Download Bioinformatics course 2009 - ILRI Research Computing

Bioinformatics Course
May 2009
In the following example, a mismatch limit of 2 means that up to 2 of 5 bases may
mismatch and the 5 base window will still be classified as a match; when mismatch limit
is set to 0, all 5 bases must match perfectly in order for the windows to match.
Notice the patterns on either side of the main diagnonals that are generated by these
repetitive regions. Notice also the random scattering of dots reflecting small regions that
match fairly closely by chance. Most of these would disappear if the mismatch limit was
set lower or the window size higher.
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