The UGENE Genome Aligner is a fast short read aligner. It aligns DNA sequences of various lengths to the reference genome with configurable mismatch rate.
It is available from the submenu of the main menu.
<img src="/wiki/download/attachments/17467779/Short read aligner.png"/>
Select the Align short reads item to align short reads to a DNA sequence or Build index item to build an index for a DNA sequence which can be used to optimize aligning short reads to the sequence.