Homologous Recombination Primer Design

Paste vector and insert sequences to detect common restriction sites and generate PCR primers with homology arms.

Sequence Input

One DNA sequence or FASTA record per input; A/C/G/T only. Ambiguity and multiple records are rejected.

Real sequence example

pUC19 · M77789.2 · 2686 bp + TkA01G000070 · TK1151 CDS 1170 bp

pUC19 demonstrates sequence input and cut-site calculation; it is not presented as a plant-expression vector. The insert comes from the site’s TK1151 reference CDS.

Vector sequence Insert sequence

Inspect restriction sites and eligibility

Only a unique site in a complete circular vector and absent from the insert is supported. Double digests, repeated sites and end repair are not modeled. Check the calculated overlap against the actual linearized-vector ends.

Primer Result

Paste sequences to generate results.