TotalRepeats

Tool for rapid de novo identification, masking, visualization and clustering of all repeated sequences at the genomic scale. The tool can quickly and accurately detect repeated 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 repeats 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, including complex sequence variants and implicit or mixed types of repeat blocks.

An alternative command line Java application TotalRepeats for local use without restrictions on genome size and the number of files to be analyzed.

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.
Size Limitations: the length of the query sequence and the size of the batch file are theoretically unlimited.

The results will appear instantly in the output fields (lower windows) - repetitive sequences in upper case. To export the results: select all (Ctrl-A), copy (Ctrl-C) and paste (Ctrl-V) to Excel sheet: