  A new perspective is introduced regarding the analysis of Multiple Sequence
Alignments (MSA), representing aligned data defined over a finite alphabet of
symbols. The framework is designed to produce a block decomposition of an MSA,
where each block is comprised of sequences exhibiting a certain site-coherence.
The key component of this framework is an information theoretical potential
defined on pairs of sites (links) within the MSA. This potential quantifies the
expected drop in variation of information between the two constituent sites,
where the expectation is taken with respect to all possible sub-alignments,
obtained by removing a finite, fixed collection of rows. It is proved that the
potential is zero for linked sites representing columns, whose symbols are in
bijective correspondence and it is strictly positive, otherwise. It is
furthermore shown that the potential assumes its unique minimum for links at
which each symbol pair appears with the same multiplicity. Finally, an
application is presented regarding anomaly detection in an MSA, composed of
inverse fold solutions of a fixed tRNA secondary structure, where the anomalies
are represented by inverse fold solutions of a different RNA structure.
