Input to the program consists of a sequence file and the following
- 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.
- 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.
- 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.
- Definition of an ATR.
Last revised December 5, 2002
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