[maker-devel] MAKER RepeatMasker outputs incompatible annotations for single feature

[Carson Holt]

This is the RepBase entry (from this file …/RepeatMasker/Libraries/RepeatMasker.lib) —>

>RLG_scAle_3_1-LTR#LTR/Copia @Saccharum_hybrid_cultivar  [S:] RepbaseID: RLG_scAle_3_1-LTR
tgttagaagattatgttaatatcttctgtataaggtaggggatctgtgtg
accacgagatccggtggattggcttgcaagtcaagttgtaatctatgtaa
atctaaccttcttgttgtacaagcccaaggggctatatattaacatgtac
cgagtacctgagaggtatctcgttccatctatttctaca

There are 64 RLG entries associated with Copia in the RepBase library for RepeatMasker. I’m not a repeat expert, so I can’t address whether this is an error or not. But if you think there is something amiss, you could contact RepBase.

—Carson


> On Apr 2, 2017, at 8:19 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
> 
> TE Superfamily RLG are aka Gypsy, but RLG is associated with Copia annotations in our RepeatMasker annotations. Has anyone else seen this before?
> 
> 
> Azfi_s0077  repeatmasker match
> 1400976 1401715
> 521 +
> . ID=Azfi_s0077:hit:59234:1.3.0.14;Name=species:RLG_scAle_3_1-I|genus:LTR%252FCopia;Target=species:RLG_scAle_3_1-I|genus:LTR%252FCopia1522 2556 +
> 
> 
> 
> Matt Simenc
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