If you really want help with this problem, put together a small test suite that gives some inputs and some sample outputs (that you tabulate by hand) and wait for someone to produce a MATLAB function to do what you want.
This is an interesting problem. Acting as an administrator, I cleaned it up and added some tests.
DNA N-Gram Distribution
Find matching parenthesis
Reindex a vector
Generate a random matrix A of (1,-1)
subtract central cross
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