This tool enables the rapid de novo identification, masking and clustering of all repeated sequences on a genomic scale. It can quickly and accurately detect any repeated sequences in genomic sequences, whether they are interspersed or clustered. It can detect direct and inverted repeat elements, perfect and imperfect microsatellite and telomere repeats, as well as any short or long tandem repeat belonging to a variety of higher-order repeat structures, such as telomeres or large satellite sequences. It can identify numerous forms of repeat sequences and complex patterns, even for complex sequence variants and implicit or mixed types of repeat blocks.
Alternative: For unlimited genome sizes, use the TotalRepeats advanced Java application via the command line.
- 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 by NCBI accession (e.g. PQ145547) from NCBI's nucleotide database.
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.