Fig. 3
From: Global exact optimisations for chloroplast structural haplotype scaffolding
With time, a repeat may degrade so that its occurrences differ. a and c show two common quadripartite structures with an IR and a DR, respectively. b and d highlight the impact of a degeneration on their structures. We give the bellow region orders according to the LSC arrow’s direction. In b, the degeneration results in two IRs: \(IR_1 = (i, j)\) and \(IR_2 = (k, l)\), such that \(i\) is before \(k\) and \(l\) precedes \(j\). In d it results in two DRs: \(DR_1 = (i, j)\) and \(IR_2 = (k, l)\), such that \(i\) is before \(k\) and \(j\) precedes \(l\)