Table 2. Selection criteria for 2 rounds of pairwise alignment.

Step of Filtering	1st pairwise alignment		2nd pairwise alignment
Segment of LTR tail used for alignment	5A	3A	5B	3B
Length of the LTR tail segment in bp	30	63	19	19
Minimum alignment length in bp	20	43	12	12
Minimum identity level in percent	90	90	80	80