AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_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 HI0967 25 H. influenzae predicted coding region HI0967 #2 HI0970 57 3-dehydroquinase (aroQ) #3 HI0971 152 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) #4 HI0972 174 acetyl-CoA carboxylase, biotin carboxylase (accC) Motif number 1 CAAAAATCGAAAAAACCAGTATAATGTGCCACA 2 20 1 AAAAACGTTA 0.932468 -38 GAAAATCGAGTATTTTTGGCGAAA 3 2 1 AAAATCGTTT 0.87556 -151 AATTTGCGATAAAATTCTGTGAATTTCGCCAAA 3 25 0 AAAATTGTAA 0.969067 -128 CAAATTTGAAAAAATTAAGGTAATCTTTGCAAC 3 52 1 AAAATTGGAA 0.966995 -101 TTTGCAACACAAAAGTAAGTTTATTCATAACCG 3 77 1 AAAAGTGTTA 0.991821 -76 TTTTAAAGGAAAAAGTGCGGTTATGAATAAACT 3 94 0 AAAAGTGGTA 0.991546 -59 TTTTTCCTTTAAAAGTGCGGTTAAAATTTCAAT 3 113 1 AAAAGTGGTA 0.991546 -40 CCGCCCGACAAAAATATTGGAAA 4 1 0 AAAATAGGAA 0.840011 -174 AATTCGCTCTAATTGTTTGTATATGAAATACGG 4 42 0 AATTGTGTTA 0.814091 -133 GCCTACATAAAAATTCACGTCTATCTGACTAAA 4 141 1 AAATTCGTTA 0.932863 -34 AAAAGAGTCCGTTTAGTCAGATAGA 4 160 0 AAGAGTGTTA 0.963167 -15 ****** ** ** Masking position 2 Map Score: 13.7602 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 456 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 ATTCTCACTTTTATAAGGATCAAAT 1 4 0 TCTTTTAGGA 0.991205 -22 ACTGGTTTTTTCGATTTTTGGTGGTCGAA 2 2 0 TCTTTGTGGA 0.988286 -56 TTTTAATCCTTTTTGTGTGGCACATTATACTGGT 2 34 0 TCTTTTTGGA 0.996865 -24 GAAAATCGAGTATTTTTGGCGAAATTCACAGAA 3 6 1 TCGTTTTGGA 0.994477 -147 ATGAATAAACTTACTTTTGTGTTGCAAAGATTACCTTA 3 67 0 TTTTTTTTGA 0.890386 -86 GGTTAAAATTTCAATCTTTTTAGGAAGAACGT 3 131 1 TCTCTTAGGA 0.968143 -22 TTCGCTCTAATTGTTTGTATATGAAATACGGACTAAAG 4 35 0 TTTTTTTGAA 0.942578 -140 ACATAAAAATTCACGTCTATCTGACTAAACGGACTCTT 4 145 1 TCGTTTTGAA 0.97627 -30 ** ** * * *** * Masking position 18 Map Score: 9.09484 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 200 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 CCTTAATTTTTTCAAATTTGCGATAAAATT 3 42 0 TTCAAATTTG 0.972751 -111 CCTAAAAAGATTGAAATTTTAACCGCACTT 3 125 0 TTGAAATTTT 0.970648 -28 TTTCCAATATTTTTGTCGGGC 4 2 1 TTCCAATATT 0.841735 -173 TTGTTTGTATATGAAATACGGACTAAAGTC 4 33 0 ATGAAATACG 0.901406 -142 GCGATATAAATTGAAATCTGTTCACGCCAA 4 83 1 TTGAAATCTG 0.975647 -92 TGTTCTCCCTATAAAATTTGGCGTGAACAG 4 100 0 ATAAAATTTG 0.850605 -75 ATGTAGGCTCTTGAAATATTGTTCTCCCTA 4 119 0 TTGAAATATT 0.970649 -56 ********** Masking position 5 Map Score: 4.61059 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 282 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 ATTCTCACTTTTATAAGGAT 1 16 0 ATTCTCACTT 0.959017 -10 GTTTATTCATAACCGCACTTTTTCCTTTAA 3 95 1 AACCGCACTT 0.962011 -58 TTGAAATTTTAACCGCACTTTTAAAGGAAA 3 115 0 AACCGCACTT 0.962011 -38 ACGTTCTTCCTAAAAAGATTGA 3 141 0 GTTCTTCCTA 0.882419 -12 ACGGACTAAAGTCCGCCCGACAAAAATATT 4 16 0 GTCCGCCCGA 0.977975 -159 CCTACGATAAATTCGCTCTAATTGTTTGTA 4 54 0 ATTCGCTCTA 0.961399 -121 TTGAAATATTGTTCTCCCTATAAAATTTGG 4 109 0 GTTCTCCCTA 0.98301 -66 ********** Masking position 4 Map Score: 4.93072 Number of sites scoring better than the average of aligned sites = 1200 Number in coding regions = 839 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 5 ATTTGATCCTTATAAAAGTGAGAAT 1 8 1 CCTAAAATGA 0.98129 -18 TTCGACCACCAAAAATCGAAAAAACCAGT 2 6 1 CCACAAACGA 0.978709 -52 GTATAATGTGCCACACAAAAAGGATTAAAA 2 38 1 CCAAAAAGGA 0.984746 -20 GTGAATTTCGCCAAAAATACTCGATTTTC 3 6 0 CCAAAACCGA 0.989894 -147 GTAATCTTTGCAACACAAAAGTAAGTTTATTCAT 3 71 1 CAAAAAATAA 0.785431 -82 ACGTTCTTCCTAAAAAGATTGAAATTTTAACC 3 131 0 CCTAAGATGA 0.933044 -22 AGTCCGTATTTCATATACAAACAATTAGAGCGAA 4 39 1 TCAAAAACAA 0.900534 -136 GTCCGTTTAGTCAGATAGACGTGAATTTTTATGT 4 145 0 TCAAAACTGA 0.946476 -30 *** * * ** *** Masking position 7 Map Score: 4.60808 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 289 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 ********** No masking Map Score: -6.86222e-14 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: -6.86222e-14 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: -6.86222e-14 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