Table 1.

The amount of initial and cleaned pairwise alignments for each of 7 domestic species investigated

Species	Initial alignments	Cleaned alignments
Cattle	63,978	16,402
Pig	902,537	20,000
Horse	70,532	14,841
Rabbit	338,613	54,768
Goat	54,933	14,403
Sheep	107,362	11,719
Chicken	111,922	25,823

The initial WGAC pairwise alignments were filtered by custom Perl programs. Duplications with 50 or more copies within the genome or present on 3 or more chromosomes were removed, generating cleaned pairwise alignments