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4.8 Repeat Mask Viewer

4.8.1 How to read the results of Repeat Mask Viewer

In this viewer are listed all best matches between the query sequence and any of the sequences in the repeat database or containing low complexity DNA. The term "best matches" reflects that a match is not shown if its domain is over 80% contained within the domain of a higher scoring match, where the "domain" of a match is the region in the query sequence that is defined by the alignment start and stop. These domains are indicated in small letters in the lower left frame with the title "Masked Sequence" in this viewer. The information for these domains is shown in the upper frame. The original cDNA sequence is shown in the lower right frame with the title "Original Sequence". We used the following version:
RepeatMasker version 2004/03/06, default mode run with cross_match version 0.990329. RepBase Update 8.12, RM database version 20040306

4.8.2 Information on repetitive sequences in the upper frame;

No.: Number assigned to each repetitive sequence in the cDNA
SW score: Smith-Waterman score of the match, usually complexity adjusted The SW scores are not always directly comparable. Sometimes the complexity adjustment has been turned off, and a variety of scoring matrices are used dependent on repeat age and GC level.
perc div.: % substitutions in matching region compared to the consensus.
perc del.: % of bases opposite a gap in the query sequence (deleted bp).
perc ins.: % of bases opposite a gap in the repeat consensus (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): no. of bases in query sequence past the ending position of match.
strand: the strand of the repeat consensus sequence in the alignment with the query sequence
matching repeat: name of the matching interspersed repeat.
repeat class/family: the class of the repeat.
position in repeat
begin: starting position of match in repeat consensus sequence.
end: ending position of match in repeat consensus sequence.
(left): no. of bases in (complement of) the repeat consensus sequence prior to beginning of the match (0 means that the match extended all the way to the end of the repeat consensus sequence).
ID: unique identifier for individual insertions.

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  3. Jurka, J. Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 8, 333-7 (1998).
  4. Smit, A. F. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6, 743-8 (1996).
  5. Smit, A. F. Origin and evolution of mammalian interspersed repeats. PhD dissertation, USC (1995).
Revised: March 30, 2007