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MAKER RepeatMasker outputs incompatible annotations for single feature

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MAKER RepeatMasker outputs incompatible annotations for single feature

Matt Simenc
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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Re: MAKER RepeatMasker outputs incompatible annotations for single feature

Carson Holt-2
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 <[hidden email]> 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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