The gap character being used for the shared alphabet between the reference and query sequence.

Original sequence

Original sequence #2

Columns in ScoreTable

This array keeps track of the length of gaps up to a point along the horizontal axis. Only used with the affine gap model

The query sequence being aligned (sequence #2)

The reference sequence being aligned (sequence #1)

Rows in ScoreTable

Generated score table - this is filled in with the scoring matrix when debugging

Traceback table built during the matrix creation step

A variable to keep track of whether the traceback table was constructed with an affine gap model.

This array keeps track of the length of gaps up to a point along the vertical axis. nly used with the affine gap model.