-j,

-J,

The three parameters control the extension of LTRs. An example of 2 neighbouring LTR pairs is shown in Figure 3. If and are similar enough, we extend LTRs from and to and .

and are pre-sorted so that , and . Since and are two exact match
pairs, we know

Obviously, the gap lengthes between them are

Introduce , number of base differences resulting from extension, as

where is the number of different(mismatches and indels) bases from global alignment of and . The similarity of merged loci is then:

When LTR_FINDER decides whether two neighboring pairs should be merged, it first calculates , make sure that it does not exceed the value of extension max gap, then calculates . If , pair extension will stop here, will be reported as a candidate for LTR element; If , new pair and inter-pair regions will be linked to the previous one to construct a longer new pair , and LTR_FINDER continues to find next neighboring pairs; if , it means we are not sure whether continue to extend or stop. So LTR_FINDER first report a LTR element candidate while at the same time, the extension process will continue.