TABLE 5.

Repetitive element classification for final assembly (Canu Hi-C) as reported by RepeatMasker.

Repeat classa	Repeat name	Count	bp masked	Masked (%)
DNA		2,937	2,206,004	0.23
	CMC-EnSpm	24,140	13,861,122	1.44
	Crypton	972	83,799	0.01
	MULE-MuDR	13,906	6,550,989	0.68
	MuLE-MuDR	2,306	1,334,054	0.14
	PIF-Harbinger	1,772	892,861	0.09
	TcMar-Mogwai	1,261	652,191	0.07
	TcMar-Stowaway	32,881	5,565,216	0.58
	hAT	548	112,059	0.01
	hAT-Ac	10,241	2,812,539	0.29
	hAT-Tag1	1,772	308,038	0.03
	hAT-Tip100	6,258	7,096,629	0.74
LINE
	CRE-II	447	335,625	0.03
	Jockey	2,157	567,406	0.06
	L1	8,788	7,141,529	0.74
	L2	14,243	21,727,481	2.25
	Penelope	2,431	992,653	0.10
	R1	566	220,850	0.02
	RTE-BovB	6,587	2,055,784	0.21
LTR		7,950	1,885,731	0.20
	Caulimovirus	351	589,622	0.06
	Copia	62,884	107,371,058	11.13
	DIRS	4591	1,952,514	0.20
	Gypsy	167,590	307,636,295	31.9
	Pao	76	7,473	0.00
	Caulimovirus	7,950	1,885,731	0.20
RC
	Helitron	6,262	2,307,357	0.24
SINE
	tRNA	418	50,479	0.01
Unknown		451,250	143,307,912	14.86
Total interspersed		835,585	639,625,270	66.33
Low_complexity		31,237	1,603,682	0.17
Satellite		128	11,962	0.00
Simple repeatb		216,414	47,610,726	4.94
rRNA		598	309,846	0.03
Total		1,083,962	6,89,161,486	71.46

^aLINE, long interspersed nuclear elements; LTR, long terminal repeat; RC, Rolling circle. ^bThe most common mono- di-, tri-, and tetra- nucleotide repeat motifs were (T)n, (TA)n, (ATT)n, (TTTA)n, respectively.