RepeatMasker Server

RepeatMasker is a program that screens DNA sequences for low complexity DNA sequences and interspersed repeats.
The masked out sequence can be used for example BLAST searches. Repeats are stored in the database Repbase update.

HomeHOME Contact UsContact Us HelpHelp RepBase UpdateRepBase Update RepeatMasker version: 4.0.7
Libraries version: 20170127 (Dfam_Consensus, RepBase)
Enter the file to process
Select file :
Or paste the sequence(s) in FASTA format

Or input your userid for retrieval of your result
userid :

DNA Source is from

Running Options
Fast (quick search; 5-10% less sensitive, 3-4 times faster)
Default (default search)
Slow (slow search; 0-5% more sensitive, 2.5 times slower)

Repeat Options
Do not mask low_complexity DNA or simple repeats
only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)
only masks low complex/simple repeats (no interspersed repeats)

Output Options
Show Alignments
Mask with X's to distinguish masked regions from Ns already in query
Produce an annotation table with fixed width columns

Input your e-mail (Optional)
E-mail :


RepeatMasker written and supported by Arian Smit.
RepeatMasker Web site designed by Dillon Chan.

Last Modified: 2017/09/06
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