Reverse complement
Generate the reverse, complement or reverse complement of a sequence.
Result
0 nt
3'→5' complement, read 5'→3'- IUPAC nucleotide ambiguity codes — Nucleic Acids Research, 1985
When to use this
Use this to get the complement, the reverse, or the reverse complement of a DNA or RNA sequence. The reverse complement is the one you almost always want: it is the opposite strand written the conventional way, and it is what a reverse primer has to be.
Worked example
You need the reverse primer for a region beginning 5′-ATGGCTAGCTAG-3′.
- Sequence
- 5′-ATGGCTAGCTAG-3′
Result
That is the sequence to order. The plain complement, CATCGATCGATC, anneals to nothing useful because it is written backwards.
What people get wrong
- Ordering the complement instead of the reverse complement. It looks like a plausible sequence and anneals nowhere, and the error only surfaces after a failed PCR.
- Losing the strand convention. Sequences are written 5′ to 3′; a reverse complement written the other way round is the same molecule described unusably.
- Assuming ambiguity codes are handled elsewhere. This tool is IUPAC-aware, so N, R, Y and the rest complement correctly rather than being dropped.
Questions
+What is the difference between complement and reverse complement?
The complement swaps each base for its partner in place. The reverse complement does that and then reverses the order, which is how the opposite strand is actually written.
+Does it handle RNA?
Yes — U is treated as T for pairing, and you can ask for the RNA form of the output.
+Are lower case and line breaks a problem?
No. Whitespace, numbers and case are cleaned up; FASTA headers are ignored.
Related tools
- GC content calculator — Measure GC content and base composition of a nucleotide sequence.
- DNA translation — Translate a nucleotide sequence into protein in any reading frame.
Science last reviewed .