Table 3.

Major factors of variations in synonymous codon usages in TEs and host nuclear genes

Subject	Source of variation	Axis 1		Axis 2
		Total variability	Correlation coefficient (r-value)	Total variability	Correlation coefficient (r-value)
A. thaliana nuclear genes	A3	9.89	−0.64	7.42	0.11
	C3		0.85		−0.20
	G3		–		0.37
	T3		−0.50		−0.26
	GC3		0.81		0.11
	GC		0.71		–
	ENC		–		0.34
A. thaliana TEs	A3	35.17	0.31	7.47	−0.53
	C3		−0.93		–
	G3		−0.15		–
	T3		0.76		0.51
	GC3		−0.83		–
	GC		−0.80		–
	ENC		−0.67		–
O. sativa nuclear genes	A3	50.78	−0.96	4.64	0.13
	C3		0.94		−0.23
	G3		0.84		0.27
	T3		−0.98		–
	GC3		1.00		–
	GC		0.96		–
	ENC		−0.91		–
O. sativa TEs	A3	30.14	−0.79	9.47	−0.47
	C3		0.94		–
	G3		0.76		–
	T3		−0.92		0.32
	GC3		0.99		–
	GC		0.95		–
	ENC		0.21		−0.29

Note: Only significant correlation coefficients are listed (P<0.0001).