Table 2.

Log-likelihood-ratio scoring matrices

Gg/Hs Rfam 70% identity, 54% A+T					Tr/Hs Rfam 66% identity, 53% A+T					At/Os Rfam 69% identity, 55% A+T
	a	c	g	t		a	c	g	t		a	c	g	t
a	86	-110	-48	-94	a	87	-93	-49	-79	a	79	-92	-57	-69
c	-110	100	-118	-48	c	-93	100	-107	-49	c	-92	100	-117	-57
g	-48	-118	100	-110	g	-49	-107	100	-93	g	-57	-117	100	-92
t	-94	-48	-110	86	t	-79	-49	-93	87	t	-69	-57	-92	79
Gg/Hs TreeFam 65% identity, 49% A+T					Tr/Hs TreeFam 57% identity, 46% A+T					Sc/Sp TreeFam 49% identity, 60% A+T
	a	c	g	t		a	c	g	t		a	c	g	t
a	100	-99	-46	-113	a	100	-75	-38	-92	a	71	-55	-28	-60
c	-99	92	-82	-46	c	-75	82	-63	-38	c	-55	100	-58	-28
g	-46	-82	92	-99	g	-38	-63	82	-75	g	-28	-58	100	-55
t	-113	-46	-99	100	t	-92	-38	-75	100	t	-60	-28	-55	71

Scoring matrices derived from Rfam (top row) or TreeFam (bottom row) based gold standards for the indicated genome pairs are shown. Species names abbreviated as: Gg: G. gallus, Hs: H. sapiens, Tr: T. rubripes, At: A. thaliana, Os: O. sativa, Sc: S. cerevisiae, Sp: S. pombe. Additional file 1, Table S2 shows corresponding matrices for other genome pairs.