| A compressed alignments 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.
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: |