EDTA have problem to identify LTR-RT when an intact LTR-RT close with a solo LTR-RT that is from the same family.

[qjiangzhao]

Hi Shujun,

I found a problem for EDTA to identify LTR-RT when an intact LTR-RT close with a solo LTR-RT that is from the same family.

For example, the longer LTR-RT (repeat_region_580) share the same left TSD and left LTR. Actually, the shorter LTR-RT (repeat_region_579) contains all required domains, which means it should be an intact LTR-RT.

On the other hand, I don't think two intact LTR-RT should share same TSD and LTR.

I found many annotation like from my data.

scaffold_9 EDTA repeat_region 1825990 1837407 . + . ID=repeat_region_580;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000657;ltr_identity=0.9935;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA target_site_duplication 1825990 1825994 . + . ID=lTSD_580;Parent=repeat_region_580;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000434;ltr_identity=0.9935;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA long_terminal_repeat 1825995 1826147 . + . ID=lLTR_579;Parent=repeat_region_579;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000286;ltr_identity=1.0000;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA Gypsy_LTR_retrotransposon 1825995 1832268 . + . ID=LTRRT_579;Parent=repeat_region_579;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0002265;ltr_identity=1.0000;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA long_terminal_repeat 1825995 1826147 . + . ID=lLTR_580;Parent=repeat_region_580;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000286;ltr_identity=0.9935;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA Gypsy_LTR_retrotransposon 1825995 1837402 . + . ID=LTRRT_580;Parent=repeat_region_580;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0002265;ltr_identity=0.9935;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA long_terminal_repeat 1832116 1832268 . + . ID=rLTR_579;Parent=repeat_region_579;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000286;ltr_identity=1.0000;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA target_site_duplication 1832269 1832273 . + . ID=rTSD_579;Parent=repeat_region_579;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000434;ltr_identity=1.0000;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA long_terminal_repeat 1837250 1837402 . + . ID=rLTR_580;Parent=repeat_region_580;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000286;ltr_identity=0.9935;Method=structural;motif=TGCA;tsd=TTCAC scaffold_9 EDTA target_site_duplication 1837403 1837407 . + . ID=rTSD_580;Parent=repeat_region_580;Name=TE_00001108;Classification=LTR/Gypsy;Sequence_ontology=SO:0000434;ltr_identity=0.9935;Method=structural;motif=TGCA;tsd=TTCAC

Yours sincerely Jiangzhao