Table 4 Summary of interspersed repeats from homology-based identification

			Full-length			All repeats
Class	Order	Superfamily	No. of elements	Length (bp)	% genome	No. of elements	Length (bp)	% genome
I	LTR	Gypsy	49,183	264,644,712	1.14	5,127,514	2,544,140,822	10.98
I	LTR	Copia	36,952	207,086,169	0.89	4,385,545	2,119,375,506	9.14
Total LTR	LTR		179,367	962,249,326	4.15	17,432,917	9,660,836,674	41.68
I	DIRS (Dictyostelium transposable element)		4,935	26,820,856	0.12	596,008	335,540,558	1.45
I	Penelope		4,966	13,456,930	0.06	422,276	188,350,501	0.81
I	LINE		15,353	53,411,263	0.23	906,403	545,648,705	2.35
I	SINE		137	68,023	0.00	670	182,264	0.00
Total RT(Retrotransposon)			262,028	1,299,761,701	5.61	25,166,637	13,577,984,814	58.58
II	TIR		7,932	20,499,522	0.09	420,769	185,871,618	0.80
II	Helitron		1,105	3,500,491	0.02	47,003	22,396,711	0.10
Total DNA			11,026	31,035,610	0.13	519,708	240,545,369	1.04
Uncategorized			56,024	110,604,852	0.48	3,164,894	1,172,394,606	5.06
Total interspersed			336,037	1,458,952,566	6.29	29,249,206	15,145,555,948	65.34
Tandem repeats				210,810,342	0.91		210,810,342	0.91
Total				1,669,762,908	7.20		15,356,366,290	66.25