Hello. I am currently using RepeatExplorer in order to identify repetitive sequences in genomic data. In the TAREAN annotation, one of the generated clusters was classified as a putative LTR element, but no primer binding site (PBS) or protein domain were detected. The monomer is composed of 349 nucleotides and the generated graph is very similar to that characteristic of satellite DNAs. I am wondering if there could be any mistakes on the TAREAN annotation or if there is something else I can analyse on the outputs to better understand this element…
Hello @mhelena
One idea is to compare to the results with RepeatMasker.
GTN Tutorial with a simplified example → Hands-on: Masking repeats with RepeatMasker / Masking repeats with RepeatMasker / Genome Annotation
Hope this helps! 