Table 7. RepeatMasker results for C. canadensis assembly CP2-3.

	Number of Elementsa	Length Occupied (bp)	Percentage of Sequence (%)
SINEs	1,526,194	167,113,901	6.64
Alu/B1	320,643	31,356,476	1.25
B2-B4	124,373	7,917,276	0.31
IDs	441,613	37,889,991	1.50
MIRs	232,410	32,110,048	1.28
LINEs	584,641	379,985,492	15.09
LINE1	420,271	340,564,285	13.52
LINE2	143,179	35,333,421	1.40
L3/CR1	16,864	3,272,497	0.13
LTR elements	358,396	123,574,660	4.91
ERVL	72,861	26,961,457	1.07
ERVL-MaLRs	200,863	68,820,344	2.73
ERV_classI	43,815	20,130,270	0.80
ERV_classII	28,700	4,316,563	0.17
DNA elements	221,280	48,541,417	1.93
hAT-Charlie	123,347	24,927,384	0.99
TcMar-Tigger	45,279	12,145,600	0.48
Unclassified	6,070	1,176,346	0.05
Total interspersed repeats		720,391,816	28.61
Small RNA	59,721	4,937,299	0.20
Satellites	5,814	820,000	0.03
Simple repeats	655,839	31,533,733	1.25
Low complexity	159,452	9,064,948	0.36

The query species was assumed to be rodentia. RepeatMasker version open-4.0.5, rushjob mode run with rmblastn version 2.2.27+, RepBase Update 20140131, RM database version 20140131. File name: cp3.scaff.assembly.fasta; sequences, 21,170; total length, 2,518,060,007 bp (2,517,076,473 bp excluding N/X-runs); GC level, 39.72%; and bases masked, 765,530,353 bp (30.40%).

^aMost repeats fragmented by insertions or deletions have been counted as one element.