My plasmid library
Local browser storageStarter reference: pUC19, accession M77789.2 (2,686 bp). A second entry is clearly marked as a virtual teaching construct. Other references can be downloaded and imported from pBR322 (J01749.1) or other authorized sources; they are not silently bundled. Imported sequences stay in this browser unless exported.
Selected plasmid
Select a record—Length, bp
—GC, %
—Annotations
Select a plasmid.
Synonymous codon recoding
Research screeningUses illustrative host codon preferences and a greedy heuristic—not validated usage frequencies, CAI, RNA thermodynamics or expression predictions. Protein identity is checked. Evaluate mRNA folding, motifs, cryptic splice sites, sequence chemistry and IP independently.
Optimized sequence
Export FASTA / report—DNA length
—Output GC
—Synonymous codons changed
Run the optimizer to see the coding sequence.
In-silico construct design
Sequence-level simulationComputational assembly only. Restriction mode does not validate sticky-end compatibility or ligation chemistry. Overlap mode proposes primer tails; it does not check genome specificity or experimental performance. Confirm with full construct sequencing before use.
Assembled plasmid
Virtual design—Construct bp
—GC %
—Inserted bp
Choose a library vector and run a virtual assembly.
Candidate PCR primer pairs
Nearest-neighbor estimateScreening only: approximate SantaLucia nearest-neighbor Tm at 50 mM monovalent salt and 250 nM oligo; approximate complementarity; exact matches only within submitted template. Does not check genome-wide off-target priming, Mg²⁺, mismatches or full secondary-structure thermodynamics. Confirm with Primer3/Primer-BLAST and experimental testing.
Ranked primer candidates
Top six pairsLoad or paste a DNA template, specify your target region, and select “Find candidate pairs.”
Privacy and scientific scope: Analysis runs locally in the browser; imported library sequences are stored in this browser's local storage and can be deleted by clearing site data. Do not paste confidential or regulated genetic sequences into a shared device. This free educational/research tool is not a replacement for DNASTAR, Primer3, a validated codon-optimization pipeline, or clinical/GMP bioinformatics. For public plasmid reference data, see GenBank M77789.2. Addgene's bulk-data API requires appropriate permission and is not silently used.