AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -iarcA_mpneu_opreg_100.orf -g0.400 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 1673933 141 D02_orf109 Protein #2 pdhC 300 dihydrolipoamide acetyltransferase component (E2); similar to Swiss-Prot Accession Number P35489, from A. laidlawii Motif number 1 AAAATAAGTCAAAAATGGAACTGTTAAACAG 1 35 0 AAAATGGAAC 0.845432 -107 TAAGAGCTTTAAAAATAAGTCAAAAATGGAA 1 46 0 AAAATAAGTC 0.962105 -96 CGTAAATCTGGAAATTCAAACAGGATAGTAG 1 93 1 GAAATCAAAC 0.912776 -49 TTATTCTAACAAACCCCAAACTTATTTCAAA 2 19 0 AAACCCAAAC 0.918947 -282 CTGTGGTTGCAAAACCGAAACAGCTAACTGC 2 131 1 AAAACGAAAC 0.966004 -170 AAATGCTGCCAAAAATAAGGCGAAATTTCTC 2 186 1 AAAATAAGGC 0.964798 -115 GTTTTAGATAAAAAGCCAGTCGTAAGACTGG 2 225 1 AAAACCAGTC 0.977593 -76 AATGCAAATAAAAAACCAGTCTTACGACTGG 2 240 0 AAAACCAGTC 0.977593 -61 GATTTAAAGCAAAAGTAATGCAAATAAAAAA 2 256 0 AAAATAATGC 0.840048 -45 CTTTAAATCTAAAATTAAAACAGTTTTTATA 2 278 1 AAAATAAAAC 0.969359 -23 **** ****** Masking position 3 Map Score: 9.64827 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 199 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 GAACGCGTAATTTTAGCTAAGAGCTTTAAA 1 64 0 TTTTAGCTAA 0.978833 -78 TCAAACAGGATAGTAGATAACAAATAATGT 1 108 1 TAGTAGATAA 0.917599 -34 TCAAGCCATTTGAAATAAGTTTGGGGTT 2 9 1 TTTGAAATAA 0.967326 -292 CACCTAGTTTTTTTAACTAAAAGTTGAGAA 2 53 1 TTTTAACTAA 0.967326 -248 TCCATCTTAATATGAAATAAATGGTGTTCC 2 89 0 TATGAAATAA 0.94137 -212 CTAAATTTCGTTTTAGATAAAAAGCCAGTC 2 216 1 TTTTAGATAA 0.982242 -85 ********** Masking position 5 Map Score: 6.07958 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 58 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 3 ATAAGTCAAAAATGGAACTGTTAAACAGCT 1 33 0 AATGGAACTG 0.969012 -109 CCCCAAACTTATTTCAAATGGCTTGA 2 7 0 ATTTCAAATG 0.930641 -294 TGTTAGAATAATTGCACCTAGTTTTTTTAA 2 39 1 ATTGCACCTA 0.94398 -262 AACTGCAGTAAATGCAACTGTGGCGGTTGC 2 156 1 AATGCAACTG 0.99272 -145 AACTGTGGCGGTTGCAAATGCTGCCAAAAA 2 171 1 GTTGCAAATG 0.969432 -130 AAGCAAAAGTAATGCAAATAAAAAACCAGT 2 251 0 AATGCAAATA 0.966983 -50 ********** Masking position 6 Map Score: 5.2118 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 69 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 CTGTTAAACAGCTAAATTACAACAAAAAAT 1 16 0 GCTAAATTAC 0.960439 -126 ATTTACGAACGCGTAATTTTAGCTAAGAGC 1 70 0 GCGTAATTTT 0.943428 -72 TCAAAATTTTCCCTACATTA 1 132 0 TCAAAATTTT 0.899273 -10 CAAAAATAAGGCGAAATTTCTCTAAATTTC 2 195 1 GCGAAATTTC 0.991952 -106 GCGAAATTTCTCTAAATTTCGTTTTAGATA 2 205 1 TCTAAATTTC 0.97258 -96 ********** Masking position 5 Map Score: 2.97481 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 38 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 AAACAGCTAAATTACAACAAAAAATAACCG 1 11 0 ATTACAACAA 0.964544 -131 AAATCTGGAAATTCAAACAGGATAGTAGAT 1 96 1 ATTCAAACAG 0.987251 -46 AGGTGCAATTATTCTAACAAACCCCAAACT 2 28 0 ATTCTAACAA 0.965972 -273 TAAATCTAAAATTAAAACAGTTTTTATATC 2 281 1 ATTAAAACAG 0.980417 -20 ********** Masking position 6 Map Score: 2.57444 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 32 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 CGGTTATTTTTTGTTGTAATTTAG 1 5 1 TATTTTTTGT 0.942633 -137 ATTTTCCCTACATTATTTGTTATCTACTAT 1 117 0 CATTATTTGT 0.97884 -25 TAATTGCACCTAGTTTTTTTAACTAAAAGT 2 47 1 TAGTTTTTTT 0.875496 -254 GCAACCACAGCATTTCTTGTCTTCCATCTT 2 111 0 CATTTCTTGT 0.975923 -190 AGAAATTTCGCCTTATTTTTGGCAGCATTT 2 186 0 CCTTATTTTT 0.900519 -115 TTTTTATTTGCATTACTTTTGCTTTAAATC 2 257 1 CATTACTTTT 0.951915 -44 AAAATTAAAACAGTTTTTATATC 2 288 1 CAGTTTTTAT 0.910729 -13 ********** Masking position 4 Map Score: 5.32554 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 93 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ********** No masking Map Score: 2.29806e-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: 2.29806e-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: 2.29806e-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