School of
Electrical Engineering
and Computer Science

Binary Repeat Align server

by Lars Arvestad and Peter Savolainen

At this site you find software and an online service for aligning tandem repeat regions for which the repeats can be treated as marked by mutations.


Tandem repeat regions are abundant in many genomes. Normally not very informative, except for various fingerprinting techniques using length statistics, regions where the repeats are marked, that is, there are slight variations of the basic repeat, remarkable patterns can occur. These patterns can be utilized for evolutionary analysis, as has been demonstrated in (Savolainen et al, 2000a), and forensic analysis (Savolainen et al, 2000b).

Tandem repeats are believed to arise mainly from replication slippage, which causes repeats to be duplicated: A subsequence is copied twice during replication and the twin copies are found next to each other in the product. To take advantage this evolutionary artifact, we wrote two special computer programs.

Available services

The web service is out-of-service at this point. Please contact Lars Arvestad if you are interested in this service!
General repeat alignmentMother-Child alignment
Press Here Press Here


The software, intended for Unix systems, is available under the GNU General Public License. It contains code for two programs, bra and mcbra. The former computes a simple global alignment under the mentioned restrictions, and the latter performs a Mother-Child alignment.

Simple instructions are available using the '-u' option.

Download from here.


Savolainen P, Arvestad L, Lundeberg J (2000a) mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats. Mol Biol Evol 17(4), 474—478
Savolainen P, Arvestad L, Lundeberg J (2000b) A novel method for forensic DNA investigations: repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs. J Forensic Sci 45(5), 990—999
Published by: Lars Arvestad <>
Updated 2014-09-24