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Tandem looks for multiple tandem repeats of a given size in a nucleotide sequence.


Tandem looks for tandem repeats in a sequence. For repeated motifs with a gap between, use ERepeat.


This program was originally written by Richard Durbin and Jean Thierry-Mieg as part of the ACEDB genome database package.

This version was modified for inclusion in EGCG by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).


Here is a sample session with Tandem

  % tandem
   TANDEM uses nucleotide sequence data
   TANDEM of what sequence ?  GenEMBL:hhtetra
                Start (* 1 *) ?
                End (* 1272 *) ?
   Minimum repeat size (* 10 *) ?  6
   Maximum repeat size (* 6 *) ?
   What threshold score (* 20 *) ?
   Allow N as a mismatch (* No *) ?
   Allow uniform consensus (* No *) ?
   What should I call the output file (* hhtetra.tan *) ?


The output from Tandem is a simple report of hits in the sequence.

  TANDEM of em_vi:hhtetra check: 7108
   Score      Start        End Length Copies Percent ..
120        793        936      6     24    93.8 ACCCTA
 90        283        420      6     23    84.8 TAACCC
 38        432        485      6      9    90.7 CCCTAA
 26        494        529      6      6    94.4 CCCTAA
 24        568        597      6      5   100.0 AACCCT



The input file for Tandem is a GCG nucleotide sequence file.


All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  Minimum Syntax: % tandem [-INfile=]GenEmbl:hhtetra -Default
  Prompted Parameters:
  -BEGin=1 -END=100           Range of interest
  [-OUTfile=]hhtetra.tan   Output file
  -THRESHold=20            Score threshold
  -MISmatch                Treat ambiguous positions as mismatches
  -UNIform                 Allow a uniform consensus
  -MINREPeat=10            Minimum repeat length
  -MAXREPeat=10            Maximum repeat length
  Local Data Files: None
  Optional Parameters:
  -ORIGinal=stdout         Produce original mimimal output format


The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.


requests the output format of the original tandem program, optionally with an output file name (the default is to write to the terminal).

Printed: April 22, 1996 15:55 (1162)