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4.8 Repeat Mask Viewer -反復配列情報

4.8.1 Repeat Mask Viewer表示情報

Repeat Mask Viewerは、RepBaseに登録された反復配列検出結果を表示する画面です。Repeat Mask ViewerはcDNA viewの”cDNA information”セクションからリンクしています。解析対象の入力塩基配列"Original Sequence"は左下フレームに表示されます。塩基配列上に検出された反復配列は右下フレーム"Masked Sequence"では赤でマークされています。反復配列の情報は上フレームに表形式で表示されています。

4.8.2 反復配列情報テーブル(上フレーム)


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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