Tool for rapid de novo identification, masking and clustering of all repeated sequences at the genomic scale. The tool can quickly and accurately detect any repeated sequences in genomic sequences in interspersed or clustered repeats. Direct and inverted repeat elements, perfect and imperfect microsatellite and telomere repeats, and any short or long tandem repeat belonging to a variety of higher order repeat structures of telomers or large satellite sequences can be detected. Numerous forms of repeat sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks.
Alternative: For unlimited genome sizes, use the command-line TotalRepeats Java application.
- Detected repeats: Direct and inverted repeats, perfect and imperfect microsatellites, telomere repeats, tandem repeats, complex patterns
- Size limit: Theoretically unlimited; practical limit ~100 MB due to browser RAM constraints
- Input format: sequence(s) can be pasted or uploaded as a file in FASTA format or retrieved sequence (NCBI’s accession, e.g. PQ145547) from NCBI’s "nuccore" nucleotide database.
Upload or paste sequence(s) in FASTA format:
Input sequence(s) in FASTA format:
Masked sequence(s)
Report (Tab-separated values)
Picture
Detection Parameters
Quick Help
- Paste/upload FASTA or retrieve by accession; for large inputs prefer files to reduce browser overhead.
- Use the visualization controls (canvas size, export/save) to inspect repeat blocks and masked sequence.