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Synteny is the conserved order of aligned genomic blocks between species. It is calculated from the pairwise genome alignments created by Ensembl, when both species have a chromosome-level assembly.

The search is run in two phases:

  1. We search for alignment blocks that are in the same order in the two genomes. Syntenic alignments that are closer than 200 kb are grouped into a synteny block.
  2. Groups that are in synteny are linked, provided that no more than two non-syntenic groups are found between them and they are less than 3 Mb apart.