Analysis of direct repeat (DR) motifs in mitochondrial genomes.

<p>Abundance, distribution and free energy of DRs in mtDNA and random DNA sequences (<i>n</i> = 100) with the same base composition (R1) as corresponding mtDNA. (A) Frequency of DR pairs (≥6 bp) in the mtDNA of human, rhesus monkey, mouse and rat. The DR frequency is normalized with respect to the mtDNA length in each species. (B) The distribution of left and right DR sequences in the minor and major arcs of human mtDNA and the mean distribution of DRs in R1 random sequences. (C) DR sizes and DR free energies in human mtDNA and the corresponding R1 random sequences. The lower the free energy of a DR, i.e. the more negative, the more stable is the DNA duplex formed. (D) Distribution of free energies of DNA duplex formed by DRs (≥6 bp) in native mtDNA and random sequences (R1) of human, rhesus monkey, mouse and rat.