AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i121_Acriflavin_Resistance_pump_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 HI0885 191 thiol:disulfide interchange protein (dsbD) #2 HI0886 111 H. influenzae predicted coding region HI0886 #3 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #4 HI0888 95 phosphoribosylamine--glycine ligase (purD) #5 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #6 HI0890 58 conserved hypothetical protein #7 HI0891 40 conserved hypothetical protein #8 HI0892 108 ATP-dependent RNA helicase (rhlB) #9 HI0893 241 transcriptional repressor (Bm3R1) #10 HI0894 79 lipoprotein, putative Motif number 1 ATGATTTAGATCACAAAAAGGAAAATCAGGTAA 1 104 0 TACAAAAGAA 0.968675 -88 AAAATACTTTTTACCAAAAGTAAAAAATAA 2 8 0 TACAAAAGAA 0.968642 -104 AGTTAAACAATAATTAAAATTGAAAAATACTTT 2 31 0 TATAAAATGA 0.815667 -81 AATTCATCTTTAAACAAAAGGAAAGCAA 2 94 1 TAAAAAAGAA 0.980148 -18 TTTTAACTATTTAATGAAAGGAAAATACA 3 169 1 TAAGAAAGAA 0.962061 -19 TATGCCTAATTTAAAAAAAGTACGGCTATTTTT 4 58 0 TAAAAAAGAC 0.971398 -38 TTTCATCACTTAAATGAAATTAATTCATCATAA 5 20 0 TAAGAAATAA 0.917666 -104 TTCATTTAAGTGATGAAAATTTAGGAATGAAAT 5 35 1 TATAAAATTA 0.740988 -89 GATAAAAATTTAATTAAAATTTCATTCCTAAAT 5 53 0 TATAAAATTC 0.663065 -71 AACCATATAATCAACGAAAGAAAATAAA 6 6 0 TAAGAAAGAA 0.962063 -53 AGATTAACCGATAGGAAACCCTATCGG 8 5 1 TACGATAGAA 0.705577 -104 AGCACCGCACTTATAAAAATTAACCGATAGGGT 8 28 0 TATAAAATAA 0.942803 -81 GGAAAAATCCTCAAAAAAAGCACCGCACTTATA 8 46 0 TAAAAAAGAC 0.971399 -63 GTTTATTTAATGATGAAAAGTGCGGTTAATTTT 9 29 1 TATAAAAGGC 0.87379 -213 AAGTAGGATATAAAAAATAGGAATATAAAATGC 9 66 0 TAAAATAGAA 0.881649 -176 AAACAAAAAATAAATAAAATGAACGCTCATTCA 9 178 1 TAAAAAATAA 0.95596 -64 TAAAGCTCCGTTATAAAAATAACAACAA 10 6 0 TATAAAATAC 0.918956 -74 * ** ***** ** Masking position 7 Map Score: 21.945 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 325 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 GATAGCATACGCCAAAATAAGTATAAGGATG 1 15 0 GCAAAATAAG 0.937696 -177 GGAAAATCAGGTAAAAAATCACCGCACTTTT 1 87 0 GTAAAAATCA 0.93598 -105 TTTACCAAAAGTAAAAAATAA 2 1 0 GTAAAAATAA 0.94681 -111 ATAAATGTGGGCAAAAATAAGGATAAAATTA 3 27 0 GCAAAATAAG 0.937696 -161 TAAATTTCAGGCATAAAAAAGCCCACATAAA 3 53 0 GCTAAAAAAG 0.783336 -135 TTAAAGTGCGGTAAAAATACGATAAATTTCA 3 75 0 GTAAAATACG 0.937696 -113 TCATTAAATAGTTAAAAATAAGCGATGAGAA 3 155 0 GTAAAAATAA 0.94681 -33 GGAATTGCAGGTAAAAAATAGCCGTACTTTT 4 45 1 GTAAAAATAG 0.976905 -51 GTATGCCTAATTTAAAAAAAGTACGGCTATT 4 61 0 TTAAAAAAAG 0.760029 -35 TGTCCGATTTGCCAAAAATCG 7 30 1 GCAAAAATCG 0.966141 -11 AGGAAAAATCCTCAAAAAAAGCACCGCACTT 8 49 0 CTAAAAAAAG 0.824381 -60 ATAAAATGCAGTCAAAATTAACCGCACTTTT 9 44 0 GTAAAATTAA 0.871522 -198 AAAGTAGGATATAAAAAATAGGAATATAAAA 9 69 0 ATAAAAATAG 0.735873 -173 TTTTTGGCAAGTTAAAAAACAAAAAACGTAA 9 149 0 GTAAAAAACA 0.943247 -93 TTTTTAACTTGCCAAAAAACAAAAAATAAAT 9 162 1 GCAAAAAACA 0.931744 -80 ** ******** Masking position 6 Map Score: 19.217 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 512 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 CAGGTAAAAAATCACCGCACTTTTTTATTGTT 1 79 0 ATCCGCACTT 0.986595 -113 TTTCATAATTTTATCCTTATTTTTGCCCACAT 3 22 1 TTCCTTATTT 0.793655 -166 ATCCTTATTTTTGCCCACATTTATGTGGGCTT 3 34 1 TTCCACATTT 0.939495 -154 TTATCGTATTTTTACCGCACTTTAAGAAATTA 3 81 1 TTCCGCACTT 0.994617 -107 ATATTTAATCTTTTCTATATTTAAGCAAACGT 3 112 1 TTCTATATTT 0.520441 -76 CGGCTATTTTTTACCTGCAATTCCCCCTCTTT 4 37 0 TTCTGCAATT 0.871177 -59 CAGGTAAAAAATAGCCGTACTTTTTTTAAATT 4 52 1 ATCCGTACTT 0.948001 -44 CATTCCTAAATTTTCATCACTTAAATGAAATT 5 32 0 TTCATCACTT 0.802493 -92 CCTCAAAAAAAGCACCGCACTTATAAAAATTA 8 39 0 AGCCGCACTT 0.932707 -70 GCAGTCAAAATTAACCGCACTTTTCATCATTA 9 36 0 TTCCGCACTT 0.994617 -206 GCGGTTAATTTTGACTGCATTTTATATTCCTA 9 50 1 TTCTGCATTT 0.956988 -192 ** ******** Masking position 9 Map Score: 12.1203 Number of sites scoring better than the average of aligned sites = 1753 Number in coding regions = 1223 Number in noncoding regions = 530 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 4 ACATTATTGTAACAATAAAAAAGTGCGGTGA 1 69 1 AACAAAAAAA 0.816999 -123 CGGGTAGTTAAACAATAATTAAAATTGAAAA 2 38 0 AACAAAATTA 0.933896 -74 CTTTTGTTTAAAGATGAATTAAAACGGCGTC 2 83 0 AAGATAATTA 0.929403 -29 AAATATAGAAAAGATTAAATATAATTTCTTA 3 103 0 AAGATAAATA 0.929403 -85 CCATATCATTATGATGAATTAATTTCATTTA 5 12 1 ATGATAATTA 0.746814 -112 CGCACTTTTCATCATTAAATAAACGCGTGGA 9 22 0 ATCATAAATA 0.81335 -220 GTAAACCCACAAGATGAATGATGAACAAAGT 9 95 0 AAGATAATGA 0.9036 -147 CAAAAAACGTAACAATACTTATCTGTAGGTA 9 130 0 AACAAACTTA 0.708054 -112 TGGCAAGTTAAAAAACAAAAAACGTAACAAT 9 145 0 AAAAAAAAAA 0.505227 -97 CTTGCCAAAAAACAAAAAATAAATAAAATGA 9 169 1 AACAAAAATA 0.933896 -73 TAATTGCTCAAAAATGAATGAGCGTTCATTT 9 194 0 AAAATAATGA 0.760037 -48 AGTCAAACTCAACATCAAAGACCAAAACGCT 10 45 1 AACATAAAGA 0.932649 -35 ***** ***** Masking position 7 Map Score: 5.78674 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 318 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 GATTTTTTACCTGATTTTCCTTTTTGTGATC 1 98 1 CGATTTTCCT 0.916039 -94 TTTTAGGTATTCAAATTTCTTTGTGATAGAA 1 139 1 TAAATTTCTT 0.758191 -53 AAAGATTAAATATAATTTCTTAAAGTGCGGT 3 94 0 TTAATTTCTT 0.895392 -94 TGTATTTTCCTTTCATTAAAT 3 177 0 TTATTTTCCT 0.977265 -11 ATTTCATTCCTAAATTTTCATCACTTAAATG 5 37 0 TAATTTTCAT 0.750985 -87 TTTATTTTCTTTCGTTGATTA 6 1 1 TTATTTTCTT 0.964417 -58 TTGACTGCATTTTATATTCCTATTTTTTATA 9 60 1 TTATATTCCT 0.871414 -182 ATTATTGCTCCTTATTTTACTCAAGGATCTT 9 221 1 CTATTTTACT 0.776602 -21 AAAACGCTCACATATTTTCTTG 10 68 1 CTATTTTCTT 0.957183 -12 * ********* Masking position 7 Map Score: 4.17947 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 237 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 GCCAAAATAAGTATAAGGATGGAAA 1 6 0 GTATAAGGAT 0.964082 -186 AGAATTGAGTATAAAAATATAGATGCTC 1 174 0 GTATAAAAAT 0.72531 -18 CTTTCCTTTTGTTTAAAGATGAATTAAAAC 2 89 0 GTTTAAAGAT 0.96955 -23 TAGTTTAACTGTTTATGGATAAAAATTTAA 5 73 0 GTTTATGGAT 0.938346 -51 CATCTTGTGGGTTTACGGCTTACCTACAGA 9 110 1 GTTTACGGCT 0.949247 -132 TTTGACTCATGTTTAAAGCTCCGTTATAAA 10 22 0 GTTTAAAGCT 0.963508 -58 ********** Masking position 5 Map Score: 2.15571 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 42 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -2.95996e-13 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 8 ********** No masking Map Score: -2.95996e-13 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 9 ATATAGATGCTCGAAATTCTATCACAAAGAAA 1 154 0 TCGAATTTAT 0.958336 -38 AGTTGTAGTTTCATAATTTTATCCTTATTTTT 3 14 1 TCAAATTTAT 0.954869 -174 ACCGCACTTTAAGAAATTATATTTAATCTTTT 3 94 1 AAGAATTTAT 0.731646 -94 AATTAATTCATCATAATGATATGGA 5 4 0 TCAAATGTAT 0.93793 -120 GATGAAAATTTAGGAATGAAATTTTAATTAAA 5 46 1 TAGAATGAAT 0.82683 -78 TGTTTATGGATAAAAATTTAATTAAAATTTCA 5 62 0 TAAAATTAAT 0.860906 -62 GGATTTTTCCTAAAAATGCTATGCTAAACGTA 8 69 1 TAAAATGTAT 0.865781 -40 GCTATGCTAAACGTAATTTTATTATTCTAAAA 8 86 1 ACGAATTTAT 0.864544 -23 ACCGCACTTTTCATCATTAAATAAACGCGTGG 9 23 0 TCACATTAAT 0.751537 -219 CAATAATTGCTCAAAAATGAATGAGCGTTCAT 9 196 0 TCAAAATAAT 0.671146 -46 *** **** *** Masking position 6 Map Score: 3.11152 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 154 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 ********** No masking Map Score: -2.95996e-13 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: -2.95996e-13 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 12 ********** No masking Map Score: -2.95996e-13 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