Figure 1.

Flowchart of LIR searching algorithm in Lirex

For a pair of seeds located in a DNA window of a defined size, pairing seeds are extended both inward and outward. If seeds extend to >30 bp with GC >20% and repeat identity >85%, the seeds are considered as the primary LIRs. A final list of LIRs was generated after filtering and merging the redundant LIRs. When the ratio of repeat length to internal spacer, δ, is greater or equal to mismatch rate between repeat copies, the LIR is considered to be recombinogenic. LIR, long inverted repeat.