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This view shows whole genome sequence aligments between two or more species, termed pairwise and multi-species alignments, respectively. Read more about alignments here.

Only one species is shown by default. Click the "Select an alignment" roll-down menu at the top of the sequence in order to choose an alignment to view. Pairwise alignments between two species, or multi-species alignments, may be chosen.

Chromosomes and scaffolds in the alignment are listed for each species. Then, sequence is shown. Red highlighted nucleotides are located in exons. By default, identical base pairs are highlighted. Click on the "Configure this page" link at the left of the view to add or change the display. Customisable options are as follows:

  • Flanking sequence View the sequence upstream and downstream of the gene.
  • Number of base pairs per row Define how many base pairs shown per line.
  • Exons Highlight exons from Ensembl, Vega, or ab initio analysis.
  • Exons on strand Highlight exons on the forward, reverse or both strands of the chromosome.
  • Show variations Show all variations.
  • Line numbering Select line numbering. Relative to this sequence starts from 1 for the region displayed, and relative to the coordinate system shows the base pair position using genomic coordinates.
  • Conservation regions Highlight regions in which more than 75% of bases match in the alignment.
  • Codons Display codons for start and stop translation.
  • Display pop-up information on mouseover

Note: Ancestral sequences may be turned off using "Configure this page".

If the sequence is not known, nucleotides are replaced by dots.