AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_dna_polymerase_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 HI0856 148 DNA polymerase I (polA) #2 HI0885 191 thiol:disulfide interchange protein (dsbD) #3 HI0886 111 H. influenzae predicted coding region HI0886 #4 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #5 HI0888 95 phosphoribosylamine--glycine ligase (purD) #6 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #7 HI0890 58 conserved hypothetical protein Motif number 1 TCAAATATTTAATTTAAGGAAATCAA 1 1 0 AAAGGAACAA 0.977142 -148 GCTATGGCATAATATCAGCCATTCAAATATTTAATT 1 23 0 AAAGCATCAA 0.95218 -126 ACGCCAAAATAAGTATAAGGATGGAAA 2 2 0 AAAAGATGAA 0.823256 -190 TGTGCAACATTATTGTAACAATAAAAAAGTGCGGTG 2 63 1 TAAACATAAA 0.711709 -129 CACAAAAAGGAAAATCAGGTAAAAAATCACCGCACT 2 90 0 AAAGGAAAAA 0.981149 -102 TCTAAATCATAGTTTTAGGTATTCAAATTTCTTTGT 2 127 1 AGAGGATCAA 0.898558 -65 AAATACTTTTTACCAAAAGTAAAAAATAA 3 4 0 TAAAGAAAAA 0.841272 -108 TTCATCTTTAAACAAAAGGAAAGCAA 3 96 1 AAAGGAACAA 0.977142 -16 AAATGTGGGCAAAAATAAGGATAAAATTATGAAACT 4 20 0 AAAAGATAAA 0.961141 -168 AAATACGATAAATTTCAGGCATAAAAAAGCCCACAT 4 56 0 AAAGGATAAA 0.988378 -132 TTTGCTTAAATATAGAAAAGATTAAATATAATTTCT 4 105 0 TAAAAATAAA 0.522829 -83 TAAATAGTTAAAAATAAGCGATGAGAATTATAACGC 4 146 0 AAAGCATAGA 0.754572 -42 AAAGAGGGGGAATTGCAGGTAAAAAATAGCCGTACT 5 37 1 AAAGGAAAAA 0.981149 -59 AAATTAGGCATACGCAAGGACTACAAC 5 79 1 TAAGGCTCAA 0.756178 -17 TAAGTGATGAAAATTTAGGAATGAAATTTTAATTAA 6 41 1 AAAGGATAAA 0.988378 -83 CCATATAATCAACGAAAGAAAATAAA 7 1 0 AAAGAAAAAA 0.868167 -58 ** *** ** *** Masking position 7 Map Score: 20.2729 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 394 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 ATTATGCCATAGCAAAAAATATTCGTCATAA 1 46 1 AGAAAAAATA 0.969589 -103 AGGAAAATCAGGTAAAAAATCACCGCACTTT 2 88 0 GGAAAAAATC 0.959292 -104 AGAATTGAGTATAAAAATATAGATGCTCG 2 173 0 GTTAAAAATA 0.899024 -19 TTTTACCAAAAGTAAAAAATAA 3 2 0 AGAAAAAATA 0.969589 -110 TTTTACTTTTGGTAAAAAGTATTTTTCAATT 3 16 1 GGAAAAAGTA 0.959292 -96 GCAAAAATAAGGATAAAATTATGAAACTACA 4 17 0 GGTAAAATTA 0.940827 -171 ACATAAATGTGGGCAAAAATAAGGATAAAAT 4 29 0 GGCAAAAATA 0.976369 -159 TCTTAAAGTGCGGTAAAAATACGATAAATTT 4 77 0 CGTAAAAATA 0.949243 -111 TTCATTAAATAGTTAAAAATAAGCGATGAGA 4 156 0 AGTAAAAATA 0.969589 -32 GGGAATTGCAGGTAAAAAATAGCCGTACTTT 5 44 1 GGAAAAAATA 0.991228 -52 AACTGTTTATGGATAAAAATTTAATTAAAAT 6 66 0 GGTAAAAATT 0.940827 -58 ** ******** Masking position 6 Map Score: 18.3348 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 134 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TTAAACTGAAAAATGTGGGCATTATAGCGT 1 117 0 AAATGTGGGC 0.97261 -32 GTAACAATAAAAAAGTGCGGTGATTTTTTA 2 77 1 AAAAGTGCGG 0.993828 -115 AAGCCCACATAAATGTGGGCAAAAATAAGG 4 36 0 AAATGTGGGC 0.97261 -152 TATAATTTCTTAAAGTGCGGTAAAAATACG 4 85 0 TAAAGTGCGG 0.983318 -103 CCCTCTTTTGTAAAGAGGGGGATAGTTAGA 5 15 0 TAAAGAGGGG 0.973505 -81 CCCTCTTTACAAAAGAGGGGGAATTGCAGG 5 26 1 AAAAGAGGGG 0.990135 -70 CTAATTTAAAAAAAGTACGGCTATTTTTTA 5 56 0 AAAAGTACGG 0.947314 -40 AAAAAATAAGCGGCGATATTAAT 7 46 0 AAATAAGCGG 0.874791 -13 ********** Masking position 3 Map Score: 12.9546 Number of sites scoring better than the average of aligned sites = 1477 Number in coding regions = 978 Number in noncoding regions = 499 Number of orfs with sites within 600 bp upstream = 319 Fraction of orfs with sites within 600 bp upstream = 0.0512367 Motif number 4 GATTTCCTTAAATTAAATATTTGAATGGCT 1 13 1 AATTAAATAT 0.809517 -136 TTCAGTTTAAAACGAGATTTTT 1 137 1 AACGAGATTT 0.80702 -12 ATTCTATCACAAAGAAATTTGAATACCTAA 2 141 0 AAAGAAATTT 0.928277 -51 GTTAAACAATAATTAAAATTGAAAAATACT 3 33 0 AATTAAAATT 0.901699 -79 ATATAGAAAAGATTAAATATAATTTCTTAA 4 102 0 GATTAAATAT 0.726978 -86 AAAAATAAGCGATGAGAATTATAACGCAAA 4 143 0 GATGAGAATT 0.868583 -45 TCATCACTTAAATGAAATTAATTCATCATA 6 21 0 AATGAAATTA 0.920453 -103 TCATTTAAGTGATGAAAATTTAGGAATGAA 6 36 1 GATGAAAATT 0.945113 -88 AAAATTTAGGAATGAAATTTTAATTAAATT 6 50 1 AATGAAATTT 0.978939 -74 ATGAAATTTTAATTAAATTTTTATCCATAA 6 61 1 AATTAAATTT 0.942447 -63 ATAATCAACGAAAGAAAATAAA 7 3 0 AAAGAAAATA 0.654749 -56 ********** Masking position 5 Map Score: 8.56988 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 498 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 AAAAATATTCGTCATAAATTTTACATTAAAC 1 60 1 GTCATAATTT 0.802738 -89 TTCGCTCATCACCATAAATTACGCTATAATG 1 97 1 ACCATAATTA 0.961185 -52 CGGGTAGTTAAACAATAATTAAAATTGAAAA 3 38 0 AACAAAATTA 0.687186 -74 CTACCCGTTAAAGATTAATATGACGCCGTTT 3 62 1 AAGATAATAT 0.814095 -50 CTTTTGTTTAAAGATGAATTAAAACGGCGTC 3 83 0 AAGATAATTA 0.958444 -29 CGGTAAAAATACGATAAATTTCAGGCATAAA 4 67 0 ACGATAATTT 0.961521 -121 AAATATAGAAAAGATTAAATATAATTTCTTA 4 103 0 AAGATAAATA 0.764449 -85 CCATATCATTATGATGAATTAATTTCATTTA 6 12 1 ATGATAATTA 0.925159 -112 TAAACTATCTGCCATAAATTACATAACAGGA 6 96 1 GCCATAATTA 0.946328 -28 ATGGTTAGCGGCGATTAATATCGCCGCTTAT 7 33 1 GCGATAATAT 0.831811 -26 ***** ***** Masking position 7 Map Score: 4.86667 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 378 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AATAAAAAAGTGCGGTGATTTTTTACCTGA 2 82 1 TGCGGTGATT 0.980485 -110 TTAAAAAAAGTACGGCTATTTTTTACCTGC 5 51 0 TACGGCTATT 0.926557 -45 TTATATGGTTAGCGGCGATTAATATCGCCG 7 29 1 AGCGGCGATT 0.994984 -30 AAAAAATAAGCGGCGATATTAATCGCCG 7 41 0 AGCGGCGATA 0.987469 -18 ********** Masking position 8 Map Score: 1.84805 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 41 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GCCATTCAAATATTTAATTTAAGGAAATCA 1 12 0 TATTTAATTT 0.784506 -137 TTCGTCATAAATTTTACATTAAACCCGCCA 1 67 1 ATTTTACATT 0.883986 -82 AATGCCCACATTTTTCAGTTTAAAACGAGA 1 124 1 TTTTTCAGTT 0.869816 -25 TTTTTACCTGATTTTCCTTTTTGTGATCTA 2 101 1 ATTTTCCTTT 0.959227 -91 TTATTTTTTACTTTTGGTAAAAAG 3 5 1 TTTTTACTTT 0.936513 -107 GTAAAAAGTATTTTTCAATTTTAATTATTG 3 27 1 TTTTTCAATT 0.919065 -85 TGTATTTTCCTTTCATTAAATAG 4 175 0 ATTTTCCTTT 0.959227 -13 AGCCGTACTTTTTTTAAATTAGGCATACGC 5 64 1 TTTTTAAATT 0.869958 -32 ATGATGAATTAATTTCATTTAAGTGATGAA 6 22 1 AATTTCATTT 0.856349 -102 TAGGAATGAAATTTTAATTAAATTTTTATC 6 56 1 ATTTTAATTA 0.655898 -68 ********** Masking position 5 Map Score: 8.40496 Number of sites scoring better than the average of aligned sites = 777 Number in coding regions = 602 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 8 TTGATTTCCTTAAATTAAATATTTGA 1 6 1 TTCTTAAATT 0.910588 -143 ATTTTAATTATTGTTTAACTACCCGTTAAAG 3 44 1 TTGTTAACTA 0.947811 -68 CGTCATATTAATCTTTAACGGGTAGTTAAAC 3 56 0 ATCTTAACGG 0.488524 -56 TGCTTTCCTTTTGTTTAAAGATGAATTAAAA 3 90 0 TTGTTAAAGA 0.923982 -22 AAATATAGAAAAGATTAAATATAATTTCTTA 4 103 0 AAGTTAAATA 0.660301 -85 ACGCAAACGTTTGCTTAAATATAGAAAAGAT 4 119 0 TTGTTAAATA 0.969404 -69 GTATTTTCCTTTCATTAAATAGTTAAAAATA 4 166 0 TTCTTAAATA 0.942319 -22 TAGCCGTACTTTTTTTAAATTAGGCATACGC 5 63 1 TTTTTAAATT 0.719196 -33 GAATGAAATTTTAATTAAATTTTTATCCATA 6 59 1 TTATTAAATT 0.719361 -65 TTATGGCAGATAGTTTAACTGTTTATGGATA 6 82 0 TAGTTAACTG 0.824756 -42 TTTTCTTTCGTTGATTATATGGTTAGCGGCG 7 15 1 TTGTTATATG 0.797909 -44 *** ******* Masking position 7 Map Score: 2.74929 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 335 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 ********** No masking Map Score: -1.24102e-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: -1.24102e-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: -1.24102e-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