You have been very polite and my inclination is to help you. Please make it easier to do so.

You have provided us with your current solution to a problem, but you haven't specified what that problem is. It is difficult to identify what areas might be unneccesary or wasteful in this situation.

Some inline documentation would be useful, as would some additional comments in this thread. Here are a few things that would be nice to know:

• Why is $distance_index and $window random
• More sample data. The $sequence provided is 7 characters, but in this comment you state that it can be over 1000 characters in length. The size of the input data will help determine which algorithm is appropriate.
• How often will this function be called

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