AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ipdhR_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP460 146 DIHYDROLIPOAMIDE DEHYDROGENASE PRECURSOR (pdhD) #2 RP530 125 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (pdhC) #3 RP805 249 DIHYDROLIPOAMIDE DEHYDROGENASE (pdhD) Motif number 1 TGTTTATAATATTGTAGTATTGTAA 1 1 1 TTTTAATATT 0.987013 -146 ATAATAATCTTTTTTAAAATATCGTAGTCACACAA 1 42 0 TTTTAATATT 0.987026 -105 CGGTATCTAATCTTTATAATAATCTTTTTTAAAAT 1 57 0 TTTTAATAAT 0.967919 -90 TAGTTATAATATAATCACGTGTGTT 2 1 1 TGTTAATATT 0.932908 -125 TTTATTGAGATTTATGTTATTATTTTTTTTGCATA 2 99 0 TTATTATTAT 0.716778 -27 TTTGTATCGTTGTTTTATATTTTTTAGTTTTTAAG 3 20 1 TTTTTATTTT 0.962417 -230 AAGAGCTAAATGTTTTATATTTCTTAACTGCAATA 3 65 0 TTTTTATTTT 0.962417 -185 AACATTTAGCTCTTTTAAAGATCATCTACTAAATT 3 86 1 TTTTAAGATT 0.935009 -164 ACTGAAAAAATATATAGAATTTAGTAGATGATCTT 3 103 0 TTATAATTTT 0.941004 -147 GATTTCACCTTTTTTGGAATAATTTATACCTTAAA 3 200 1 TTTTAATAAT 0.968183 -50 TTTATTTTTATTTTATTGGTTCTATTT 3 233 0 TTTTATTTTT 0.890932 -17 * *** ***** * Masking position 5 Map Score: 13.5149 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 450 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 TCTTGGCATATTTAACCTTATGATCCTTAT 1 117 0 TTTAACCTTA 0.990063 -30 ACTTCAGGATATAAACCTTATAATACTAGA 2 46 0 ATAAACCTTA 0.929448 -80 AACACTTGATTTTAACCTTTACTGAAAAAA 3 128 0 TTTAACCTTT 0.981617 -122 GGTTATCTCATTTTACCATAGATTTCACCT 3 180 1 TTTTACCATA 0.944915 -70 TTACCATAGATTTCACCTTTTTTGGAATAA 3 192 1 TTTCACCTTT 0.969062 -58 TTGGAATAATTTATACCTTAAAATAGAACC 3 213 1 TTATACCTTA 0.973867 -37 ********** Masking position 5 Map Score: 7.12934 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 40 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 GCATTACAATACTACAATATTATAAACA 1 9 0 ACTACAATAT 0.984261 -138 CTGTTGTGTGACTACGATATTTTAAAAAAG 1 39 1 ACTACGATAT 0.992926 -108 CCGTATATTGACTACGGTATCTAATCTTTA 1 76 0 ACTACGGTAT 0.984463 -71 AAAATATAAAACAACGATACAAATTTTTCA 3 13 0 ACAACGATAC 0.978802 -237 ATATTTCTTAACTGCAATACATACTAGTAC 3 54 0 ACTGCAATAC 0.968166 -196 ********** Masking position 8 Map Score: 6.0437 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 4 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 CGATATTTTAAAAAAGATTATTATAAAGAT 1 53 1 AAAAAGATTA 0.855438 -94 AGGCTTATGCAAAAAAAATAATAACATAAA 2 94 1 AAAAAAAATA 0.973822 -32 CTTAAAAACTAAAAAATATAAAACAACGAT 3 25 0 AAAAAATATA 0.979746 -225 TATTGCAGTTAAGAAATATAAAACATTTAG 3 65 1 AAGAAATATA 0.975701 -185 ACCTTTACTGAAAAAATATATAGAATTTAG 3 114 0 AAAAAATATA 0.979746 -136 TCAGCATTTAAAGAACTTTATCAACACTTG 3 150 0 AAGAACTTTA 0.864636 -100 GAACCAATAAAATAAAAATAAA 3 238 1 AATAAAAATA 0.918746 -12 ********** Masking position 5 Map Score: 7.61043 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 195 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 TGTTTATAATATTGTAGTATTGTA 1 5 1 TATAATATTG 0.607236 -142 AATATTGTAGTATTGTAATGCCTGTTGTGT 1 18 1 TATTGTAATG 0.944388 -129 GTGACTACGATATTTTAAAAAAGATTATTA 1 46 1 TATTTTAAAA 0.7741 -101 TAAAAAAGATTATTATAAAGATTAGATACC 1 61 1 TATTATAAAG 0.955656 -86 TGTGTTCTAGTATTATAAGGTTTATATCCT 2 41 1 TATTATAAGG 0.91929 -85 AACATTTAGCTCTTTTAAAGATCATCTACT 3 86 1 TCTTTTAAAG 0.948694 -164 TTGATAAAGTTCTTTAAATGCTGAGGTTAT 3 156 1 TCTTTAAATG 0.777202 -94 TTATTGGTTCTATTTTAAGGTATAAATTAT 3 218 0 TATTTTAAGG 0.968847 -32 TTTATTTTTATTTTATTGGTTCTATTTT 3 232 0 TATTTTATTG 0.939756 -18 ********** Masking position 7 Map Score: 8.59173 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 255 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 AGGCATTACAATACTACAATATTATAAACA 1 11 0 ATACTACAAT 0.906028 -136 ACACGTGATTATATTATAACTA 2 3 0 ATATTATAAC 0.867029 -123 AAACCTTATAATACTAGAACACAGTGTCAA 2 34 0 ATACTAGAAC 0.981164 -92 ACTAAAAAATATAAAACAACGATACAAATT 3 18 0 ATAAAACAAC 0.88573 -232 ACTGCAATACATACTAGTACTTAAAAACTA 3 44 0 ATACTAGTAC 0.82875 -206 TTTATACCTTAAAATAGAACCAATAAAATA 3 222 1 AAAATAGAAC 0.918533 -28 ********** Masking position 6 Map Score: 2.48719 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 115 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 ********** No masking Map Score: -9.78117e-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: -9.78117e-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: -9.78117e-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