Program Parameters

Input to the program consists of a sequence file and the following parameters:

  1. Alignment Parameters. Scores for match, mismatch, indel (insertion or deletion) and terminal indels. These parameters represents the probability such a mutation occurs in nature. A lower penalty score (interpreted as negative numbers) for a mutation allows alignments with more mutations of this kind. Match score is positive and stands as a reference to the mutation scores.
  2. Minimum Similarity level/Alignment Score. The similarity level or alignment score (depends on the definition of an ATR chosen) must meet or exceed this value for the repeat to be reported.
  3. Maximum Motif Length. Only repeats with motif length shorter than or equal to this value are reported. Motif length is the length of the repeated pattern found by the program.
  4. Definition of an ATR.


 Last revised December 5, 2002
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