Ryan's Blog


Posted in Uncategorized by ryanlayer on January 14, 2010
  1. Sequence name
  2. Sequence
  3. Type of match: NM – no match found. QC – no matching done: QC failure (too many Ns basically). RM – no matching done: repeat masked (may be seen if repeatFile.txt was specified). U0 – Best match found was a unique exact match. U1 – Best match found was a unique 1-error match. U2 – Best match found was a unique 2-error match. R0 – Multiple exact matches found. R1 – Multiple 1-error matches found, no exact matches. R2 – Multiple 2-error matches found, no exact or 1-error matches.
  4. x:y:z where x, y, and z are the number of exact, single-error, and 2-error matches found
  5. Blank, if no matches found or if too many matches found, or the following: BAC_plus_vector.fa:163022R1,170128F2,E_coli.fa:3909847R1 This says there are two matches to BAC_plus_vector.fa: one in the reverse direction starting at position 160322 with one error, one in the forward direction starting at position 170128 with two errors. There is also a single-error match to E_coli.fa.
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