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. The threshold score can be set on the command-line using the -threshold qualifier, the default is 20. For perfect repeats, the score is the length of the repeat (except for the first copy). Reduce the threshold score a little if you wish to to allow mismatches. Each mismatch scores -1 instead of +1 so it scores 2 less than a perfect match of the same number of bases.
Running with a wide range of repeat sizes is inefficient. That is why equicktandem was written - to give a rapid estimate of the major repeat sizes.
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By default etandem writes a 'table' report file.
Running with a wide range of repeat sizes is inefficient. That is why equicktandem was written - to give a rapid estimate of the major repeat sizes.
This application was modified for inclusion in EMBOSS by