We used the Arabidopsis genome as the reference and obtained pair-wise genome alignment chain files from the Plant Ensembl to obtain synthetic regions between other genomes and the reference genome. Then coordinates of PACs of all other species were converted to coordinates of the reference genome. We adopted the reciprocal best match method to determine conserved PACs. Briefly, two PACs from two species was considered as orthologous if their distance was smaller than 25 nt based on the whole genome alignment. For each PAC in each species, the information of conservation is recorded, including the species where the conserved sites are found and the corresponding PACs. More...