sigma-align - 1.1.3-9+b1 main

Sigma (“Simple greedy multiple alignment”) is an alignment program. It's
algorithm and scoring scheme are designed specifically for non-coding
DNA sequence.
.
It uses a strategy of seeking the best possible gapless local
alignments. This happens at each step making the best possible alignment
consistent with existing alignments. It scores the significance of the
alignment based on the lengths of the aligned fragments and a background
model. These may be supplied or estimated from an auxiliary file of
intergenic DNA.