Fig. 2.

Searching for repeat unit boundary based on the global alignment. s and e are the current repeat boundaries. Two anchors $A_1(s_1,e_1)$ and $A_2(s_2,e_2)$ are selected as their starting positions are the closest to e. Two subsequences starting from s₁ to s₂ and from e₁ to e₂ are extracted to perform an end-to-end global alignment. The next repeat unit boundary $e\prime$ can be calculated based on the alignment result. In this example, the base G of e is matched with the G in subsequence $[e_1:e_2]$, whose coordinate is then considered as the putative next boundary $e\prime$