This website supplements the DIMACS Educational Module, entitled "Finding Repeats Within Strings."   Enter a sequence in the textbox and the repeats in the string will be shown. The Smith-Waterman algorithm aligns the string with itself using dynamic programming. You can view the matrices, in which the path of the optimal alignment is marked with a * and the "affected" cells are marked with a $. For more details, see the complete module at http://dimacs.rutgers.edu/Publications/Modules/moduleslist.html.
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Match Score
Mismatch Score
Gap Penalty
Error Threshold
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