Homologous matches of an candidate. The lines represent matches generated by whole-genome homology search of a reference candidate. Some matches are made of several pieces (segments on the same horizontal line). All the matches are categorized into Part I and Part II. Part I (Rset) consists of the matches that cover both the LTR region and the internal domain. They are reliable copies of the reference candidate. Part II is further classified into pseudo-copies and "copies in part II". Pseudo-copies are the matches that correspond to unrelated sequences. Unrelated sequences (dark grey regions) are the subregions that have significantly high matches (grey stripes) or that match some LTR elements well (not showing here). At last, "copies in part II" and Rset are combined to obtain the total copies of the candidate.