NEXUS SeqFold v0.6 | Precision Workflows

Primer evaluation

Nonclinical PCR design

DNA template (A/C/G/T)

Region start (1-based)

Region end (blank = end)

Target Tm (°C)

Min product length (bp)

Max product length (bp)

Input template and run primer screening.

Scientific limits: SantaLucia-style nearest-neighbor Tm approximations, screening of 3′ complementarity and simple hairpin motifs. This is not Primer3 or Primer-BLAST; no genome-wide uniqueness, full oligonucleotide secondary-structure ΔG, off-target amplification or experimentally validated PCR outcomes.

Ranked primer pairs

Review warnings before ordering

#	Forward / Tm	Reverse / Tm	Amplicon	3′ cross	Score
No pairs yet

Per-pair analysis

No primer data.

RNA nested hairpin screening

Max 220 nt

RNA sequence (A/C/G/U; T accepted)

Minimum hairpin loop (nt)

Ready.

Not ViennaRNA RNAfold. The model scores hairpins, stacked base pairs and limited internal loops only; no multiloop thermodynamics, dangling ends, complete experimental parameter tables, ensemble or base-pair probabilities. Score is an uncalibrated relative number, not ΔG (kcal/mol). Do not compare scores across RNAs as binding affinity or stability.

RNA structure output

Dot-bracket and arcs

—Base pairs

—Relative score (not kcal/mol)

Calculate a structure.

Reference-guided multi-read consensus

2–12 Sanger reads

Expected target/reference DNA (≤1,200 bp)

Paste multiple FASTA records (optional)

For pasted FASTA, add |R or "reverse" to the name to set reverse orientation; check each selection below.

Or add AB1 / FASTA / FASTQ files

Read	Bases	Quality	Orientation
No reads loaded.

Minimum agreeing read depth

Select reads and orientations, then assemble.

Reference-guided only: does not construct reference-free contigs. Potential indels are reported but not incorporated into consensus. Weak or conflicting evidence produces N. Stored instrument basecalls are used, not re-basecalled. This is not a clinical variant caller or validated Sanger assembly system.

Consensus evidence

Uncertainty retained

—Reference positions

—Accepted reads

—Unresolved N

—Depth-qualified sites

Consensus

Awaiting reads.

Candidate substitutions

Position	Reference	Consensus	Depth	Base counts
No calls.

Accepted reads and warnings

No analysis yet.

Source-traceable plasmid catalogue

NCBI GenBank references

The reference catalogue distinguishes a bundled verified sequence from links to external official records. No vendor-specific maps or accession-only sequences have been reconstructed.

Bundled pUC19 source sequence

Open annotated plasmid editor ↗

Bundled reference sequence (read-only for copy/export)

Only pUC19 sequence is bundled; other accessions link to official records for manual import.