This tool rapidly identifies, masks, and clusters repeated sequences at genome scale. It detects interspersed or clustered repeats, including direct and inverted elements, perfect and imperfect microsatellites and telomeres, and tandem repeats of any length across diverse higher-order structures.
Alternative: For unlimited genome sizes, use the TotalRepeats advanced Java application via the command line.
Retrieve sequence from NCBI by accession
— chromosomes (NC_), mRNA (NM_), RefSeq contigs
Upload local FASTA file
— plain FASTA, multi-FASTA, or sequences
Detection Parameters
- 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.