Oligo Sequence Analyzer
Paste your oligonucleotide sequence and get Tm, GC%, secondary structures, molecular weight, and quality score — all at once. No signup. Runs entirely in your browser.
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 a full OligoAnalyzer-style workflow with parameter presets, hetero-dimer checks, BLAST handoff, mismatch effects, and deeper primer review, use the Primer Analyzer. All computations run entirely client-side in your browser; your sequences are never transmitted to any server.
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
- Paste your oligonucleotide sequence (5′→3′, DNA only: A, T, C, G) into the input field. Spaces and line breaks are automatically removed.
- Click "Analyze" or press Enter. All six analyses run simultaneously in your browser from a single sequence input.
- Review the Quality Score (A–D) at the top for an instant pass/fail assessment of your primer.
- Check individual cards for Tm (with three alternative methods for comparison), GC%, secondary structures, molecular weight, and extinction coefficient.
- If issues are flagged, follow the recommendations and use the linked specialized tools for deeper analysis.
- 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 workflow: parameter presets, hairpin, self-dimer, hetero-dimer, BLAST handoff, 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 handoff, 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 up to 10,000 sequences — Tm uniformity, GC distribution, and pass/fail reports.
Project Review
Check a Result or Ordering Step
Send the calculation, settings, or pool submission detail that needs a second look.
Next Pages to Open
Continue with the page or tool that matches the next decision in your experiment.