Free AI-Assisted
Oligo QC Instant
Paste or upload up to 100 primers for instant GC%, multi-method Tm, and traffic-light QC—no login, no upload.
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Key facts
| Fact | Value |
|---|---|
| Inputs | Plain text, FASTA, or CSV (name + sequence); pair mode with forward and reverse |
| Batch limit | Up to 100 primers per run |
| Tm methods | Wallace rule, SantaLucia 1998 NN, Owczarzy 2008 salt-corrected NN |
| Structure QC | Hairpin ΔG, self-dimer ΔG; pair mode adds heterodimer and 3′ overlap |
| Polymerase presets | Q5, Phusion, Taq, KAPA HiFi, Custom buffer |
| Export | CSV download and TSV copy to clipboard |
| Runs in browser | Yes — sequences not uploaded |
| Account required | No |
| History | Last 10 runs stored locally in browser |
What it does
Validating a primer panel before ordering means bouncing between IDT, NEB, and spreadsheets—one oligo at a time, with no batch export and no plain-English warnings when hairpins or dimers look risky. Oligo QC Instant accepts plain text, FASTA, or CSV (up to 100 primers), runs entirely in your browser, and returns a sortable QC table with GC%, three Tm methods side by side, hairpin and self-dimer ΔG, and PASS / CAUTION / FAIL badges you can click for guidance.
Switch between Single / Batch and Primer pair mode. In pair mode, enter forward and reverse sequences to see ΔTm, heterodimer ΔG, 3′ overlap, and a recommended annealing temperature for your polymerase buffer preset (Q5, Phusion, Taq, KAPA, or Custom Na⁺/Mg²⁺/dNTP). Results auto-update for five or fewer sequences; click Analyze for larger batches. Export CSV or copy the table to a spreadsheet; reload the last 10 sessions from the History tab.
Why researchers use it
- QC up to 100 primers in one paste or upload
- See Wallace, NN, and salt-corrected Tm together
- Get plain-English warnings for hairpins and dimers
- Check primer pairs for ΔTm and heterodimer risk
- Keep sequences private with client-side calculation
- Export QC tables for lab notebooks or LIMS
Best for
- Multiplex PCR primer panels before ordering
- Core facility intake QC on submitted oligos
- Graduate students validating primer lists from literature
- Quick pair checks when NEB or IDT login is inconvenient
- Spreadsheet-free batch GC% and Tm review at the bench
When to use this vs alternatives
Choose Oligo QC Instant for fast batch primer QC with exportable pass/fail flags and no account. Use the Primer Tm Calculator when you need co-solvent correction, larger batch pair limits, and detailed Ta rules per polymerase. IDT OligoAnalyzer remains the reference for deep single-oligo analysis when server-side BLAST and extinction coefficients are required.
What makes it different
IDT OligoAnalyzer is accurate but requires login, runs one oligo at a time, and sends sequences to IDT servers. NEB Tm Calculator matches polymerase buffers but lacks batch mode and secondary-structure QC. Legacy oligo calculators use Wallace rule only and skip dimer checks.
Oligo QC Instant combines no-login batch input, three Tm methods with tooltips, traffic-light severity badges with corrective suggestions, primer-pair mode with recommended Ta, and CSV export—without uploading sequences. Use the [Primer Tm Calculator](/tools/tm-annealing-temperature-calculator) when you need DMSO/formamide correction, up to 200 pairs, and detailed method comparison for annealing temperature planning.
How to get started
- Open the workspace on the Oligo QC tab.
- Choose Single / Batch or Primer pair mode.
- Paste sequences, FASTA, or CSV—or upload a file.
- Select polymerase buffer and primer concentration (default 250 nM).
- Click Analyze (auto-runs for ≤5 sequences in batch mode).
- Click badges for plain-English guidance; Export CSV or Copy table.
Frequently asked questions
Which Tm value should I use for PCR?
What do PASS, CAUTION, and FAIL mean?
Are my sequences sent to a server?
Client source code & registry
Last updated . Pepkio builds free lab calculators alongside bioinformatics CRO services.