Input Sequence

💡 Quick Summary

Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. The full IUPAC DNA alphabet is supported (including degenerate bases), and the case of each input character is preserved. You may want the reverse-complement of a sequence if it contains an ORF on the reverse strand.

📋 How to Use

Paste a raw DNA sequence or one or more FASTA sequences into the input area. Input limit is 100,000,000 characters.
Choose an Operation: Reverse complement reverses and complements the sequence; Reverse reverses it without complementing; Complement complements without reversing.
Click Run. Each input sequence is output as a FASTA entry with the operation name appended to the title.
The Summary panel shows how many sequences were processed and the total input and output lengths.
Use the Copy button to copy all output sequences to your clipboard.
Click Load Example to try with sample IUPAC-coded sequences.
Click Clear to reset.

🧮 Formulas & Logic

Reverse complement

output = reverse( complement( input ) )

Reverse

output = reverse( input )

Complement

output = complement( input ) — each base replaced by its Watson-Crick partner, no reversal

IUPAC complement

A↔T, G↔C, R↔Y, K↔M, B↔V, D↔H, S↔S, W↔W, N↔N (case preserved)

📊 Result Interpretation

Sequences Processed

Number of FASTA entries (or bare sequences) successfully transformed.

Input Length

Total number of valid IUPAC DNA characters across all input sequences (non-DNA characters are ignored).

Output Length

Total number of characters in the transformed output — always equal to Input Length.

🔬 Applications

Finding the coding sequence on the reverse strand of a genomic region
Designing reverse primers — the primer sequence is the reverse complement of the template strand
Checking whether a restriction site spans the reverse strand
Converting antisense constructs to their sense orientation
Verifying sequencing reads that were assembled on the opposite strand

⚠️ Common Mistakes & Warnings

Non-DNA characters are silently removed

Any character that is not a valid IUPAC DNA/RNA letter (A, T, G, C, U, R, Y, S, W, K, M, B, D, H, V, N, X) is stripped before transformation. This includes spaces, digits, and punctuation.

RNA "U" is treated as a DNA base

Uracil (U) is kept as-is and its complement is Adenine (A). If your input is RNA you may want to convert U→T before using this tool.

❓ Frequently Asked Questions

What is the difference between reverse, complement, and reverse complement?

"Reverse" simply reads the sequence backwards (5'→3' becomes 3'→5'). "Complement" replaces each base with its Watson-Crick partner without changing the order (A↔T, G↔C). "Reverse complement" does both — it produces the sequence of the opposite strand read in the 5'→3' direction, which is the most common operation in molecular biology.

Which operation should I use for primer design?

Use "Reverse complement". A reverse primer anneals to the coding (sense) strand, so its sequence is the reverse complement of the region immediately downstream of your target.

Are degenerate (IUPAC) bases supported?

Yes. All IUPAC degenerate bases are complemented correctly: R↔Y, K↔M, B↔V, D↔H, S↔S, W↔W, N↔N. The case of each character is preserved — lowercase input produces lowercase output.

Can I process multiple sequences at once?

Yes. Paste any number of FASTA-formatted sequences (each starting with ">title") and all will be processed in a single run. Each output entry has the operation name appended to its title.

What happens to non-DNA characters in my sequence?

Any character that is not a recognised IUPAC DNA/RNA letter is silently removed before the transformation. Spaces, digits, dashes, and newlines in the sequence body are all stripped automatically.