ETANDEM

Looks for tandem repeats in a nucleotide sequence

etandem looks for tandem repeats in a sequence. It is normally used afterequicktandem has been run to identify potential repeat sizes.It calculates a consensus for the repeat region and gives a score forhow many matches there are to the consensus - the number of mismatches.

Input sequences are converted into ACGT or N (so ambiguity codes are ignored).
The score is +1 for a match, -1 for a mismatch.
The first copy of a repeat is ignored.
The highest score is kept for each start position and repeat size.

The lowest score to be reported is set by the threshold score. Thethreshold score can be set on the command-line using the-threshold qualifier, the default is 20. For perfect repeats, thescore is the length of the repeat (except for the first copy). Reducethe threshold score a little if you wish to to allow mismatches. Eachmismatch scores -1 instead of +1 so it scores 2 less than a perfectmatch of the same number of bases.

Running with a wide range of repeat sizes is inefficient. That is whyequicktandem was written - to give a rapid estimate of the major repeatsizes.