Table 3.

Classification of repeat elements generated from RepeatMasker

	Number of elementsa	Length occupied (bp)	Percentage of sequence (%)
Retroelements	160 425	112 810 688	20.6
SINEs	17 580	3 242 835	0.59
Penelope	1155	97 740	0.02
LINEs	20 303	6 704 697	1.22
CRE/SLACS	37	1672	0
L2/CR1/Rex	4680	678 218	0.12
R1/LOA/Jockey	340	22 011	0
R2/R4/NeSL	70	3992	0
RTE/Bov-B	3670	1 765 787	0.32
L1/CIN4	9180	3 982 099	0.73
LTR elements	122 542	102 863 156	18.79
BEL/Pao	622	98 414	0.02
Ty1/Copia	49 026	41 614 407	7.6
Gypsy/DIRS1	62 124	58 039 401	10.6
Retroviral	3184	346 807	0.06
DNA transposons	288 141	58 683 503	10.72
hobo-Activator	43 650	10 654 515	1.95
Tc1-IS630-Pogo	4515	615 692	0.11
En-Spm	0	0	0
MuDR-IS905	54	53 928	0.01
PiggyBac	121	6007	0
Tourist/harbinger	4780	1 700 494	0.31
Other (mirage, P-element, P-element, Transib)	695	43 698	0.01
Rolling-circles	4313	1 802 302	0.33
Unclassified	373 015	120 296 966	21.97
Total interspersed repeats		291 791 157	53.29
Small RNA	19 997	17 205 637	3.14
Satellites	2056	628 418	0.11
Simple repeats	121 138	6 848 295	1.25
Low complexity	17 346	833 121	0.15

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