etandem looks for tandem repeats in a sequence.

Here is a sample session with etandem. The input sequence is the human herpes virus tandem repeat:

% etandem
Input sequence: embl:hhtetra
Output file [hhtetra.tan]: 
Minimum repeat size [10]: 6
Maximum repeat size [6]:

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

-minrepeat (integer)

Minimum repeat size.

-maxrepeat (integer)

Maximum repeat size.

[-outfile] (report)

Output report filename.

Advanced qualifiers:

-threshold (integer)

Threshold score.

-mismatch (boolean)

Allow N as a mismatch.

-uniform (boolean)

Allow uniform consensus.

-origfile (outfile)

Output filename.