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. 2020 Oct 27;11:560332. doi: 10.3389/fmicb.2020.560332

FIGURE 3.

FIGURE 3

Comparison of a segment of the mtDNA genomic sequence surrounding the longest insert (25 + 2 nt, red letters) observed in the clade IV haplotype from Colombia and Venezuela (bottom), in the intergenic region between NAD5 and tRNA-Ser, and the corresponding sequence of reference clade I isolate B8441 from Pakistan (top). Stemloop diagrams show one of the predicted optimal structures of the clade IV sequence, obtained using UNAFold with default settings (Markham and Zuker, 2008), which has a more complex stemloop component that is absent among the simpler optimal structures predicted for the B8441 sequence. A subsequence that is repeated in the clade IV haplotype but not in the B8441 isolate is underlined. A possible C–G pairing that could thermodynamically lead to the different folding shown for the clade IV haplotype is shown in blue letters. Red letters and bars indicate, respectively, the bases of the clade IV haplotype that are absent in the clade I haplotype, and the corresponding positions in the clade I haplotype (B8441 mtDNA genome coordinates 14,285 and 14,291).