[Feedback] Site Feedback: Repeats for v4 genome

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Subject     : Repeats for v4 genome

Name        : Maciej Jonczyk

Email       : mjonczyk at biol.uw.edu.pl

Organization: University of Warsaw

Comments    : Dear Gramene Team,
I've found nice repeat annotation for v5 maize genome (Zm-B73-REFERENCE-NAM-5.0.TE.gff3.gz). It contains great repeat and TE annotation, from which I used repeats: centromeric_repeat, long_terminal_repeat, low_complexity and repeat_region.

Now I switched back to v4 genome. Tere is also gff with TEs (B73v4.TE.filtered.gff3) but it contains mainly transposons.

My question is, where could I find better repeat annotation for v4 maize genome.
Alternatively, hov could I repeat TE annotation for v4 version which has been done for v5 version (i.e. generate similar file to Zm-B73-REFERENCE-NAM-5.0.TE.gff3.gz but for v4 genome)?

I've tried using repeatmasker for masking simple repeats but it masked only about 29000000 bp.

http://www.warelab.org/bugs/view.php?id=6037