Reverse complement calculator (single or FASTA batch)
Maintained by the Talindrew team · Last updated
The reverse complement of a DNA sequence is the opposite strand read 5′→3′: complement every base (A↔T, G↔C), then reverse the order. It is the sequence a reverse primer must match and what the antisense strand reads. IUPAC ambiguity codes complement in pairs (R↔Y, K↔M; S, W and N map to themselves).
Result
The reverse complement is the sequence of the opposite strand read 5′→3′, what you order as the reverse primer's template match. Paste several sequences as FASTA to convert them all at once. IUPAC codes complement per Cornish-Bowden 1985.
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What it looks like
Formula
revcomp(s) = reverse(complement(s)), A↔T · G↔C · R↔Y · K↔M · B↔V · D↔H · S,W,N ↔ themselves
Worked example
Given: 5′-ATGGCTAGC-3′
- 1.Complement each base: TACCGATCG (read 3′→5′).
- 2.Reverse the order: GCTAGCCAT.
Reverse complement = 5′-GCTAGCCAT-3′
How the calculation flows
Units & constants
| Alphabet | A C G T (U → T) plus all IUPAC ambiguity codes |
|---|---|
| Outputs | Reverse complement, complement (3′→5′), reverse |
| Input cleanup | Whitespace, line numbers and FASTA breaks stripped automatically |
| Typical uses | Reverse-primer design, antisense probes, reading the minus strand |
| Price | Free |
Which output do you actually want?
Almost always the reverse complement. The plain complement (3′→5′) is chemically the other strand but written backwards from how oligos are ordered; the plain reverse is rarely meaningful biologically. If you are ordering a reverse primer against a displayed top strand, take the reverse complement of the region the primer should cover: that is the sequence you paste into the order form, 5′→3′.
How do ambiguity codes complement?
Each IUPAC code maps to the code for the complementary base set: R (A/G) ↔ Y (C/T), K (G/T) ↔ M (A/C), B (not-A) ↔ V (not-T), D (not-C) ↔ H (not-G). S (G/C), W (A/T) and N are their own complements because their base sets are self-complementary. Degenerate primer designs survive reverse-complementation unchanged in degeneracy.
Frequently asked questions
Yes, for a coding (sense) sequence: the antisense strand is its reverse complement. mRNA-targeting probes and reverse primers are designed as reverse complements of the sense sequence.
U is accepted and treated as T on input. Output is written in DNA alphabet; for an RNA reverse complement, replace T with U in the result.
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