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 n C. 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
