Table 3. Optimal TSD length and number of de novo insertion sites based on Illumina data.

Order	Superfamily	Family	Modal TSD length	Insertion sites	Insertion sites with modal TSD length	% Insertion sites with modal TSD length
TIR	hAT	hobo	8	1,198	1,196	99.83
TIR	P	1360	7	279	274	98.21
TIR	P	P-element	8	1,226	1,207	98.45
TIR	Pogo	pogo	2	895	883	98.66
TIR	Tc1	S-element	2	25	25	100
TIR	Transib	hopper	5	533	532	99.81
TIR	Transib	transib2	5	7	7	100
LTR	Copia	Dm88	3	1	1	100
LTR	Gypsy	297	4	19	18	94.74
LTR	Gypsy	412	4	498	494	99.20
LTR	Gypsy	accord	4	3	3	100
LTR	Gypsy	blood	4	378	376	99.47
LTR	Gypsy	Burdock	4	481	471	97.92
LTR	Gypsy	gtwin	4	19	18	94.74
LTR	Gypsy	gypsy	4	92	92	100
LTR	Gypsy	gypsy12	4	1	1	100
LTR	Gypsy	gypsy2	4	2	2	100
LTR	Gypsy	gypsy5	4	6	6	100
LTR	Gypsy	HMS-Beagle	4	320	311	97.19
LTR	Gypsy	Idefix	5	1	1	100
LTR	Gypsy	invader3	4	1	1	100
LTR	Gypsy	invader6	4	1	1	100
LTR	Gypsy	mdg1	4	146	146	100
LTR	Gypsy	mdg3	4	5	5	100
LTR	Gypsy	micropia	4	1	1	100
LTR	Gypsy	opus	4	1,030	976	94.76
LTR	Gypsy	Quasimodo	4	9	8	88.89
LTR	Gypsy	rover	4	3	3	100
LTR	Gypsy	Stalker2	4	84	82	97.62
LTR	Gypsy	Tabor	4	138	138	100
LTR	Gypsy	Tirant	2	2	2	100
LTR	Gypsy	Transpac	4	202	202	100
LTR	Gypsy	ZAM	4	3	3	100
LTR	Pao	3S18	5	119	113	94.96
LTR	Pao	aurora-element	17–18	2	2	100
LTR	Pao	Max-element	5	100	96	96.00
LTR	Pao	roo	5	193	182	94.30
LTR	Pao	rooA	13	1	1	100

Families with fewer than eight insertion sites were excluded from further analyses of TSD and TSM structure, but often show similar modal TSD length to related TE families.