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DNA Reverse Complement Tool
Paste a DNA or RNA sequence, single or multi-record FASTA, and get its reverse complement, complement or reverse instantly. IUPAC ambiguity codes, gaps and letter case are handled correctly.
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Reverse complement
Strand view
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How to use the DNA Reverse Complement Tool
- Paste your sequence into the input box. Plain sequence, numbered GenBank text or FASTA with one or many records all work.
- Choose the operation: Reverse complement (the opposite strand read 5'→3'), Complement or Reverse.
- Pick the output options: DNA or RNA letters, line width, and whether to add a note to FASTA headers.
- Check the warnings. Unusual characters are listed with their positions so you can spot typos.
- Copy or download the result as a .fasta file.
How the reverse complement is calculated
DNA is a double helix of two antiparallel strands. Each base pairs with a fixed partner: adenine (A) with thymine (T), or uracil (U) in RNA, and guanine (G) with cytosine (C). Because the strands run in opposite directions, the partner strand of 5'-ATGCC-3' is 3'-TACGG-5'. Sequences are always written 5'→3', so that strand is written backwards as 5'-GGCAT-3'. That is the reverse complement.
- Complement: swap each base for its partner and keep the order. This is the other strand written 3'→5'.
- Reverse: keep the bases but read them backwards. This is the same strand written 3'→5'. It is rarely needed for biology but useful for checking palindromes and reading traces.
- Reverse complement: complement and reverse. Use it to design reverse primers, read the minus strand of a gene, or check whether a sequence matches the opposite strand of a reference.
IUPAC nucleotide codes and their complements
| Code | Meaning | Bases | Complement |
|---|---|---|---|
| A | Adenine | A | T (U in RNA) |
| C | Cytosine | C | G |
| G | Guanine | G | C |
| T / U | Thymine / Uracil | T or U | A |
| R | Purine | A or G | Y |
| Y | Pyrimidine | C or T | R |
| S | Strong (3 H-bonds) | G or C | S |
| W | Weak (2 H-bonds) | A or T | W |
| K | Keto | G or T | M |
| M | Amino | A or C | K |
| B | Not A | C, G or T | V |
| D | Not C | A, G or T | H |
| H | Not G | A, C or T | D |
| V | Not T | A, C or G | B |
| N | Any base | A, C, G or T | N |
| - or . | Gap | none | kept as gap |
Tips for working with sequences
- Reverse primers: to make a reverse primer that binds the end of your target, take the last 18–25 bases of the target's top strand and use their reverse complement. Check its melting temperature with the Primer Tm Calculator.
- Palindromes: many restriction sites are their own reverse complement. EcoRI's site GAATTC, for example, reads the same on both strands.
- Soft-masking: genome files often mark repeats in lowercase. Keep the "Keep as typed" case option so that masking stays where it belongs.
- Translating the minus strand: the three reverse reading frames of a sequence are the forward frames of its reverse complement. The DNA to Protein Translator shows all six frames at once.
Frequently asked questions
What is a reverse complement?
It is the sequence of the opposite DNA strand, written in the normal 5' to 3' direction. You swap every base for its partner (A with T, C with G) and then read the result backwards. For 5'-ATGCC-3' the reverse complement is 5'-GGCAT-3'.
Why do I need the reverse complement and not just the complement?
DNA strands are antiparallel. The plain complement is written 3' to 5' under the original, but sequences are always written 5' to 3', so you also reverse it. Reverse primers, probes on the minus strand and genes on the reverse strand are all written as reverse complements.
How are IUPAC ambiguity codes complemented?
Each code stands for a set of bases and becomes the code for the complementary 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 (any base) are their own complements.
Does it work with RNA?
Yes. U is treated as the partner of A. If the input contains U and no T the output uses U automatically, or you can force DNA (T) or RNA (U) output with the Output letters option.
Can I paste a FASTA file with several sequences?
Yes. Every record is processed separately, headers are kept and the sequence lines are re-wrapped at the width you choose. You can optionally add a note such as "reverse complement" to each header.
What happens to numbers, spaces and lowercase letters?
Numbers, spaces and line breaks are removed, so sequences copied from GenBank or a text editor work directly. Lowercase letters stay lowercase, which preserves soft-masked repeat regions. Gaps (- and .) are kept in place.
Is my sequence uploaded anywhere?
No. The conversion runs entirely in your browser with JavaScript; nothing is sent to a server.
Are all the tools on FreeToolCabin tested for quality and accuracy?
Yes! Every tool on our site undergoes automated Q/A testing in real browser environments to ensure high precision, correct output, and zero errors. If you happen to spot a bug or have a suggestion, please contact us at [email protected] and our team will review it right away.
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