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Sequence Alignment Game


  • Try to get as many matches and as few mismatches and gaps as possible
  • Drag a nucleotide to the right to add a gap.
  • Drag to the left to remove a gap.
  • A gap appearing in both sequences at the same location will be automatically removed.
Level 1. Length: 10, Probability of mutation: 20%, Maximum # of deletions: 2
Level 2. Length: 12, Probability of mutation: 30%, Maximum # of deletions: 3
Level 3. Length: 15, Probability of mutation: 40%, Maximum # of deletions: 4

If you wish, you can change the default Match, Mismatch, and Gap scores in the below textboxes.

# A C G T
Match Score
Mismatch Score
Gap Score

Your cumulative score

Created by Minji Kim, Yeonsung Kim, Lei Qian, and Jun S. Song.