AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #2 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #3 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #4 HI1661 102 2-oxoglutarate dehydrogenase E2 component, dihydrolipoamide succinyltransferase(sucB) #5 HI1662 157 2-oxoglutarate dehydrogenase E1 component (sucA) #6 HI1664 27 conserved hypothetical protein #7 HI1665 53 H. influenzae predicted coding region HI1665 #8 HI1667 73 conserved hypothetical protein #9 HI1668 21 tail specific protease (prc) #10 HI1669 38 conserved hypothetical protein #11 HI1670 183 H. influenzae predicted coding region HI1670 Motif number 1 GTTAAAAATATTGACCGCACTTTTACGGTCT 1 76 0 TTACCGCACT 0.999203 -38 ACAATGTTTTTTGACCGCAGTTTTCATCAA 2 10 0 TTACCGCAGT 0.993219 -53 ATTGTGTTTTATGACCGCACTTTAAAAGGAA 2 36 1 ATACCGCACT 0.999053 -27 ACACAAAAAAATTACCGCACTTTCAAATAAT 3 103 1 ATACCGCACT 0.999049 -197 CTTTATTAAATTAACCGCACT 4 1 0 TTACCGCACT 0.999203 -102 ACAAGTAAAAATAACCGCACTTTGTTTAAGA 5 19 1 ATACCGCACT 0.999053 -139 CAAACAATAAAAAACCGCACTTCATCTCTTA 5 45 0 AAACCGCACT 0.992598 -113 AAATGTAAAATTAACCGCACTTTT 6 14 1 TTACCGCACT 0.999203 -14 CTAAATGGTTTTGACCGCACTTTGTTTGAGA 8 14 1 TTACCGCACT 0.999203 -60 CTTTATTAAAATCACCGCACTTGTTGCTTTT 8 44 0 ATACCGCACT 0.999053 -30 ATTTGCCTAGTTTATCGCACTTTTTACAAAA 11 131 0 TTATCGCACT 0.989982 -53 ** ******** Masking position 4 Map Score: 50.9641 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 496 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 2 TAAAGACCGTAAAAGTGCGGTCAATATTTT 1 73 1 AAAAGTGCGG 0.998795 -41 TTGATGAAAACTGCGGTCAAAAAACA 2 7 1 AAAACTGCGG 0.990768 -56 TTGTTCCTTTTAAAGTGCGGTCATAAAACA 2 40 0 TAAAGTGCGG 0.997234 -23 ATAATTATTTGAAAGTGCGGTAATTTTTTT 3 107 0 GAAAGTGCGG 0.996711 -193 ATCTCTTAAACAAAGTGCGGTTATTTTTAC 5 23 0 CAAAGTGCGG 0.99821 -135 GTTTAAGAGATGAAGTGCGGTTTTTTATTG 5 42 1 TGAAGTGCGG 0.988269 -116 AAAAGTGCGGTTAATTTTAC 6 18 0 AAAAGTGCGG 0.998795 -10 TTTTCTCAAACAAAGTGCGGTCAAAACCAT 8 18 0 CAAAGTGCGG 0.99821 -56 GAGAAAAGCAACAAGTGCGGTGATTTTAAT 8 41 1 ACAAGTGCGG 0.994863 -33 TAATTTTGTAAAAAGTGCGATAAACTAGGC 11 128 1 AAAAGTGCGA 0.986378 -56 ********** Masking position 6 Map Score: 36.7221 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 809 Number in noncoding regions = 448 Number of orfs with sites within 600 bp upstream = 296 Fraction of orfs with sites within 600 bp upstream = 0.0475426 Motif number 3 TTTTTGTTCCTTTTAAAGTGCGGTCAT 2 46 0 TTTTCTTAAA 0.835584 -17 TGCTGAGTCCTTTTTGAAAAAAATCTGAA 3 4 1 TGGCTTTAAA 0.899354 -296 TGCATTCCATCGGGCTTTGTTTTAAAGTTTTTTCAG 3 35 0 CGGTTTTAAA 0.952094 -265 TTTTTGTGTTTTTTTGTTCGCTAAAATAACCAGTAA 3 76 0 TTTTTGTAAA 0.939635 -224 TGATTTGATATGATGATTTGATGAAAATTCACTATC 3 149 1 TGTTTGTAAA 0.96183 -151 TGAAAATTCACTATCTTTATCTCAAAAAATCTTCTA 3 170 1 CTTTTTTAAA 0.956999 -130 GTATTCGTGTTTAGCCTTGTCTAAACTAATATTCAC 3 251 1 TTGTTTTAAC 0.847492 -49 GTGCGGTTATTTTTACTTGTATTAAAAT 5 3 0 TTTTTTTAAA 0.975591 -155 GAAGTGCGGTTTTTTATTGTTTGAAATCTAAAGAGT 5 53 1 TTTTTTTAAA 0.975649 -105 GTTACAAATTTGTGATCTAGTTCAAACTCTTTAGAT 5 78 0 TGGCTGTAAA 0.748153 -80 TCACCGCACTTGTTGCTTTTCTCAAACAAAGTGCGG 8 28 0 TGTTTTTAAA 0.984719 -46 GCAACAAGTGCGGTGATTTTAATAAAGGTTTAGGAA 8 48 1 CGTTTTAAAA 0.753822 -26 GCTTGTGGTCTTTCTTTATAAATCAAAAACG 11 6 1 TGTTTTTTAA 0.846481 -178 ACGTGCCATTCTATCGTTGTTTTAACGTATTTGTGA 11 39 1 CTTTTTTAAC 0.847493 -145 AGTCTTGGCGTTATTTTTGTGTGAAATTTATTCAGC 11 75 1 TTTTTTTAAA 0.975654 -109 CGGGATCCGTTGTTAATTTTGTAAAAAGTGCGATAA 11 115 1 TGTTTTTAAA 0.984711 -69 ** * ** * * *** Masking position 15 Map Score: 20.5572 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 265 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 TACCTCGTAAAAACGTTAAAAATATTGACCG 1 90 0 AAACGTAAAA 0.968816 -24 ACCGCACTTTAAAAGGAACAAAAA 2 49 1 AAAAGAACAA 0.93712 -14 AAATCTGAAAAAACTTTAAAACAAAGCCCGA 3 31 1 AAACTTAAAA 0.889551 -269 GCGAACAAAAAAACACAAAAAAATTACCGCA 3 91 1 AAACAAAAAA 0.81191 -209 AAAATCTTCTAAAATTTACAAGATTTGTTAA 3 195 1 AAAATTACAA 0.794386 -105 AATGTTTGTGAAAAGCAAATATTGCCGTATT 3 225 1 AAAAGAAATA 0.799202 -75 CAGAGGAAAGCAAAGATAAAAACCTTTATTA 4 24 0 CAAAGTAAAA 0.931939 -79 AAAAAAGAAGAAAAGGAAAAATAAA 4 88 1 AAAAGAAAAA 0.961023 -15 ATTTTAATACAAGTAAAAATAACCGCACT 5 9 1 ACAAGAAAAA 0.769868 -149 TTTAGATTTCAAACAATAAAAAACCGCACTT 5 54 0 AAACATAAAA 0.81191 -104 CATAGGATTGCAACGGAAATAAGCCTCTTAT 5 122 0 CAACGAAATA 0.73581 -36 AACAAATGTAAAATTAACCGCAC 6 3 1 CAAATTAAAA 0.780202 -25 TTTGTTTGAGAAAAGCAACAAGTGCGGTGAT 8 34 1 AAAAGAACAA 0.93712 -40 TACGTTAAAACAACGATAGAATGGCACGTTT 11 37 0 CAACGTAGAA 0.747595 -147 GACTTCACAAATACGTTAAAACAACGATAGA 11 48 0 ATACGTAAAA 0.739861 -136 CACTTTTTACAAAATTAACAACGGATCCCGT 11 114 0 AAAATAACAA 0.794386 -70 ***** ***** Masking position 8 Map Score: 15.8005 Number of sites scoring better than the average of aligned sites = 1011 Number in coding regions = 759 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 5 CAAATCTTGTAAATTTTAGAAGATTTTTTGA 3 191 0 AATTTTAGAA 0.834862 -109 AAAATTTACAAGATTTGTTAAATGTTTGTGA 3 205 1 AATTTGTTAA 0.870839 -95 GATTTGTTAAATGTTTGTGAAAAGCAAATAT 3 216 1 AGTTTGTGAA 0.983383 -84 AAATTGTTACAAATTTGTGATCTAGTTCAAA 5 88 0 AATTTGTGAT 0.956716 -70 TGACCGCACTTTGTTTGAGAAAAGCAACAAG 8 25 1 TGTTTGAGAA 0.818109 -49 GAACCAACAGAAATTTGTGAAAAATCAACCG 10 14 0 AATTTGTGAA 0.983707 -25 ATAGAATGGCACGTTTTTGATTTATAAAGAA 11 22 0 AGTTTTTGAT 0.832083 -162 TTGTTTTAACGTATTTGTGAAGTCTTGGCGT 11 55 1 GATTTGTGAA 0.948922 -129 * ********* Masking position 10 Map Score: 4.98578 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 127 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 CATTCCATCGGGCTTTGTTTTAAAGTTTTT 3 39 0 GGCTTTGTTT 0.925442 -261 AAAATTCACTATCTTTATCTCAAAAAATCT 3 172 1 ATCTTTATCT 0.820161 -128 GAATACGGCAATATTTGCTTTTCACAAACA 3 227 0 ATATTTGCTT 0.696937 -73 ATTCGTGTTTAGCCTTGTCTAAACTAATAT 3 253 1 AGCCTTGTCT 0.501418 -47 AGGTTTTCCTTAATCTGTTTT 3 289 0 GGTTTTCCTT 0.714894 -11 AAAGGTTTTTATCTTTGCTTTCCTCTGTAA 4 28 1 ATCTTTGCTT 0.959113 -75 TTTATTTTTCCTTTTCTTCTTTT 4 90 0 ATTTTTCCTT 0.823021 -13 AAGTGCGGTTATTTTTACTTGTATTAAAAT 5 11 0 ATTTTTACTT 0.825919 -147 TTCCGAGTCAATTTTTATTTA 9 2 0 ATTTTTATTT 0.823196 -20 GCTTGTGGTCTTTCTTTATAAATCAAA 11 8 1 GTCTTTCTTT 0.912201 -176 GTGCCATTCTATCGTTGTTTTAACGTATTT 11 41 1 ATCGTTGTTT 0.888618 -143 GTGAAGTCTTGGCGTTATTTTTGTGTGAAA 11 71 1 GGCGTTATTT 0.729548 -113 AACTAGGCAAATCTTTATTTTATTAATGCC 11 150 1 ATCTTTATTT 0.935213 -34 ********** Masking position 5 Map Score: 6.25288 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 498 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 GTGGGCTTAAAGCCCACCTACAGA 1 5 0 AGCCCACCTA 0.994273 -109 GTGGGCTTTAAGCCCACCGATTAATGAAAT 1 18 1 AGCCCACCGA 0.996129 -96 GATGGGTTTCTGCCCACCAAAGATTTCATT 1 40 0 TGCCCACCAA 0.989945 -74 ********** Masking position 6 Map Score: 1.62617 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 9 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 CAAGGCTAAACACGAATACGGCAATATTTG 3 240 0 CACGAATACG 0.974375 -60 TGAACTAGATCACAAATTTGTAACAATTTC 5 90 1 CACAAATTTG 0.975415 -68 GTTGATTTTTCACAAATTTCTGTTGGTTCT 10 16 1 CACAAATTTC 0.939838 -23 GCCAAGACTTCACAAATACGTTAAAACAAC 11 54 0 CACAAATACG 0.984718 -130 ********** Masking position 5 Map Score: 0.329338 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 38 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ********** No masking Map Score: -1.34049e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: -1.34049e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: -1.34049e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0