Fig. 2

Secondary structure of mtDNA. A Clusters of deletions within the major arc. The majority of clusters are located close to each other within the potential contact zone. The colors on the scheme on top correspond to the clusters. The vertical density plots on the right part of the figure demonstrate the distribution of deletion centers: real (observed) and random (expected). B Realized (red) versus non-realized (gray) repeats tend to be enriched in the potential contact zone. Mosaic-plot of repeats (realized versus non-realized) within and outside the potential contact zone. C Bottom-left: heatmap of the microhomologies between 100 bp windows within the major arc. Microhomology alone poorly explains the distribution of the deletions (empty circles). Top right: heatmap of the data-driven contact zone, based on the AIC of the compared models. D In silico approach for major arc global folding prediction. Bottom left triangle: contact matrix derived from the in silico folding estimation of the major arc's whole single-stranded heavy chain; top right triangle: contact matrix derived from the in silico folding estimation of 100 bp windows of the single-stranded heavy chain of the major arc