AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_hinf_reg_100.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 HI0058 70 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) #2 HI0059 72 conserved hypothetical protein #3 HI0060 40 ABC transporter, ATP-binding protein (msbA) #4 HI0061 258 recombination protein (rec2) #5 HI1279 104 acylneuraminate cytidylyltransferase (neuA) Motif number 1 TTTATTCCTTATTCTTTAATATTTCAGCTTT 1 48 0 ATTCTTTATA 0.797843 -23 AGAAAATCCTTTCTAATAAGTGCGG 2 58 0 AATCCTTCTA 0.92444 -15 CAATGCGTGCAATTTTTACTATTAGATAGCG 3 17 1 AATTTTTCTA 0.981867 -24 TTAGGAACCCAATTTTTGCGGGCGGTATAAA 4 94 1 AATTTTTCGG 0.961868 -165 CGTAAAAATAAATTTTTCAGGAAAATTTACT 4 149 0 AATTTTTAGG 0.915001 -110 CTGAAAAATTTATTTTTACGATATGGATCGC 4 160 1 TATTTTTCGA 0.891947 -99 CGGTTGCTTCAAATTTTGCGATCCATATCGT 4 177 0 AAATTTTCGA 0.891947 -82 GGCTGGAATTAATCTTTTATAAAA 4 245 1 AATCTTTATA 0.961591 -14 AGCAAAAACTAATCTTTAATATGGCACCACA 5 37 0 AATCTTTATA 0.961588 -68 ATTAAAGATTAGTTTTTGCTAAAACAAGGGA 5 48 1 AGTTTTTCTA 0.926748 -57 ******* *** Masking position 6 Map Score: 10.1924 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 416 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 TTGCCGATAAAGCTGAAATATTAAAGAATA 1 40 1 AGCTGAAATA 0.942871 -31 CTCTCACTCCTAATACATACAGAATTA 4 8 1 TCCTAATACA 0.948468 -251 GTCAGGAACAAACTAAAATAACAAGACAGG 4 57 0 AACTAAAATA 0.860596 -202 AAAATTGGGTTCCTAAAATAGCAGTCAGGA 4 80 0 TCCTAAAATA 0.982569 -179 AAAATTTACTTGCTAAAACAAACAACTTCT 4 129 0 TGCTAAAACA 0.988603 -130 AAGTAAATTTTCCTGAAAAATTTATTTTTA 4 148 1 TCCTGAAAAA 0.93756 -111 GATTAGTTTTTGCTAAAACAAGGGAAAGAT 5 54 1 TGCTAAAACA 0.988603 -51 ********** Masking position 6 Map Score: 8.39396 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 169 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 AATATTAAAGAATAAGGAATAAATT 1 56 1 AAAGGAAAAA 0.870089 -15 CTTTCTAATAAGTGCGGATAAAATAACGCGAGT 2 42 0 AGGGGATAAA 0.976977 -31 TACAGAATTAAGCGTGGATTTCACGACTTCCTG 4 28 1 AGGGGATTCA 0.97381 -231 TAAAATAACAAGACAGGAAGTCGTGAAATCCAC 4 41 0 AGCGGAATCG 0.963367 -218 CTAAAATAGCAGTCAGGAACAAACTAAAATAAC 4 65 0 AGCGGAAAAA 0.989852 -194 AGGCTTAGAGAGGCTGGAATTAATCTTTTATAA 4 234 1 AGCGGAATAA 0.992188 -25 TTTGTTTAACAAAGAGGAAATAAA 5 2 0 AAGGGAATAA 0.971949 -103 ** * **** *** Masking position 8 Map Score: 5.05539 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 68 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CAATCAAAACAACTGGGGATTAATCCTT 1 9 0 AACTGGGGAT 0.972083 -62 CGAGTTTTTCAACTCGCGTTTTCGATAATC 2 17 0 AACTCGCGTT 0.647014 -56 CGAGTTGAAAAACTCGCGTTATTTTATCCG 2 31 1 AACTCGCGTT 0.647014 -42 CCGCCCGCAAAAATTGGGTTCCTAAAATAG 4 89 0 AAATTGGGTT 0.943043 -170 ********** Masking position 4 Map Score: 2.60557 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 31 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 ********** No masking Map Score: -1.0847e-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 6 ********** No masking Map Score: -1.0847e-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 7 ********** No masking Map Score: -1.0847e-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