See also
Sequence identity
show_termgaps option
Terminal gaps
A terminal gap is an alignment gap which starts in the first column
or ends in the last column. Local alignments
never have terminal gaps.
Internal gaps
An internal gap is any gap that is not a terminal gap. Local alignments may
have internal gaps.
Example
The global alignment below has terminal and internal gaps indicated. The -show_termgaps
option was used for the ‑alnout output file. Note
that the number of columns (302 in this example) is always reported without
terminal gaps, as these are the columns used to calculate
identity.
