Parsing a pair of sequences (X, Y) using the Inside algorithm involves iterating over subsequence-pairs (Xij, Ykl) specified by four indices (i, j, k, l). In the constrained Inside algorithm, these indices are only valid if the fold envelopes (triangular grids) include the respective subsequences (i, j) and (k, l) (shown as black circles) and the alignment envelope (rectangular grid) includes both cutpoints (i, k) and (j, l) (shown as short diagonal lines). The filled cells in the rectangular grid show the aligned nucleotides. Note that the co-ordinates (i, j, k, l) lie on the grid-lines between the nucleotides.
Holmes BMC Bioinformatics 2005 6:73 doi:10.1186/1471-2105-6-73