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Compressed alignments

A compressed alignment represents an alignment in a compact format that does not include the sequence letters. The representation uses run-length encoding, as follows. Each column in the alignment is classified as M, D or I.
Column   Description
M   Match. A pair of letters.
D   Delete. A gap in the target.
I   Insert. A gap in the query.

If there are n consecutive columns of type C, this is represented as nC. For example, 123M is 123 consecutive matches. As a special case, if n=1 then n is omitted. So for example, D5M2I3M represents an alignment of this form:
   Query    XXXXXX--XXX
  Target   -XXXXXXXXXX