In principle one can have the following alignment:

XXXXXXXXXXA--------
----------AYYYYYYYY

It has a 100% sequence identity! The previously implemented logic of gap
thresholds was also not very helpfil to filter out these cases as it
operated on fraction of gaps between first and last aligned column in
the alignment. That's 0.0 and thus perfect.

This commit simplifies this logic and simply checks for a sequence identity
threshold and a minimum number of aligned columns when grouping sequences
together. This should make grouping these cases together very unlikely.