Reverse complement calculator

What is the reverse complement of a DNA sequence?

The reverse complement is the sequence of the opposite strand of double-stranded DNA, written in the usual 5′→3′ direction. To get it you swap every base for its Watson–Crick partner (A↔T, C↔G) and then reverse the order. For example, the reverse complement of ATGGAATTCGCTAGC is GCTAGCGAATTCCAT. Because both strands are antiparallel, the reverse complement is what a reverse primer, an antisense probe or a read from the other strand actually looks like.

How to find the reverse complement

1. Paste the DNA or RNA sequence into the box above. Plain text, GenBank-style numbered text and single or multi-record FASTA all work.
2. Keep the Reverse complement tab selected. The result appears as you type, wrapped at 60 characters, with length and GC content shown above it.
3. Press Copy to take the reverse-complemented sequence into a primer design tool, a cloning map or a sequence editor.

By hand, write the sequence backwards and replace each base with its complement. The tool does the same thing for sequences of any length and keeps FASTA headers with the record they belong to.

Reverse complement vs complement vs reverse

The three operations are easy to mix up, and only one of them gives the other strand in its natural orientation:

Use Complement when you want the paired strand written 3′→5′ under the original, and Both strands when you want the two of them drawn together. Use Reverseonly to flip reading direction without changing bases.

Double-stranded display: seeing both strands at once

The Both strands tab draws the duplex instead of a single line of letters: the sequence you pasted runs 5′→3′ along the top, its partner runs 3′→5′ underneath, and a rung joins every base pair. That is the same layout a cloning map or a figure in a paper uses, and it is the quickest way to check an overhang, a restriction site or the orientation of a primer, because the pairing is in front of you rather than in your head.

The bottom strand is the complement, not the reverse complement: each column is a real base pair, so reading the bottom line right to left gives the reverse complement that the first tab prints. The figure is cut into blocks that fit the width you have, so it stays in line on a phone instead of scrolling sideways, and the block size is shown next to the result. FASTA headers are kept and each record gets its own figure.

Degenerate positions get a : instead of a |, since R over Y is a pair of ambiguity codes rather than a single hydrogen-bonded pair. Pressing Copy takes the whole display as plain text, ready to paste into a lab notebook, a protocol or a slide in any monospaced font.

Worked example. "Try an example" loads a 102 nt GFP fragment at65.7% GC. On the Both strands tab it comes back as six blocks of 20 bases (the last one holds the two remaining bases), the first of which is the figure above.

Reverse complement of RNA

RNA is detected automatically: if a sequence contains U and no T, complements are written with U instead of T, so the output is a valid RNA strand. This gives the antisense RNA of an mRNA, siRNA or guide sequence directly. Mixed and lower-case input keeps its case, which is useful for marking primers, overhangs or exons.

IUPAC ambiguity codes in degenerate primers

Degenerate bases are complemented correctly, so the reverse complement of a degenerate primer is still a valid degenerate primer. The full table:

When you need the reverse complement

• Primer design. A reverse PCR primer is the reverse complement of the template at the 3′ end of the amplicon.
• Cloning and Gibson assembly. Checking insert orientation and building overlaps on the opposite strand.
• Sequencing reads. Reads from the minus strand must be reverse-complemented before they align to the reference.
• Restriction sites and palindromes. A site is palindromic when it equals its own reverse complement, as EcoRI GAATTC does.
• Antisense oligos, probes and guide RNAs that must pair with a target strand.

Frequently asked questions

How do I get the reverse complement of a primer?

Paste the primer as written, 5′ to 3′. The result is the strand it anneals to, also written 5′ to 3′. To design a reverse primer, take the last 18 to 25 bases of the amplicon on the top strand and reverse complement them.

Is there a length limit?

No fixed limit. Whole plasmids and multi-record FASTA files of many thousands of bases are handled instantly.

What happens to characters that are not nucleotides?

Whitespace, line breaks and digits from numbered formats are ignored. Any other character is skipped and reported in a notice above the result, so a stray letter never silently changes the output.

Why does the reverse complement of GAATTC equal GAATTC?

Because GAATTC is palindromic: complementing gives CTTAAG, and reversing that gives GAATTC again. Most type II restriction enzyme sites are palindromes for this reason.