Transposons where detected and classified by an homology search against the REdat_9.7_Poaceae section of the PGSB transposon library [pmid 26527721].
The program vmatch (http://www.vmatch.de) was used for that purpose as a fast and efficient matching tool suited for large and highly repetitive genomes with
the following parameters: identity>=70%, minimal hit length 75 bp, seedlength 12 bp (exact commandline: -d -p -l 75 -identity 70 -seedlength 12 -exdrop 5).To
obtain an overlap free annotation the vmatch output was filtered for redundant hits via a priority based approach. Higher scoring matches where assigned first
and lower scoring hits at overlapping positions where either shortened (<90% coverage and >=50bp rest length) or removed.

Hover over the different structures in the image below to see more information in the tooltip.