Oligo Sequence Analyzer

Paste your oligonucleotide sequence and get Tm, GC%, secondary structures, molecular weight, and quality score all at once. No signup. Browser by default; History may save snapshots.

DNA only (A, T, C, G) • 6–500 nt • Standard PCR conditions: 50 mM Na⁺, 1.5 mM Mg²⁺, 250 nM oligo

What Is the Sequence Playground?

The Sequence Playground is a quick single-paste QC surface that calculates six useful checks from one sequence input: melting temperature (Tm) using SantaLucia 1998 nearest-neighbor thermodynamics, GC content with risk assessment, secondary structure prediction (hairpins and self-dimers with ΔG values), molecular weight, molar extinction coefficient (ε₂₆₀), and an overall primer quality score graded A through D.

Use this page when you want a fast exploratory check. For parameter presets, hetero-dimer checks, BLAST preparation, mismatch effects, and deeper primer review, use the Primer Analyzer. The computation runs in your browser by default; optional account saves use the site History flow described in the privacy policy.

The quality scoring algorithm evaluates your oligo against five criteria used by experienced primer designers: Tm range (55–65°C optimal), GC content (40–60% optimal), hairpin stability (ΔG > -3 kcal/mol), self-dimer stability (ΔG > -5 kcal/mol), and appropriate length (15–35 nt for standard primers).

How to Use the Sequence Playground

  1. Paste your oligonucleotide sequence (5′→3′, DNA only: A, T, C, G) into the input field. Spaces and line breaks are automatically removed.
  2. Click "Analyze" or press Enter. All six analyses run simultaneously in your browser from a single sequence input.
  3. Review the Quality Score (A–D) at the top for a quick primer-readiness signal.
  4. Check individual cards for Tm (with three alternative methods for comparison), GC%, secondary structures, molecular weight, and extinction coefficient.
  5. If issues are flagged, follow the recommendations and use the linked specialized tools for deeper analysis.
  6. For batch analysis of multiple sequences, use the Batch Sequence QC tool linked at the bottom.

Frequently Asked Questions

How does this differ from IDT OligoAnalyzer?
This playground is a fast single-sequence QC surface. Use the Primer Analyzer for the full report: parameter presets, hairpin, self-dimer, hetero-dimer, BLAST preparation, and mismatch analysis. This page remains useful when you want a quick client-side quality score without opening a deeper primer review.
What does the quality score measure?
The quality score evaluates five parameters: Tm range (optimal 55–65°C), GC content (optimal 40–60%), hairpin ΔG (threshold -3 kcal/mol), self-dimer ΔG (threshold -5 kcal/mol), and length (optimal 15–35 nt). Grade A = all optimal, B = minor deviations, C = significant issues, D = major redesign recommended.
Can I analyze RNA sequences?
Currently the Sequence Playground supports DNA sequences only (A, T, C, G). For RNA analysis, use the individual Tm Calculator which supports both DNA and RNA inputs.
Why are three Tm values shown?
The three methods — Nearest-Neighbor (±1–2°C), %GC Method (±3–5°C), and Wallace Rule (±5–10°C) — have different accuracies. Nearest-Neighbor is recommended for primers 15–70 nt. The comparison helps you understand the uncertainty range. For a deeper comparison of 5 methods, use the Tm Method Comparison tool on the Tm Calculator page.

Related Tools

Primer Analyzer

Full primer review with parameter presets, hetero-dimer checks, BLAST preparation, and mismatch effects.

Tm Calculator

Detailed Tm analysis with salt corrections, DMSO/formamide adjustment, and batch processing.

Secondary Structure Predictor

Full hairpin, self-dimer, and cross-dimer analysis with structure visualization.

GC Content Analyzer

Detailed GC analysis with sliding window, dinucleotide frequencies, and batch mode.

Batch Sequence QC

Quality control for 1,000 free or 50,000 member sequences, including Tm uniformity, GC distribution, and exportable review reports.

Review request

Check a result or ordering detail

Send the calculation, settings, or pool submission detail that needs a second look.

Related reading

Continue with the page or tool that matches the next decision in your experiment.

Primer Design ChecklistSecondary Structure Method PathAccuracy Validation MethodsDesign Guide