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Compare a reference and query sequence to list substitutions, insertions, and deletions after pairwise alignment. Use the same molecule type on both sides (DNA/RNA with DNA/RNA, or protein with protein) and overlapping regions for interpretable results.
NC_045512.2) and Fetch. Wait until the status line confirms loading.
> header; sequence is read from the body.Scope: Output reflects a local pairwise alignment (a strong matching segment), not necessarily whole-chromosome end-to-end alignment. For database-wide similarity, use BLAST Sequence Search. For research and teaching, not clinical use.
This tool can compare DNA and RNA sequences in various formats, including FASTA and plain text. You can directly upload sequence files or fetch sequences from NCBI using their accession IDs.
The tool runs a local pairwise alignment: it finds a strong matching segment between your reference and query, not necessarily full end-to-end alignment of both entire sequences. Differences in that aligned segment are reported as substitutions, insertions, or deletions. Summary statistics and charts (for example mutation distribution) refer to that aligned region, as noted on the results page.
Yes. Use the checkboxes to show all mutations or only substitutions, insertions, or deletions. There are no separate controls to filter by base-pair position range; trim your sequences before upload or fetch if you need a specific window.
The PDF report includes comprehensive analysis details: summary statistics, sequence metadata, a visualization of mutation distribution, a complete table of all mutations with their positions and types, and citation information for academic use.
You can cite this tool using standard academic formats (APA, MLA, Chicago) with the DOI: https://doi.org/10.5281/zenodo.15069907. Citation formats are provided at the bottom of the results page and included in the generated PDF reports.
Many comparisons complete comfortably in the kilobase to low megabase range. NCBI fetch limits depend on server configuration (often on the order of a few million base pairs). Longer sequences may run slowly, time out, or trigger warnings in the UI; multi-megabase or chromosome-scale jobs are better suited to specialized desktop tools.