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 |