Check Primers Against Template
Paste or upload primer pairs (FASTA, CSV, TSV, or Primer-BLAST report). The tool aligns them against your template sequence and provides full thermodynamic analysis — Tm, GC%, hairpin ΔG, self-dimer ΔG, cross-dimer ΔG — with ranked recommendations.
VigyanLLM is a free online PCR analysis tool that checks primer pairs against any DNA template sequence using the Tm nearest-neighbor model (SantaLucia 1998) and primer3-based ΔG calculations. Unlike standard web primer checkers, it supports Primer-BLAST reports, VigyanLLM auto-design CSV exports, and CSV/TSV/FASTA formats with automatic detection.
| Input | Output |
|---|---|
| Template sequence (DNA 5'→3') | Alignment identity %, mismatch count, start position on template |
| Primer pairs (FASTA/CSV/TSV/Primer-BLAST) | Forward/reverse Tm (°C), GC%, hairpin ΔG, self-dimer ΔG, 3' GC clamp |
| Batch primer list (multiple pairs) | Cross-dimer ΔG, Tm delta, suggested annealing Ta, ranked score, warnings |
| Primer-BLAST export report | Automatic format detection, parsed forward/reverse sequences, downloadable CSV |
Template Sequence
Primers to Check
Scientific References
1. Bustin S.A. et al. (2009). The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem, 55(4), 611–622.
2. Rozen S. & Skaletsky H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol, 132, 365–386.