Table 1.

Characteristics of Species That Were Used for Phylogenetic Footprinting With S. aureus

	Average identity between aligned upstream regions of orthologous genesa,b							Number of orthologs with S. aureus (total no. of ORFs in genome)
	Target genome
Query genome	Spyg	Lmon	Saur	Llac	Spne	Bhal	Bsub
Spyg	100	48	50	50	52	47	47	1180 (1697)
Lmon	49	100	51	50	50	48	49	1493 (2846)
Saur	50	51	100	51	50	48	49	— (2594)
Llac	50	50	51	100	51	47	48	1302 (2267)
Spne	50	48	49	49	100	46	46	1204 (2094)
Bhal	47	48	48	48	48	100	49	1523 (4066)
Bsub	48	49	49	48	48	49	100	1593 (4112)

^aBecause the sets of orthologous upstream sequences were based on the COG classification of the genes (see Methods), the composition of the sets between two genomes depends on which of the two genomes is used as the query genome and which is used as the target genome. This asymmetrical definition of orthologous upstream sequences leads to an asymmetrical calculated average identity between genomes.

^bThe standard deviation from the mean was, in all cases, around 10%.