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What are the lower case grey letters in the query sequence in BLAST results?

April 26, 2017blast Case Grey letters lower query results sequence

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What are the lower case grey letters in the query sequence in BLAST results?

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You are seeing the result of automatic filtering of your query for low-complexity sequence. This filter is on by default on most pages in order to prevent alignments that many consider to be artifacts. The filter substitutes any low-complexity sequence with lowercase grey characters. This allows you to see the sequence that was filtered instead of the “X”s and “N”s of the previous BLAST output.