAGCATTGAAG 0 91 0 CAATTCAGGCTGAACTGAATAATTTGCACTCA 1 120 1 TTTTTCTCGTTAAACTAAAAAAGATATTTTTA 7 24 0 TAATGCCTTAGAAAGTAAAAAACTGCCGTTCA 7 143 0 CAATATATAATCAAGTAAATAACGTTTAATCG 9 102 1 AAATGTCAGATCAAATAAATAAGGCGGAATAA 0 35 1 GATTATATATTGAAATAAATAACAATCATATA 9 82 0 AAATTGATATTTAGATGAAAAACAAAACGGTA 1 40 0 CTTGCGTGCGTGAACTGAAAAGTTCACATTCC 2 80 1 TTGCGTGCGTGTATTTGAAAAAATTCACGCAC 2 18 1 CAATCATATAGCAAAAGAAAAATTATTTAGTA 9 60 0 CGTCAGATTGAAAAATGAAAAAAATTGGGTAA 8 148 0 CTTAGCAAGAGAAATTTAAAAATGCTTTTCTT 4 53 1 AGAACTATTTGCATTTAAATAAAATTAGGCAT 1 78 1 AGCAAAACTATTAGCAGAAAAAGCAAGTGTGC 1 205 0 * ** ******* MAP Score: 6.6576 Motif 11 CTTCAATGCTTTTTTCAATTCAAGTAATTCACGAC 0 91 1 ACGACGTAACTGTTTCAATTCGCTTTCCATTTCAG 0 121 1 ACATAAGGAGCTTTTCAATGCAATTTAAACATTTC 1 152 1 AACTTGCTACCCTTGCGGCACACTTGCTTTTTCTG 1 188 1 GGAATGTGAACTTTTCAGTTCACGCACGCAAGCGG 2 77 0 CGCAGACCGCCATTCTGGCTCACTTTACTTATCAT 2 133 1 TGCACTTCTGCCTTCCAATGCACTTGATTACGGTT 3 240 1 TTAAAAATGCTTTTCTTGTTCCATTCGGATAGAAA 4 68 1 AAATCCATTTTCTTTTCATTCCATTTCTTATCCTT 4 234 1 ATCCTTTCTTTTTTATTACGCACTCCCTTTAATCA 4 263 1 TGCGGTGAATTTTTACCGCACTTTTATTATCTACG 5 55 1 CATTAAACAACATTCCTATGCTATTATTGTCATCA 6 18 1 CTTTGAAAGCTATTTTTATACTATTTATAAACAAA 6 116 0 AATTTACAGTTATTATAGTCCCATCTATCTTGTGA 6 254 0 GAAGGGCGGATATTTCTGCCCTTTTGTTATTATAG 8 30 1 * ** * ** * *** MAP Score: 6.28615 Motif 12 TCCGCAGAATTGACCGCACTTTGTGTTGAAA 0 233 1 CTTGCTACCCTTGCGGCACACTTGCTTTTTC 1 190 1 TTTTTTCAAATACACGCACGCAATATTTGGA 2 10 0 TTTGAAAAAATTCACGCACGCGTTTACAATT 2 31 1 AACTTTTCAGTTCACGCACGCAAGCGGTTAA 2 73 0 CAGACCGCCATTCTGGCTCACTTTACTTATC 2 135 1 CATCTCAGCCTTTCGGCACCCCGACTAAAAA 4 150 0 TTTCTTTTTTATTACGCACTCCCTTTAATCA 4 267 1 CGGTAAAAATTCACCGCACTCTTCAAAGAAA 5 42 0 CGGTGAATTTTTACCGCACTTTTATTATCTA 5 57 1 ATTCTCGCTCCTTTTAAAAATA 7 1 1 ACGAGAAATTTAACCGCACTTTCGATGAATT 7 104 0 ********* * MAP Score: 6.22031 Motif 13 ACAAGAAAAGCATTTTTAAATTTCTCTTGC 4 57 0 CATAGGCGTCTATTTTTATATGTCGCCCCT 7 206 1 CTTTGAAAGCTATTTTTATACTATTTATAA 6 121 0 CTAAAAAAGATATTTTTAAAAGGAGCGAGA 7 12 0 TTTGATCTGACATTTTAATAGTTATCATTT 0 20 0 TAATAGTTATCATTTTTATCTATAA 0 5 0 CAATTTTTTTCATTTTTCAATCTGACGCCA 8 153 1 CGCTTAATATTATTCTTAAAATGTTCTACC 6 192 1 TATATAACAATATTTATAAAATTAACGAAG 7 71 1 ATTTTTATACTATTTATAAACAAACTTTTA 6 110 0 GAAAAGTTCACATTCCTAAAAGGATTTAAC 2 96 1 GTTTACCTCTCATTCCTAAAATGCAAGGTT 6 76 0 GATTGTTATTTATTTCAATATATAATCAAG 9 87 1 GAACTATTTGCATTTAAATAAAATTAGGCA 1 79 1 AATTTCTCGTTATTTTTATGAACGGCAGTT 7 125 1 AAGCGTTATATATTTTACTAAATAATTTTT 9 45 1 AGATGTTTTCTATTTTTCTCGTTAAACTAA 7 38 0 GCAATTTAAACATTTCAAACTTGCTACCCT 1 171 1 CATTAAACAACATTCCTATGCTATTATTGT 6 18 1 ********** MAP Score: 5.67679 Motif 14 TAGGCATAGAATAGCCACAATTCAGGCTGA 1 103 1 CACGGCTATGATTGTCACGA 3 0 0 CGTGACAATCATAGCCGTGAGTAAGTATAC 3 11 1 GTGAGTAAGTATACCCACGGCTAATTATCG 3 27 1 GGCTGAGATGATACCCGTGAACCTGAAACA 4 171 1 AAAAAATATAATACTCTTGAATT 5 3 0 TTTTCCAAAAATACCCATGATGACAATAAT 6 40 0 TACTTTTGATATACTCACAAATCTTATTGT 6 223 1 TAGAATCTTAATAGTCATGAAGGGCGGATA 8 12 1 AATGTGGGATATTCCCATAAACAAGGGATT 8 83 1 ********** MAP Score: 4.69577 Motif 15 CCTTTTCCTATTATTTCTTCAATGCTTTTTT 0 75 1 ACTGTTTCAATTCGCTTTCCATTTCAGCTTG 0 129 1 ATGTACCGTTTTGTTTTTCATCTAAATATCA 1 37 1 TGCGGCACACTTGCTTTTTCTGCTAATAGTT 1 201 1 TTTGCTGATATTACCGTTTATAATGGTCAGC 1 231 1 CTGGCTCACTTTACTTATCATCTTAATCGGG 2 147 1 TCCGTTATGTTTGCCGTTTCTGTATGTCATT 2 180 1 GAAAGTCAGGTTTTCTTTACTGCGAGGTTGT 3 141 1 GGAAAGTTTTTTTGCGTTCATACAACCTCGC 3 162 0 AAAAATGCTTTTCTTGTTCCATTCGGATAGA 4 70 1 ACCTAATTGCTTGTTTTTTCTACCAAACAAG 4 102 1 AAAAATCCATTTTCTTTTCATTCCATTTCTT 4 232 1 TTTCATTCCATTTCTTATCCTTTCTTTTTTA 4 247 1 TTTAATTCGTTTACCTCTCATTCCTAAAATG 6 83 0 CTCACAAATCTTATTGTTTCACAAGATAGAT 6 236 1 ATTCTCGCTCCTTTTAAAAATA 7 1 1 AAGTAAAAAACTGCCGTTCATAAAAATAACG 7 132 0 CTTGCAGGTTTTATTTCTACTCAGTACCAAA 7 241 1 ATAGAGCATCTTACCTCTCATCAATGTGGGA 8 61 1 CCCAATTTTTTTCATTTTTCAATCTGACGCC 8 151 1 TTTGCTGTTCCTAAGTAATCCT 9 1 1 ** ******** MAP Score: 0.37067