BLAT-Based Comparative Analysis for Transposable Elements: BLATCAT

Table 2

Description of the RepeatMasker attributes.

Attribute	Description
SW score	Smith-Waterman score of the match, usually complexity adjusted
Perc div.	Percentage of substitutions in matching region compared to the consensus
Perc del.	Percentage of bases opposite a gap in the query sequence (deleted bp)
Perc ins.	Percentage of bases opposite a gap in the repeat sequence (inserted bp)
Query sequence	Name of query sequence
Position in query
Begin	Starting position of match in query sequence
End	Ending position of match in query sequence
(Left)	Number of bases in query sequence past the ending position of match
Matching repeat	Match is with the complement of the consensus sequence in the database
Repeat class/family	Name of the matching interspersed repeat
Position in repeat
Begin	The class of the repeat
End	Number of bases in (complement of) the repeat consensus sequence prior to beginning of the match
(Left)	Starting position of match in database sequence (using top-strand numbering)
ID	Ending position of match in database sequence