TimelyScholarFree Tools › Dot Plot Sequence Alignment
Compare two sequences visually. A dot marks each pair of positions where a window of the two sequences matches, so similar regions appear as diagonal lines and repeats as parallel lines.
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70 matching windows. Diagonal lines show similar regions and parallel diagonals show repeats; lines running from top-right to bottom-left show a segment in reversed order. To find reverse-complement matches (such as inverted repeats), compare sequence 1 with the reverse complement of sequence 2. Increase the window or the matches required to reduce noise.
DNA, RNA or protein; up to 3,000 letters each.
Longer windows and more required matches reduce noise.
Diagonals, repeats and breaks between them.
A dot plot places one sequence along each axis and marks positions where the sequences match. Identical sequences give a single main diagonal; insertions and deletions shift it; repeated segments give parallel diagonals.
Using a sliding window and requiring a minimum number of matches within it filters out random single-letter matches and makes real similarity stand out.
Compare the first sequence with the reverse complement of the second (use the reverse complement tool first).