Automated paleontology of repetitive DNA with REANNOTATE

BMC Genomics

Table 3 Nesting of repeats in human chromosomes Y and 2

	no. of elements^a		% chromosome^b		% nested^c		insertions/Kb^d
	Y	2	Y	2	Y	2	Y	2
SINE	10068	119383	10%	12%	46%	51%	0.48	0.63
LINE	6207	65661	25%	21%	32%	39%	0.81	1.66
LTR	5200	38395	18%	8%	43%	52%	0.57	0.68
satellite	2144	222	5%	0%	4%	37%	0.05	0.18
DNA	1464	26886	2%	3%	35%	46%	1.12	0.88
RNA	55	778	0%	0%	54%	56%	0.36	0.26
repeats total	25157	251667	59%	45%	38%	48%	0.65	1.19
non-repetitive^‡	-	-	41%	55%	-	-	1.33^†	1.00

^aNumber of repetitive elements (models) in each group. ^bPercentage of available (cytologically euchromatic) chromosome sequence. ^cPercentage of elements in each group that are inserted into any other repetitive element. ^dDensity of repetitive element insertions (of any kind) per kilo base pairs of sequence within each group. ^‡Non-repetitive sequence here means that similarity to known families of high complexity repeats was not detected, but it includes low-complexity repeats. ^†Excludes satellite repeats arrayed in tandem. (Satellites considered are high-complexity repeats).

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