PrimerCat
PRIMERCAT · ENDPOINT PCR

Endpoint PCR Primer Design

Design endpoint, colony, and high-fidelity PCR primers from DNA or FASTA templates with full amplicon and structure metrics.

DESIGN ENGINEPrimer3 · endpoint PCRCandidate sequences, amplicons, and structure metrics
01
Choose a design scenarioPresets tune design parameters; the polymerase manual still takes priority
02
Enter a DNA templatePlain DNA or one FASTA record
Advanced parameters

This release performs Primer3 design, structure checks, and an optional screen of NCBI RefSeq genomic records. A limited remote screen is not complete reference-genome validation.

OUTPUT · CANDIDATESPrimer and amplicon candidates
Awaiting input

Paste a template to see candidate sequences, amplicon positions, and quality metrics.

Full ampliconStructure metricsOrder-sheet export
PCR PRIMER DESIGN

Online PCR primer design for endpoint, colony, and high-fidelity workflows

Paste a DNA or FASTA template and PrimerCat uses Primer3 to generate PCR primer pairs with reviewable sequences, coordinates, amplicons, and structural metrics.

Choose a preset

Endpoint, colony, and high-fidelity presets use different default amplicon and Tm ranges, while advanced constraints remain editable.

Review candidates

Results report both primers 5′→3′ and expose Tm difference, GC%, hairpins, self-complementarity, end complementarity, and GC clamps.

Confirm specificity

Optional screening searches for paired hits within the declared reference scope; it does not replace laboratory validation or an exhaustive check across every genome version.

Complete computational methodsConfidence and experimental validation