I've been using RepeatExplorer from Galaxy Environment to characterize repeat elements from the genus Begonia.s I'm looking for someone who has used that before or known well this tool. What I need is how can I get the "consensus sequence" from each cluster. I mean, Repeat Explorer provides clusters of repeat elements. I want to know how can I get the consensus sequence from each cluster which is used to identify the repeat element through repeatmasker.
The main clusters are not defined by repeat masker so I would like to get the consensus sequence from each cluster to see what they look like because we know that they probably are specific repeat elements from Begonia.
Thanks very much!