Add alignment constraints to handle long sequences

[bredelings]

When aligning long sequences we need to constrain the alignment in order to avoid taking too much CPU time (and RAM).

• allow constraints that residue x[i] is within some distance of residue y[j] instead of requiring that they align exactly.
• allow alignments within some "envelope" around an initial alignment

The problem here is that dynamic programming for 3 or more sequences allows constraints like x[i] <= y[i]. However, we must then decompose the alignment of three sequences into three pairwise alignments. This relaxes the ordering imposed encoding the alignments into paths through the dynamic programming matrix.

Ideas

• Can we impose "not-less-than" constraints instead of "<=" constraints?