AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_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 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #2 HI0873 58 DTDP-glucose 4,6-dehydratase (rffG) #3 HI1534 148 conserved hypothetical protein #4 HI1537 251 lic-1 operon protein (licA) Motif number 1 AGCACTAGAACAATGAAAAAGATAAGATAA 1 40 0 CAATGAAAAA 0.905077 -261 AAGTAATAAGCAAGGAAGCAGATATAAAGC 1 67 0 CAAGGAAGCA 0.895332 -234 ATCAAAAAAGAAAGTAATAAGCAAGGAAGC 1 78 0 AAAGTAATAA 0.688148 -223 CCTTATCTTAAAATCAAAAAAGAAAGTAAT 1 90 0 AAATCAAAAA 0.916076 -211 TTTTACATATAAAACAATAAGGAAGAAGCA 3 11 0 AAAACAATAA 0.828764 -138 AAAAATATTTCAAGCAATAATTCATTTGTT 3 67 1 CAAGCAATAA 0.984511 -82 ATTAGGCAAGAAAGGAATAAAAA 3 136 1 AAAGGAATAA 0.897617 -13 TAACGTGTTAAAATCAAACAAAATTTAAAT 4 45 1 AAATCAAACA 0.953037 -207 AAATGCTATGCAATCAATCAATCAATCAAT 4 91 1 CAATCAATCA 0.993086 -161 ATCAATCAATCAATCAATCAATCAATCAAT 4 103 1 CAATCAATCA 0.993086 -149 ATCAATCAATCAATCAATCAATCAATCAAT 4 115 1 CAATCAATCA 0.993086 -137 ATCAATCAATCAATCAATCAATCAATCAAT 4 131 1 CAATCAATCA 0.993086 -121 ATCAATCAATCAATCAATCAAATTGTAGGA 4 151 1 CAATCAATCA 0.993086 -101 ********** Masking position 6 Map Score: 27.3689 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 237 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 AGATAAGATAAGATAAGATA 1 1 0 AGATAAGATA 0.990887 -300 AGATAAGATAAGATAAGATAAGATAAGATA 1 11 0 AGATAAGATA 0.990887 -290 AGATAAGATAAGATAAGATAAGATAAGATA 1 21 0 AGATAAGATA 0.990887 -280 ACAATGAAAAAGATAAGATAAGATAAGATA 1 31 0 AGATAAGATA 0.990887 -270 TTTGATTTTAAGATAAGGGATATTTTGATT 1 102 1 AGATAAGGGA 0.9837 -199 CTAAAATAGCGGATAAGAGAGATAAAATCA 1 127 0 GGATAAGAGA 0.972118 -174 CCTTTATATAGTTTAAGGTATTAATTTTCC 1 264 0 GTTTAAGGTA 0.834798 -37 GGGTTAATAAATTTAAGGTAATGCAAATAG 2 36 0 ATTTAAGGTA 0.899231 -23 ********** Masking position 5 Map Score: 15.8334 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 17 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 CTTAAAATCAAAAAAGAAAGTAATAAGCAAGGAAG 1 79 0 AAAAGAAATA 0.800897 -222 GGATAAGAGAGATAAAATCAAAATATCCCTTATCT 1 112 0 GAAAAAAATA 0.988101 -189 ATACCCACCCGAAAAAATCATAATATACTAAAATA 1 149 0 GAAAAAAATA 0.988102 -152 CAGAATATTGGACAAAATAATAATAAACCCTACCA 1 226 0 GAAAAAAATA 0.988102 -75 CAATATTCTGGAGGGAAAATTAATACCTTAAACTA 1 251 1 GAGGAAAATA 0.947688 -50 TACATATATAGAGAAAACCTTTATATAGTTTAAGG 1 276 0 GAAAAATATA 0.948931 -25 TAATAAATTTAAGGTAATGCAAATAGAAGAAATCT 2 27 0 AAGTAAAATA 0.775224 -32 TCAAAATTACTACGAAATAAAAATATTTCAAGCAA 3 49 1 TAGAAAAATA 0.949857 -100 GTTAAAATCAAACAAAATTTAAATATAAAAATGAA 4 51 1 AAAAAAAATA 0.959056 -201 TAAAAATGAATACAAAAATGCTATGCAATCAATCA 4 76 1 TAAAAATATG 0.559398 -176 GAATGCTGATGAAGAAAATGAAATACTTCCTCAGG 4 202 0 GAGAAAAATA 0.989712 -50 TCCTCCAATGGAGGAAAAAGGAATGGAATGCTGAT 4 227 0 GAGAAAAATG 0.97088 -25 ** **** **** Masking position 7 Map Score: 15.763 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 108 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 AGAGATAAAATCAAAATATCCCTTATCTTA 1 110 0 TCAAAATATC 0.800026 -191 TAAAAATATTTCAAGCAATAATTCATTTGT 3 66 1 TCAAGCAATA 0.937053 -83 TTCGACCAGTTCAGAAAATCGCGTTATTAT 3 95 1 TCAGAAAATC 0.855688 -54 CGTGTTAAAATCAAACAAAATTTAAATATA 4 48 1 TCAAACAAAA 0.800026 -204 TGCTATGCAATCAATCAATCAATCAATCAA 4 94 1 TCAATCAATC 0.995187 -158 AATCAATCAATCAATCAATCAATCAATCAA 4 106 1 TCAATCAATC 0.995187 -146 AATCAATCAATCAATCAATCAATCAATCAA 4 122 1 TCAATCAATC 0.995187 -130 AATCAATCAATCAATCAATCAATCAATCAA 4 134 1 TCAATCAATC 0.995187 -118 AATCAATCAATCAATCAATCAAATTGTAGG 4 150 1 TCAATCAATC 0.995187 -102 ********** Masking position 3 Map Score: 20.2116 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 65 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 ACAAATGAATTATTGCTTGAAATATTTTTA 3 66 0 TATTGCTTGA 0.959604 -83 TTGATTGATTGATTGATTGATTGCATAGCA 4 94 0 GATTGATTGA 0.997624 -158 TTGATTGATTGATTGATTGATTGATTGATT 4 106 0 GATTGATTGA 0.997624 -146 TTGATTGATTGATTGATTGATTGATTGATT 4 126 0 GATTGATTGA 0.997624 -126 TTGATTGATTGATTGATTGATTGATTGATT 4 138 0 GATTGATTGA 0.997624 -114 CCTACAATTTGATTGATTGATTGATTGATT 4 150 0 GATTGATTGA 0.997624 -102 ********** Masking position 4 Map Score: 21.0214 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 26 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TGTTCTAGTGCTTTATATCTGCTTCCTTGC 1 58 1 CTTTATATCT 0.964249 -243 TTGCTTATTACTTTCTTTTTTGATTTTAAG 1 84 1 CTTTCTTTTT 0.823406 -217 GATATTTTGATTTTATCTCTCTTATCCGCT 1 120 1 TTTTATCTCT 0.763901 -181 CTAATGTTAGCTATATATTTGGTAGGGTTT 1 207 1 CTATATATTT 0.884422 -94 AAGGTTTTCTCTATATATGTA 1 290 1 CTATATATGT 0.837403 -11 CGTTATTTCTTAAGTGAGAT 2 1 1 CGTTATTTCT 0.939754 -58 TTCCTTATTGTTTTATATGTAAAAATAACG 3 17 1 TTTTATATGT 0.858653 -132 AATTTTGAGTCGTTATTTTTACATATAAAA 3 27 0 CGTTATTTTT 0.940894 -122 AACACGTTAAAGTTATTTTTGTAAGGCTCT 4 24 0 AGTTATTTTT 0.673694 -228 TTGTATTCATTTTTATATTTAAATTTTGTT 4 61 0 TTTTATATTT 0.900275 -191 ********** Masking position 6 Map Score: 5.76156 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 235 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 ATACTCTATACCCACCCGAAAAAATCATAA 1 161 0 CCCACCCGAA 0.986185 -140 TAATAATAAACCCTACCAAATATATAGCTA 1 214 0 CCCTACCAAA 0.986908 -87 TATTAATTTTCCCTCCAGAATATTGGACAA 1 246 0 CCCTCCAGAA 0.991492 -55 AGATTCAGAGCCTTACAAAAATAACTTTAA 4 18 1 CCTTACAAAA 0.92462 -234 ********** Masking position 9 Map Score: 0.900305 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 28 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TATTTTAGTATATTATGATTTTTTCGGGTGGGTA 1 149 1 TTTATTTTTT 0.759079 -152 TTTTTCGGGTGGGTATAGAGTATTTGTATGAAAA 1 168 1 GGTATAGTTT 0.867532 -133 GCTATATATTTGGTAGGGTTTATTATTATTTTGT 1 216 1 TGTAGTTTTT 0.980457 -85 TATTTTTATTTCGTAGTAATTTTGAGTCGTTATT 3 40 0 TGTAGATTTG 0.952608 -109 CATAGCATTTTTGTATTCATTTTTATATTTAAAT 4 67 0 TGTATATTTT 0.969353 -185 ATCAATCAAATTGTAGGATTTGTTAAAACTTGCT 4 163 1 TGTAGTTTTT 0.980457 -89 TTCCTCAGGCTTGTAGCAAGTTTTAACAAATCCT 4 177 0 TGTAGAGTTT 0.977757 -75 * **** *** ** Masking position 5 Map Score: 1.17907 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 66 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: 6.13499e-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 10 ********** No masking Map Score: 6.13499e-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: 6.13499e-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