Dot Plot Tool - Compare Two Sequences and Find Repeats
See repeats, duplications and inversions that a single best alignment hides.
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A pairwise alignment returns one best path through two sequences, which means it has to choose - and everything it did not choose disappears from the output. A dot plot shows all of it at once: a repeat is an off-diagonal line, a tandem duplication is a line parallel to the main one, and an inversion is a line running the other way, which a normal alignment reports as nothing at all. Compare a sequence with itself to map its own internal repeats, which is the fastest way to see why a construct is unstable or why a primer has more than one binding site. The word size is chosen from your sequence lengths when you leave it blank, because too short a word fills the plot with chance matches that the eye reads as homology.
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Paste two sequences to compare. Pasting the same one twice maps its internal repeats.
How to use the Dot Plot tool
- 1Paste the first sequence, raw or as FASTA.
- 2Paste the second - or press the button to copy the first one across for a self-comparison.
- 3Leave the word size blank to have one picked from the lengths, or raise it if the plot looks noisy.
- 4Read the plot: blue runs are same-strand matches, red runs are reverse-complement matches.
Frequently asked questions
What does a dot plot show that an alignment does not?
Every match at once, rather than one best path. A pairwise alignment picks a single route through the two sequences, so a second copy of a repeated region, a tandem duplication, or an inverted segment is discarded to make that route consistent. On a dot plot each of those is its own line - and an inversion, which appears as a run on the opposite diagonal, is something a standard alignment typically does not report at all.
How do I find repeats within one sequence?
Paste the same sequence into both boxes, or use the copy button. The main diagonal is then the sequence against itself and carries no information; every line off that diagonal is an internal repeat, and a line running the other way is an inverted repeat - the kind that makes a construct unstable and a hairpin fold.
What word size should I use?
Leave it blank and one is chosen from the lengths, sized so that a word of that length recurs by chance about once in the comparison. If the plot still looks like a grey wash, raise it: a short word in long sequences produces thousands of chance matches, and density on a dot plot reads as homology whether or not it is.
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