+ // Cigar array meanings:
+ // M = match
+ // D = deletion
+ // I = insertion
+ // number preceding M/D/I is the number of residues which
+ // match/are deleted/are inserted
+ // In the CigarArray constructor only matches or deletions are created, as
+ // we are comparing a sequence to its own subsequence (the group) + hidden
+ // columns.
+
+ // no hidden columns case
+ CigarArray cig = new CigarArray(al, null, sg1);