AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #2 HI0967 25 H. influenzae predicted coding region HI0967 #3 HI0970 57 3-dehydroquinase (aroQ) #4 HI0971 152 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) #5 HI0972 174 acetyl-CoA carboxylase, biotin carboxylase (accC) Motif number 1 AGGACGAGGTCGCACATTATAACGATTTCG 1 25 0 CGCACATTAT 0.933599 -276 TCCTCCCTGACGCAGTTTTTGCGCTGCGGA 1 51 1 CGCAGTTTTT 0.953786 -250 TTAGACTTGACGGACATTGTGCAGCGATCT 1 137 0 CGGACATTGT 0.858959 -164 GAGTGGGTTCCGTACTCTTTGTTTAGTGTG 1 281 0 CGTACTCTTT 0.947654 -20 ATTCTCACTTTTATAAGGATCAA 2 13 0 CTCACTTTTA 0.917481 -13 AGAATTTTATCGCAAATTTGAAAAAATTAA 4 40 1 CGCAAATTTG 0.861413 -113 CAAAGATTACCTTAATTTTTTCAAATTTGC 4 51 0 CTTAATTTTT 0.639834 -102 TATGAATAAACTTACTTTTGTGTTGCAAAG 4 76 0 CTTACTTTTG 0.891424 -77 TATTCATAACCGCACTTTTTCCTTTAAAAG 4 98 1 CGCACTTTTT 0.993765 -55 AAATTTTAACCGCACTTTTAAAGGAAAAAG 4 112 0 CGCACTTTTA 0.980532 -41 TTTTGTCGGGCGGACTTTAGTCCGTATTTC 5 21 1 CGGACTTTAG 0.935525 -154 TCTGACTAAACGGACTCTTTT 5 164 1 CGGACTCTTT 0.966063 -11 ********** Masking position 4 Map Score: 14.9277 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 852 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 GCTGCCAATTGCTACGAAATCGTTATAATG 1 11 1 GCTACGAAAT 0.799852 -290 CACCTTTTCCGCAGCGCAAAAACTGCGTCA 1 58 0 GCAGCGCAAA 0.854971 -243 CTGCTATCCTCCGGCAAAAAACAAAATATA 1 106 0 CCGGCAAAAA 0.974978 -195 GCAGCAGATCGCTGCACAATGTCCGTCAAG 1 132 1 GCTGCACAAT 0.932273 -169 TTGACACTCTGGGGCAAAATAGACCGGCGT 1 169 1 GGGGCAAAAT 0.766797 -132 TTCGACCACCAAAAATCGAAAAAAC 3 6 1 CCACCAAAAA 0.761722 -52 ATCGAAAAAACCAGTATAATGTGCCACACA 3 25 1 CCAGTATAAT 0.589113 -33 AGTATAATGTGCCACACAAAAAGGATTAAA 3 37 1 GCCACACAAA 0.88274 -21 TTTCAAATTTGCGATAAAATTCTGTGAATT 4 33 0 GCGATAAAAT 0.911534 -120 GGTAATCTTTGCAACACAAAAGTAAGTTTA 4 70 1 GCAACACAAA 0.943538 -83 CTTTAAAAGTGCGGTTAAAATTTCAATCTT 4 119 1 GCGGTTAAAA 0.662869 -34 TAAAGTCCGCCCGACAAAAATATTGGAAA 5 10 0 CCGACAAAAA 0.969753 -165 TTTATCGTAGGCGATATAAATTGAAATCTG 5 73 1 GCGATATAAA 0.858265 -102 TATTGTTCTCCCTATAAAATTTGGCGTGAA 5 103 0 CCTATAAAAT 0.747587 -72 ATTTCAAGAGCCTACATAAAAATTCACGTC 5 132 1 CCTACATAAA 0.844958 -43 ********** Masking position 8 Map Score: 10.9451 Number of sites scoring better than the average of aligned sites = 5024 Number in coding regions = 4452 Number in noncoding regions = 572 Number of orfs with sites within 600 bp upstream = 478 Fraction of orfs with sites within 600 bp upstream = 0.0767748 Motif number 3 AAACTGCGTCAGGGAGGACGAGGTCGCACA 1 39 0 AGGGAGGACG 0.995776 -262 CAATCTTTTTAGGAAGAACGT 4 142 1 AGGAAGAACG 0.990371 -11 CAAATTTTATAGGGAGAACAATATTTCAAG 5 110 1 AGGGAGAACA 0.990371 -65 ********** Masking position 5 Map Score: 1.51891 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 GGGCAAAATAGACCGGCGTCCCGGCCTGCT 1 180 1 GACCGGCGTC 0.932065 -121 CGTATGCCCCGACAGCTGTATGCATAGCGA 1 218 0 GACAGCTGTA 0.550213 -83 ACAGGCGTTTCACCGCCGTCTGTAAAGCGT 1 245 0 CACCGCCGTC 0.881493 -56 GTGTGATTGTGACAGGCGTTTCACCGCCGT 1 256 0 GACAGGCGTT 0.969056 -45 ********** Masking position 2 Map Score: 1.02188 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 275 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AATGTCACCTTTTCCGCAGCGCAAAAACTG 1 63 0 TTTCCGCAGC 0.973458 -238 ATTTTGTTTTTTGCCGGAGGATAGCAGCAG 1 109 1 TTGCCGGAGG 0.986964 -192 TGCCGGAGGATAGCAGCAGATCGCTGCACA 1 120 1 TAGCAGCAGA 0.959095 -181 CCGGTCTATTTTGCCCCAGAGTGTCAATGT 1 166 0 TTGCCCCAGA 0.980142 -135 TAGCGATAAATTCCAGCAGGCCGGGACGCC 1 194 0 TTCCAGCAGG 0.97803 -107 ********** Masking position 8 Map Score: 0.925248 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 880 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 GCTGCCAATTGCTACGAAATC 1 2 1 CTGCCAATTG 0.842402 -299 TACCTTCGTTGCGCCAATGTCACCTTTTCC 1 78 0 GCGCCAATGT 0.970824 -223 TTGCCCCAGAGTGTCAATGTTAGACTTGAC 1 156 0 GTGTCAATGT 0.970791 -145 TCTTTGTTTAGTGTGATTGTGACAGGCGTT 1 266 0 GTGTGATTGT 0.900627 -35 CGATAAAATTCTGTGAATTTCGCCAAAAAT 4 22 0 CTGTGAATTT 0.949736 -131 CAAACAATTAGAGCGAATTTATCGTAGGCG 5 56 1 GAGCGAATTT 0.929917 -119 AGTCAGATAGACGTGAATTTTTATGTAGGC 5 141 0 ACGTGAATTT 0.851693 -34 ********** Masking position 6 Map Score: 0.75396 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 374 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 ********** No masking Map Score: -7.50743e-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: -7.50743e-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 ********** No masking Map Score: -7.50743e-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