AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ipdhR_ctra_opreg_100.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pdhA 221 Pyruvate Dehydrogenase Alpha #2 sucB_2 245 Dihydrolipoamide Succinyltransferase #3 lpdA 208 Lipoamide Dehydrogenase Motif number 1 CCAGAGTGAAATTCAAAAGATTTATTTGAA 1 158 1 ATTCAAAAGA 0.65791 -64 GGAACCCTTTATCCAAGAGAATCT 1 208 1 ATCCAAGAGA 0.895171 -14 AGATCTTTTAACGAAGAGGGTTTTCTCTC 2 10 1 AACGAAGAGG 0.959617 -236 CCTTAAAGAAAACGAAGAGAGAAAACCCTC 2 26 0 AACGAAGAGA 0.977015 -220 GTTAACTCAATATGAGAAGAAGATTATCAA 2 187 0 TATGAGAAGA 0.79768 -59 CGAGTTCAGAAATAAGGAGATTC 2 233 1 AATAAGGAGA 0.908189 -13 GGAGAAGTGGTAGCAGGAGAGAAAAAATAG 3 24 0 TAGCAGGAGA 0.910728 -185 ATAAAATCTCAATGAGGAGAAGTGGTAGCA 3 39 0 AATGAGGAGA 0.980482 -170 CTTTCTAGGAAAGGAAAAGAGAGGTCCTTC 3 105 0 AAGGAAAAGA 0.924952 -104 TAGAAAGGCTTGGAAGGAGAATCCTCTTCC 3 128 1 TGGAAGGAGA 0.688785 -81 TGATTATCTGAGGGAAGAGGATTCTCCTTC 3 140 0 AGGGAAGAGG 0.938487 -69 CTAAACACTCATTGAAGAGGAAATGTT 3 192 1 ATTGAAGAGG 0.916511 -17 ********** Masking position 5 Map Score: 11.6161 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 798 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 2 TTCGGCACTACCCAGAAAAATGGATAGAGA 1 29 0 CCCAGAAAAA 0.964442 -193 AAGTCTATGCTACAAAAAAAAACTTTTCGG 1 54 0 TACAAAAAAA 0.908733 -168 TAGAATGTCTTTCAAATAAATCTTTTGAAT 1 168 0 TTCAAATAAA 0.893366 -54 GATAAAGGGTTCCTGAAAAATTCTAGAATG 1 191 0 TCCTGAAAAA 0.842771 -31 TTTTTGAAACCACAGAAAAGACGCTTAAAC 2 55 0 CACAGAAAAG 0.86968 -191 TTTCTGTGGTTTCAAAAAATGTTTAGTGTA 2 67 1 TTCAAAAAAT 0.834645 -179 AACTGGCTTTTACAGATAAAAAATGCCTTT 2 159 0 TACAGATAAA 0.948745 -87 AGCCTTCGAGTTCAGAAATAAGGAGATTC 2 227 1 TTCAGAAATA 0.888462 -19 AGAGAGGTCCTTCAGACAAATACATTTCCC 3 88 0 TTCAGACAAA 0.945708 -121 ATCCTCTTCCCTCAGATAATCATCTCATAT 3 148 1 CTCAGATAAT 0.869817 -61 ********** Masking position 6 Map Score: 7.52828 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 418 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 3 TCGGCACTACCCAGAAAAATGGATAGAGAT 1 28 0 CCAGAAAAAT 0.871681 -194 TCTGGGTAGTGCCGAAAAGTTTTTTTTTGT 1 43 1 GCCGAAAAGT 0.977787 -179 GGAAAAGTAACCGGAAAGGTCCGGCCTTCG 1 111 0 CCGGAAAGGT 0.985954 -111 CAAGGCCGGCGCGGAAAAGTAACCGGAAAG 1 123 0 GCGGAAAAGT 0.994818 -99 ATAAAGGGTTCCTGAAAAATTCTAGAATGT 1 190 0 CCTGAAAAAT 0.871681 -32 AAATCTCAATGAGGAGAAGTGGTAGCAGGA 3 36 0 GAGGAGAAGT 0.932932 -173 ATGTACAACCCGGGAAATGTATTTGTCTGA 3 77 1 CGGGAAATGT 0.950371 -132 ACTCATTGAAGAGGAAATGTT 3 198 1 GAGGAAATGT 0.957953 -11 ********** Masking position 5 Map Score: 7.75838 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 91 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 4 TTTTAACGAAGAGGGTTTTCTCTCTTCGTT 2 16 1 GAGGGTTTTC 0.970273 -230 TCGTTTTCTTTAAGGTTTAAGCGTCTTTTC 2 41 1 TAAGGTTTAA 0.876138 -205 GTAACATAGGGAGTGCTTAACCGCCTTCAG 2 94 1 GAGTGCTTAA 0.974292 -152 AATGCCTTTTGAGGGTTTAATAACATGAAA 2 138 0 GAGGGTTTAA 0.992664 -108 TTCTGAACTCGAAGGCTTTAGTATTCTGTT 2 214 0 GAAGGCTTTA 0.950104 -32 CCTCTTCAATGAGTGTTTAGGATTGCAACG 3 182 0 GAGTGTTTAG 0.953702 -27 ********** Masking position 7 Map Score: 3.66842 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 62 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 5 ********** No masking Map Score: -1.76682e-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: -1.76682e-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: -1.76682e-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