AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_fusions002_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236198 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0036 205 ABC transporter, ATP-binding protein #1 HI0060 40 ABC transporter, ATP-binding protein (msbA) #2 HI0061 258 recombination protein (rec2) #3 HI0126 43 ferric ABC transporter, ATP-binding protein (afuC) #4 HI0129 300 H. influenzae predicted coding region HI0129 #5 HI0658 160 ABC transporter, ATP-binding protein #6 HI0660 269 H. influenzae predicted coding region HI0660 #7 HI0661_HI0663 547 HI0661: hemoglobin-binding protein, HI0663: ATP-binding transport protein (cydD) #8 HI1051 77 ABC transporter, ATP-binding protein #9 HI1052 111 transcriptional regulator, araC family, putative #10 HI1110 50 D-xylose ABC transporter, ATP-binding protein (xylG) #11 HI1111 233 D-xylose ABC transporter, periplasmic-binding protein (xylF) #12 HI1157 71 ATP-binding protein protein (cydD) #13 HI1158 73 thioredoxin reductase (trxB) #14 HI1159 284 conserved hypothetical protein #15 HI1161 300 conserved hypothetical protein #16 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #17 HI1188 300 DNA helicase II (uvrD) #18 HI1466.1 300 H. influenzae predicted coding region HI1466.1 #19 HI1467 58 ABC transporter, ATP-binding protein #20 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #21 HI1475 227 H. influenzae predicted coding region HI1475 #22 HI1476 227 transcriptional regulatory protein Motif 1 AACGTAGAGTGGGCTTCAGCCCACCAAAATATCTC 7 123 1 GTTGTAGGGTGGGCTTCAGCCCACCNACAAACAGT 7 161 0 GTTTGTNGGTGGGCTGAAGCCCACCCTACAACTAC 7 164 1 ATATTTTGGTGGGCTGAAGCCCACCCTACATTAAG 7 337 0 AATGTAGGGTGGGCTTCAGCCCACCAAAATATCTT 7 340 1 ATTGTAGGGTGGGCTTCAGCCCACCATCAAACAAT 7 378 0 GTTTGATGGTGGGCTGAAGCCCACCCTACAATTAC 7 381 1 CCCCCCTCACCTTCGGCAGCTCCCCCCATAAATGG 15 238 1 * ** ***** ** MAP Score: 29.9478 Motif 2 TGAAAAATAACCGCACTTTTTGTAAAAGGG 0 157 0 TTATTTTTCACCGCACTTTTATCTCGGATG 0 177 1 TAAAAATTTACCGCACTTTTGATTTTAGAT 6 14 0 TAAATTTTTACCGCACTTTTTCTTAAGAAA 6 34 1 CTAACCAATTCCCCTCTTTTAACTCTTTTA 12 15 1 AGAAAAAGTTCCCCTCTTTAAAAGAGTTAA 12 33 0 CTAAAATCTTCCGCACTTTGCTAAAATCAG 14 32 1 TCGCTCTTTTTCACAATTTA 14 274 0 TAAAAATTCACCGCACTCTTCAAAGAAATT 16 40 0 TGAATTTTTACCGCACTTTTATTATCTACG 16 60 1 AAATGTTCTACCCTACTTTTGATATACTCA 17 210 1 CAAACTGGCTTCGCTCTTTTTCTATTTATG 19 30 1 CGGTGCATTGCCCCTTTTTTTATTCTTAGG 21 121 0 ACCGCCAAAGCCCCTGTTTTCAATAATTCC 21 147 1 ********** MAP Score: 29.0851 Motif 3 GCTATCTAATAGTAAAAATTGCACGCATTG 1 16 0 TTATACCGCCCGCAAAAATTGGGTTCCTAA 2 93 0 CGATCCATATCGTAAAAATAAATTTTTCAG 2 159 0 CGATATGGATCGCAAAATTTGAAGCAACCG 2 177 1 TTAAGTTGTAGGTAAAAATT 3 33 1 GGCTAATTATCGTAATAGTAGTTCCCCTTT 4 45 1 GAAAAAGTGCGGTAAAAATTTACCGCACTT 6 26 0 CGATCTAGATCGCAAAAATAGCGAAAATAG 6 141 0 TGTGAAAAAACGTAATAATGGAGAAAGATT 11 129 1 TTTGTAGTTAAGTAATAATATAATGCAATA 13 41 0 TGCGTTGGCGCGTAAAAATTGATGACAAGT 14 167 0 ATAAAAGTGCGGTAAAAATTCACCGCACTC 16 52 0 CACTTACGTCCGTAAAATTTCGCCAAATTC 21 181 1 GTATATTATCCGTAATAGTTGCATGTTGCA 22 43 1 TAAAATACACCGTAATAGTTTCATTTGGCT 22 77 1 TTCTATTACGGGTAATAATTTAGTTTTTAA 22 159 1 TTTTTAATCCCGTAATAGTTGTAATTATTC 22 182 1 CCTCTTTAGTCGTAATAGTTGAATAATTAC 22 202 0 ********** MAP Score: 20.5892 Motif 4 TTAGCAAGTAAATTTTCCTGAAAAATTTATTTTTA 2 142 1 ACAAGGATAAAATAATCCAAAAATAAGCAGAATGC 4 198 0 ATCGGAATAGACTGTTCCGAGAAAAGAAAAAATAT 5 99 1 CATCATAATGATTACTCCTAAAATAAAAAGAAGTA 7 67 1 CATCATAATGATTACTCCTAAAATAAAAAGAAGTA 7 280 1 AGTGCATATTATTATAGCACAAAAACAAATCAAT 8 9 0 ATCTTTTCCTTAAAAAGAAAGGCAAC 8 61 0 ATGAAAAGTTAGTTTTTCACAAAAATACGAAAAAT 11 35 0 CAACGAACAAAATCTTACTGAAATACTGCAACAAT 14 118 1 AACTTGCTCAAGTAGTGCCAAAAAATCCGCCGATT 14 202 0 TTCACAATTTACTTTTCCAAGAATAAATTGTCCTT 14 250 0 AAACATAGATAATGTACCTAAAACAATTTAGGTTG 15 188 1 CTTCAAAGAAATTAATCGGTAAAAAATATAATACT 16 18 0 AAGGTTTCTCATTTTTCCAAAAATACCCATGATGA 17 47 0 ATCAAACATTAATCAACCAAAAAAACCAATAAAAC 18 121 1 TAGTTTTCCATAAATAGAAAAAGAGC 19 42 0 ATTTAGTCAAAATGAACCAGAAAAACTAAGAATTT 21 51 0 * * *** ***** MAP Score: 19.2404 Motif 5 TCAAGTAGTGCCAAAAAATCCGCCGATTCTTTATGC 14 194 0 TTGTATGAACGCAAAAAAACTTTCCATAATGCATTC 4 168 1 GATCTAGATCGCAAAAATAGCGAAAATAGCTTGATT 6 134 0 GCGTTGGCGCGTAAAAATTGATGACAAGTGGTTTTT 14 160 0 CTATCTAATAGTAAAAATTGCACGCATTGTACCTT 1 9 0 TAAAAGTGCGGTAAAAATTCACCGCACTCTTCAAAG 16 45 0 GATATGGATCGCAAAATTTGAAGCAACCGTTTGCAT 2 178 1 CGGCATTTGTGCAAAATCTCCTTGAAAATCAAGCTA 6 108 1 TCTCATTTTTCCAAAAATACCCATGATGACAATAAT 17 40 0 CATTAATCAACCAAAAAAACCAATAAAACACTTGGA 18 127 1 TGACCCTTTTACAAAAAGTGCGGTTATTTTTCACCG 0 154 1 CTTCAGCCCACCAAAATATCTCACGACTGTTTGTNG 7 136 1 CTTCAGCCCACCAAAATATCTTACGATTGTTTGATG 7 353 1 ACTTACGTCCGTAAAATTTCGCCAAATTCCTATTTC 21 182 1 GTGGCTGACAGCAAAAAATGGATTGGTATCACGGTG 7 220 0 GTGGCTGACAGCAAAAAATGGATTGGTGTCACG 7 7 0 TTTAAATACAGCAAATAATGAGAATAGTTTTTATTT 7 459 1 CGCCACAGTTGCAAATAATCAACATAGAAAAATTAA 11 82 0 TTAGTTTTTCACAAAAATACGAAAAATTTCATCACC 11 26 0 GATGTTAGCGATAAAAATTGAGATAAATAAGCAAGT 9 80 0 TTCCCTAAGAATAAAAAAAGGGGCAATGCACCGCCA 21 118 1 TATAAATAGTATAAAAATAGCTTTCAAAGCATATGG 17 122 1 AGCGAAAAAAATGAATTAACTCGTTAAGT 3 3 1 CCGCACTTTGCTAAAATCAGCCATTATTTTTTTCAC 14 42 1 CAGGAACAAACTAAAATAACAAGACAGGAAGTCGTG 2 48 0 TGCCTCTAAATATTCATCTGAAGTACTTTCA 4 279 0 GTTTTAGCAAGTAAATTTTCCTGAAAAATTTATTTT 2 139 1 ******* ** * MAP Score: 18.6683 Motif 6 GTCAGGAACAAACTAAAATAACAAGACAGGA 2 55 0 AAAATTGGGTTCCTAAAATAGCAGTCAGGAA 2 78 0 AAAATTTACTTGCTAAAACAAACAACTTCTG 2 127 0 GATAAAATAATCCAAAAATAAGCAGAATGCA 4 197 0 ACCTATCTAAAATCAAAAGTGCGGT 6 4 1 ATGATTACACATCAAAAATCAATAACTTATT 6 214 1 ATCTACTTATTTCAATAACCAATAAGTTATT 6 234 0 TAATGATTACTCCTAAAATAAAAAGAAGTAT 7 72 1 TAATGATTACTCCTAAAATAAAAAGAAGTAC 7 285 1 ACCCTACAATTACTAATATCAACAATCAACG 7 403 1 GAATACTTTCTCCTATAATATGT 7 534 1 TTTGTTTTTGTGCTATAATAATATGCACTTC 8 15 1 GGGGAACTTTTTCTATAATCACGACCAAAAC 12 49 1 GGTAAAACGTTTCTAAAATCTTCCGCACTTT 14 20 1 TTCCGCACTTTGCTAAAATCAGCCATTATTT 14 40 1 AGATTAGAGGTTCTAAAATAAATAATGATAA 15 34 1 TAGATAATGTACCTAAAACAATTTAGGTTGA 15 193 1 TTATAAACATTTCTATAATCAAGCCCGAATT 18 76 1 * ********* MAP Score: 16.1544 Motif 7 CCATAATGCATTCTGCTTATTTTTGGATTATTT 4 191 1 GAAATAGGAATTTGGCGAAATTTTACGGACGTA 21 185 0 AAATGATACGTTCGTCACATTTTTTCTTGCGAA 0 88 1 ATGAAACTATTACGGTGTATTTTATAGTTGCAA 22 68 0 CTTTGAAGAGTGCGGTGAATTTTTACCGCACTT 16 45 1 AAATCAAAAGTGCGGTAAATTTTTACCGCACTT 6 19 1 GAAATGACTATCTCGCCAAATTTTTAGTTTCTA 6 178 1 GGTAAATTTTTACCGCACTTTTTCTTAAGAAAG 6 32 1 TGCAAACGGTTGCTTCAAATTTTGCGATCCATA 2 180 0 TTTAGCAAAGTGCGGAAGATTTTAGAAACGTTT 14 24 0 TCTTAGTTTTTCTGGTTCATTTTGACTAAATCA 21 55 1 AACCAACTGGTGTGGCAAATTATAGGCGGATTA 9 38 1 CGCATAAAGAATCGGCGGATTTTTTGGCACTAC 14 193 1 AATAGTTTCATTTGGCTATATTTTAATCTATTG 22 90 1 TATAGGAGAATCCCGCTTAATATTATTCTTAAA 17 179 1 TTACAAAAAGTGCGGTTATTTTTCACCGCACTT 0 162 1 ATCAAGCTATTTTCGCTATTTTTGCGATCTAGA 6 135 1 TAGTTTTTATTGCGTCTTATTATACGTGGCTTT 5 45 1 GGTGATGAAATTTTTCGTATTTTTGTGAAAAAC 11 26 1 GCCTCTACAATACCGAAAATTTTTGACCCTTTT 0 131 1 TGAAAAAAATAATGGCTGATTTTAGCAAAGTGC 14 44 0 TCCTAAGGATTGTTGCAGTATTTCAGTAAGATT 14 128 0 TTTGAGGCTATTTTGCAATATTTTTTCTTTTCT 5 118 0 AAGTAAATTTTCCTGAAAAATTTATTTTTACGA 2 147 1 TCGCTCTTTTTCACAATTTACTTTTCCAA 14 265 0 TTATATTTTTTACCGATTAATTTCTTTGAAGAG 16 22 1 CTCTCCAGTTTGTTGCTCAATATCTCGAGTTGC 18 178 0 CTATGCATACTTCTTTTTATTTTAGGAGTAATC 7 76 0 CTATGCGTACTTCTTTTTATTTTAGGAGTAATC 7 289 0 GAAATTTAACTCCTTCGGATTATATCCAAGTTG 0 27 1 TGCCTCTAAATATTCATCTGAAG 4 287 0 CTATCTTTAATCTGTTTAAATTTACAGTTATTA 17 274 0 CTTGCTTATTTATCTCAATTTTTATCGCTAACA 9 81 1 AAATGCAACTTATTGCATTATATTATTACTTAA 13 31 1 CAACCTGCGTTGCCTTTCTTTTTAAGGAAAAGA 8 53 1 * **** ***** MAP Score: 14.3379 Motif 8 CCTTAACCAAACTCAAAAAATGATACGTTC 0 71 1 CTCTCACTCCTAATACATACAGAAT 2 5 1 CGTGAAATCCACGCTTAATTCTGTATGTAT 2 22 0 ACGATATGGATCGCAAAATTTGAAGCAACC 2 176 1 AAGTATACCCACGGCTAATTATCGTAATAG 4 33 1 GGTTGTATGAACGCAAAAAAACTTTCCATA 4 166 1 TCGATCTAGATCGCAAAAATAGCGAAAATA 6 142 0 AATGACTATCTCGCCAAATTTTTAGTTTCT 6 180 1 TGATAGATAAACGCCTAATTAACACGGTGG 7 39 0 CATAATGATTACTCCTAAAATAAAAAGAAG 7 70 1 TACGTTAAGTACGCATAATTCTATGCATAC 7 99 0 TGATAGATAAACGCCTAATTAACACGGTGG 7 252 0 CATAATGATTACTCCTAAAATAAAAAGAAG 7 283 1 TACATTAAGTACGCATAATTCTTTCTATGC 7 316 0 AATGTTCTCCTAAATATATTGAATT 9 5 1 ATATTTCATCACTCCAAAATTTTATTTCGC 15 154 0 CCGTAAAATTTCGCCAAATTCCTATTTCTT 21 190 1 TGCAACTATTACGGATAATATACACCACAT 22 36 0 ********** MAP Score: 13.7055 Motif 9 AGTTTTCCATAAATAGAAAAAGAGCGAAGCCAG 19 34 0 GCTTTGAAAGAGAGAGTAAAAGATAGATCCTTT 6 61 0 CAAAACAAAGAAAACAAAAGAAATAGGAATT 21 206 0 TGATTACTCCTAAAATAAAAAGAAGTATGCATA 7 75 1 TGATTACTCCTAAAATAAAAAGAAGTACGCATA 7 288 1 TGGAGTGATGAAATATTAAAAAACATAGATAAT 15 168 1 GACTGTTCCGAGAAAAGAAAAAATATTGCAAAA 5 108 1 TTTCTTTCCCTAAGAATAAAAAAAGGGGCAATG 21 113 1 CATCACTCGTAGATAATAAAAGTGCGGTAAAAA 16 64 0 ACACGGTGGCTGACAGCAAAAAATGGATTGGTG 7 15 0 ACACGGTGGCTGACAGCAAAAAATGGATTGGTA 7 228 0 ACCTATCTAAAATCAAAAGTGCGGTAAATT 6 7 1 TTTTTCACAAAAATACGAAAAATTTCATCACCT 11 25 0 AATCATAAATAGAAACTAAAAATTTGGCGAGAT 6 187 0 AATCGCTATCTAATAGTAAAAATTGCACGCATT 1 17 0 TTTTTATTCGAAATAGTAAAACAATAGATTAAA 22 111 0 AGGAACAAACTAAAATAACAAGACAGGAAGTCG 2 50 0 CTAAGAATTTAAACAAAAAAGAAAACGCCCGTT 21 28 0 ATCAAAATCAAGAAATAAAAACTATTCTCATTA 7 474 0 *** * ****** MAP Score: 12.7803 Motif 10 ACCTTAACCAAACTCAAAAAATGATACGTTCGT 0 70 1 AGCGAAAAAAATGAATTAACTCG 3 0 1 CAGAAGTGCAAACGCTAACAAGGATAAAATAAT 4 217 0 ACGGTGGCTGACAGCAAAAAATGGATTGGTGTC 7 13 0 ACGGTGGCTGACAGCAAAAAATGGATTGGTATC 7 226 0 ACGTTTAAATACAGCAAATAATGAGAATAGTTT 7 456 1 TAGTTTTCACACTTTAAAAAAGGCTTTCAATTA 11 162 0 TTATTACTTAACTACAAACAAGGATTCTTT 13 53 1 TTATCCTTGTGAAAAAAATAATGGCTGATTTTA 14 53 0 TAGAGGTTCTAAAATAAATAATGATAACTTGCC 15 38 1 AGTTTTTAAAACCTCTAATAAGCAGAAGGCAAG 15 65 0 ATATTTTCTTACTTAAAATAAGGATGTGCG 20 47 1 CTTTCCCTAAGAATAAAAAAAGGGGCAATGCAC 21 116 1 CACATAAGGTACAGCAAAAAAGGTGTATTAA 22 8 0 CGGATAATATACACCACATAAGGTACAGCAAAA 22 22 0 TACTATTTCGAATAAAAACAATGACTTAATTAG 22 126 1 ** **** **** MAP Score: 10.9533 Motif 11 ACCCTTTTACAAAAAGTGCGGTTATTTTTCAC 0 156 1 CTTTCTTAAGAAAAAGTGCGGTAAAAATTTAC 6 33 0 AGAGGTTTTAAAAACTTGCCTTCCCCTGCTTG 15 82 1 CCATCCGAGATAAAAGTGCGGTGAAAAATAAC 0 176 0 TCGTAGATAATAAAAGTGCGGTAAAAATTCAC 16 59 0 GGCTGACAGCAAAAAATGGATTGGTGTCACG 7 9 0 GGCTGACAGCAAAAAATGGATTGGTATCACGG 7 222 0 TACCGCCCGCAAAAATTGGGTTCCTAAAATAG 2 88 0 TTCACACTTTAAAAAAGGCTTTCAATTATAAA 11 158 0 AGCGAAAAAAATGAATTAACTCGTTAA 3 5 1 TAAATAGTATAAAAATAGCTTTCAAAGCATAT 17 124 1 GAAAAATGAGAAACCTTGCATTTTAGGAATGA 17 65 1 TATCTAAAATCAAAAGTGCGGTAAATTTTTAC 6 13 1 CGCAGTAAAGAAAACCTGACTTTCGCCTAGGG 4 133 0 AAACGCCATTTAAACGGGCGTTTTCTTTTTTG 21 16 1 ATAAATAATGATAACTTGCCTTCTGCTTATTA 15 51 1 ATTGGGTTCCTAAAATAGCAGTCAGGAACAAA 2 74 0 TTTCGAATAAAAACAATGACTTAATTAGTTCT 22 131 1 GAATTATTGAAAACAGGGGCTTTGGCGGTGCA 21 144 0 ***** *** ** MAP Score: 10.4998 Motif 12 CTACTTACCCTAGGCGAAAGTCAGGTTTTC 4 126 1 CTTTTTATTTTAGGAGTAATCATTATGATG 7 67 0 TGCATAGAATTATGCGTACTTAACGTAGAG 7 102 1 CTTTTTATTTTAGGAGTAATCATTATGATG 7 280 0 TAATTCTTTCTATGCGTACTTCTTTTTATT 7 301 0 TAGAAAGAATTATGCGTACTTAATGTAGGG 7 319 1 TGATTGTTGATATTAGTAATTGTAGGGTGG 7 401 0 ACATATTATAGGAGAAAGTATTCTCTCA 7 529 0 GATATAGGGATATGCGAAATAAAATTTTGG 15 141 1 GCACAGATCTTATGAGAAATAAA 18 287 1 AAATAGGAATTTGGCGAAATTTTACGGACG 21 187 0 TGGTGTATATTATCCGTAATAGTTGCATGT 22 39 1 TCATTGTTTTTATTCGAAATAGTAAAACAA 22 120 0 CTAACCTCTTTAGTCGTAATAGTTGAATAA 22 206 0 ********** MAP Score: 9.23285