About the DNA Reverse Complement Tool
This reverse complement tool converts a DNA or RNA sequence into its reverse, its complement and its reverse complement — the sequence of the opposite strand read 5′ to 3′. Paste a raw sequence or a FASTA record; spaces, line breaks, numbering and the header line are stripped automatically, and the original upper or lower case is preserved.
It is useful when designing reverse primers, checking whether a probe binds the sense or antisense strand, reading Sanger results from a reverse read, or matching restriction sites and guide RNAs. All IUPAC ambiguity codes are supported (R↔Y, K↔M, B↔V, D↔H, while S, W and N stay the same), so degenerate primers convert correctly.
Choose DNA output to write T, RNA output to write U, or Auto to follow the input: a sequence containing U but no T is treated as RNA. Characters that are not nucleotide codes are counted and dropped so you can spot copy-paste errors.
How to use the dna reverse complement tool
- 1Paste a sequence or a full FASTA record into the box.
- 2Leave the alphabet on Auto, or force DNA (T) or RNA (U) output.
- 3Copy the reverse complement, which reads the opposite strand 5′ to 3′.
- 4Check the ignored-character count to catch stray letters from copy-paste.
Formula and method
DNA strands are antiparallel and pair by Watson–Crick rules: adenine pairs with thymine (uracil in RNA) and guanine with cytosine. The complement replaces each base with its partner, giving the opposite strand written 3′→5′ underneath the input. Reversing that string gives the opposite strand in the conventional 5′→3′ direction, which is the reverse complement.
Ambiguity codes complement to the code covering the partner bases: R (A/G) becomes Y (C/T), K (G/T) becomes M (A/C), B (not A) becomes V (not T) and D (not C) becomes H (not G). S (G/C), W (A/T) and N stay the same. GC content counts G, C and S over all nucleotides.
- R / Y
- Purine (A or G) / pyrimidine (C or T)
- S / W
- Strong (G or C) / weak (A or T)
- K / M
- Keto (G or T) / amino (A or C)
- N
- Any nucleotide
Worked examples
Short DNA fragment
Each base of ATGCGTACGTTAGC is swapped for its partner to give the complement TACGCATGCAATCG, which is then read backwards to give GCTAACGTACGCAT. Seven of the 14 bases are G or C, so GC content is 50%.
RNA sequence (auto-detected)
The input contains U and no T, so it is treated as RNA and the output uses U. The complement of AUGGCUUAA is UACCGAAUU; reversed, it gives UUAAGCCAU. Three of nine bases are G or C (33.3%).
Degenerate primer with IUPAC codes and FASTA header
The header line is skipped. K complements to M, N stays N and R complements to Y, so GGRTACNNKA becomes TMNNGTAYCC when read 5′→3′ on the opposite strand.
Frequently asked questions
What is a reverse complement?+
It is the sequence of the opposite DNA strand written in the standard 5′→3′ direction. You get it by complementing every base (A↔T, G↔C) and then reversing the order. Reverse primers and antisense probes are written as reverse complements.
What is the difference between complement and reverse complement?+
The complement pairs base-for-base under the original and therefore reads 3′→5′. The reverse complement is the same strand flipped so it reads 5′→3′, which is how sequences are conventionally written, ordered and searched.
How do I get the reverse primer sequence?+
Take the target sequence at the 3′ end of the region you want to amplify, written on the top strand, and paste it here. The reverse complement is the reverse primer to order, written 5′→3′.
Does the tool handle RNA and ambiguity codes?+
Yes. U is complemented to A, and A complements to U when RNA output is chosen or detected. All IUPAC codes (R, Y, S, W, K, M, B, D, H, V, N) and gap characters are supported.
Is my sequence sent anywhere?+
No. The conversion runs entirely in your browser, so unpublished or proprietary sequences never leave your computer.