Professional bioinformatics tool: GC content, Melting Temp, ORF Finder, Restriction Sites, Translation
M = Start * = Stop +1/+2/+3 = forward -1/-2/-3 = reverse complement
Codon counts from the input sequence (all three forward reading frames combined).
Auto-suggests forward and reverse primer pairs from the input sequence. Checks Tm, GC%, length, and self-complementarity (hairpin).
Paste two DNA sequences to align. Shows identity %, mismatches, gaps, and a visual alignment.
Rewrites a protein-coding sequence using the most frequent codons for the selected organism. Input must start with ATG.
Detects direct repeats, inverted repeats, and tandem repeats in the loaded sequence.
Finds CpG-rich regions using the Gardiner-Garden & Frommer (1987) criteria: length ≥200 bp, GC% ≥50%, obs/exp CpG ratio ≥0.6.
Scores every ATG codon in the sequence against the consensus Kozak context (GCC)GCCRCCATGG. Rates each as Strong, Adequate, or Weak.
Predicts stem-loop / hairpin structures in the RNA transcript using a greedy nearest-neighbor ΔG scan. Identifies the top hairpins by free energy.
For each ORF found in the sequence, shows molecular weight, isoelectric point (pI), GRAVY hydrophobicity score, amino acid composition, and charge at pH 7.
Every calculation on this page runs in JavaScript inside your own browser. Your sequence is never uploaded, which means unpublished and patient-derived data can be analyzed without leaving your machine, and the tool keeps working on an air-gapped lab computer once the page has loaded. The site uses Google Analytics for visit statistics, which never sees the sequence you paste. Paste raw sequence or FASTA; headers, whitespace and numbering are stripped automatically.
Tm is computed with SantaLucia unified nearest-neighbor thermodynamics, which sums stacking enthalpies and entropies over adjacent base pairs rather than applying a flat GC rule. That matters most for short oligos, where a GC-percentage estimate can be several degrees off and send an annealing temperature in the wrong direction.
Candidate primers are scored on length, GC content, terminal GC clamp, 3 prime stability, poly-run content and predicted hairpin free energy. Pairs are then checked for heterodimer formation and matched on Tm, so what you get back is a ranked pair rather than a single sequence.
ORFs are called across all six frames, forward and reverse complement, from each ATG to the first in-frame stop. A minimum length cutoff filters the short spurious frames that appear by chance in any sequence of reasonable size.
The sequence is scanned against a panel of common enzymes and the result is drawn as a linear map with cut positions, per-enzyme lanes and fragment boundaries, so single and double digest strategies can be compared at a glance.
Codons are re-weighted against the host usage table using CAI and RSCU. Rare codons are flagged rather than silently swapped, since wholesale optimization can disrupt folding intermediates and regulatory motifs inside a coding sequence.
GC content is reported both globally and as a sliding window so local GC-rich and AT-rich stretches stand out. CpG islands are called using the Gardiner-Garden observed over expected ratio together with a GC threshold.