Table 2.

Annotation of LTR-retrotransposons and MITEs in rice assemblies

TE Classification	Nipponbare	MH63
LTR-all a	131,905	117,362
LTR full-length b	3733	3787
LTR- Gypsy	1354	1303
LTR- Copia	944	759
LTR- Unclassified c	1435	1725
MITE-all (1)	211,732	191,113
MITE full-length d	45,963	46,725

^a Repeatmasker fragments. Includes both intact and truncated elements

^b High confidence elements containing intact LTRs, TSDs and coding domains

^c Intact elements whose poor coding domain conservation doesn’t allow proper classification

^d Elements spanning more than 80% of its family consensus length