Annotated sequence
Working copy · 1-based coordinatesLocal project revisions
Save · restore · export| Saved at | Sequence / features | Action |
|---|---|---|
| No revisions captured. | ||
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The importer/editor supports simple contiguous forward and reverse features. Joined intervals, complex locations, remote features and full INSDC qualifiers are not round-tripped. Original GenBank metadata beyond basic features is not preserved. Always retain the source record.
Feature editor and region viewer
Editable annotation table| # | Label | Type | Interval | Strand | Action |
|---|
Add annotation
Select Edit on an annotation to update its label, coordinates or strand. Export GenBank to preserve your changes.
View nucleotide region
Virtual restriction digest
Canonical enzyme motifsThis model recognizes 10 common palindromic motifs and assumes complete cutting. It does not model methylation, enzyme buffer compatibility, partial digestion, or star activity. Gel bands are qualitative illustrations.
Fragment analysis
1-based reported sites · cut boundaries in 0-based coordinates—Unique cut sites
—Fragments
—Sum of fragment lengths
Predicted fragments
| Fragment | Length (bp) | Coordinates |
|---|
Recognized restriction sites
| Enzyme | Site start | Cleavage boundary |
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Align multiple DNA sequences
2–8 sequences · up to 700 nt eachThis is an educational reference-centered progressive alignment using constant gap penalties. It is not the MAFFT, MUSCLE or Clustal Omega algorithms; it lacks guide trees, iterative refinement and phylogenetic inference. Order matters. Validate biologically consequential results with established tools.
Consensus alignment
Aligned FASTA / Clustal-style text—Sequences
—Columns
—Mean column conservation
Paste sequences and click Calculate.
Pairwise identity, excluding gap positions
| Sequence A | Sequence B | Identity | Comparable nt |
|---|
Sequence trace import
AB1 · FASTQ · FASTA—Called bases
—Q20 bases
—Mean PHRED
Upload an AB1 file or load the synthetic training example. All analysis stays in your browser.
Research use only. AB1 analysis reads stored PBAS basecalls, PCON quality and DATA fluorescence. It does not perform independent peak deconvolution or re-basecalling. Inspect ambiguous or mixed peaks manually.
Sanger vs reference
Candidate mismatches, insertions and deletions—Aligned identity
—Candidate differences
—Trimmed bases
| Type | Reference position | Reference → read | Read base | PHRED |
|---|---|---|---|---|
| No comparison performed yet. | ||||
Global pairwise alignment is for a selected amplicon or plasmid region, not whole-plasmid mapping. Differences are candidates, not independently verified variants. Q and alignment orientation must be reviewed.
Chromatogram viewer
A green · C blue · G white · T redImport an AB1 sequencing trace to view channel intensities and called bases.
Base calls will appear here.
Forward / reverse Sanger assembly
Quality-aware overlap · 1200 bases/readNo forward read loaded
No reverse read loaded
Choose two reads. The reverse read is reverse-complemented automatically.
This is a two-read screening assembly, not independent basecalling or high-confidence variant calling. The algorithm uses free-end affine-gap alignment. Conflicts are reported and unresolved bases become N. Repetitive regions, mixed chromatograms and ambiguous overlaps need manual verification.
Compare consensus to a reference
Consensus and supporting evidence
Research-only interpretation—Consensus bases
—Overlap length
—Overlap identity
—Ambiguous calls
Consensus FASTA
Awaiting paired reads.
Read overlap alignment
No alignment yet.
Disagreement table
| # | Type | Forward | Reverse-oriented | Calls | Consensus |
|---|
Reference differences
| Type | Position | Expected | Consensus | Read coverage |
|---|
Affine-gap pairwise alignment
DNA comparison · up to 1200 nt/sequenceGotoh affine-gap dynamic programming. Scores and outputs depend on chosen penalties. Unlike a reference genome mapper this does not provide probabilistic confidence or genomic specificity; do not use it for clinical variant interpretation.
Alignment result
Research-stage interpretation—Pair identity
—Alignment score
—Comparable bases
Press Align sequences.
Enhanced GenBank import / export
Rich feature locations · research-stageThis extended interchange panel parses simple, join and complement interval locations and preserves basic qualifiers. It does not fully round-trip all INSDC record sections (references, taxonomy, remote features or complex fuzzy locations). Keep your original .gb file. The original basic annotation editor remains limited to contiguous features.
Reference plasmid catalogue
pUC19 · M77789.2 · 2,686 bpBundled exact nucleotide sequence; NCBI GenBank provenance. Can load in Plasmid workbench.View NCBI reference ↗
pBR322 · J01749.1 · 4,361 bpOfficial source linked; sequence not bundled in this release. Download official GenBank record and import here rather than using reconstructed data.View DDBJ source ↗
Annotation table and exports
Original coordinates and qualified featuresNo GenBank record imported yet.
| # | Type | Gene / label / product | INSDC location | Readiness |
|---|---|---|---|---|
| Import a GenBank record to inspect features. | ||||
Browser-local reading. No sequences transmitted to NEXUS.
Scope and privacy: All computations run on your device, without cloud storage or accounts. Browser-local projects may be lost if you clear site data. This is research-stage software, not a validated clinical analysis suite or DNASTAR substitute. Use exports for independent review.