Alignments (Image)


The top panel is similar to the gene map shown in the Region in Detail view in the Location tab.

Whole genome alignments are shown graphically in the lower panel. Alignments themselves are drawn. Note: The multi-species comparison view is a similar page that shows the chromosomes, scaffolds and contigs as they are. For example, gaps in the multi species comparison page are gaps in the genome assembly. Gaps in this align slice view may be gaps in the alignment.

Select the alignment at the top of the this panel by using the "alignment" roll-down menu. Choose multi-species alignments across more than two species, or a pairwise alignment between two species.

The Display

Horizontal bars

Horizontal blue bars represent genomic sequence as in other Ensembl views. The filled or hollow horizontal brown bars are clickable, and represent the alignments. If a bar is filled, the forward strand of the chromosome was aligned. Hollow bars represent alignments using the reverse strand of the chromosome.

Vertical shading

The brown background is there for contrast, and white vertical stripes are gaps in the alignment. Each panel shows this unique shading for a specific species. Different colours of vertical shading represent different chromosomes in the alignment.


Arrows (triangles) indicate breaks in the alignment. Click on an arrow for more information about the break.

Ancestral sequences

These are inferred from the multiple alignments. If present, the species used to determine the ancestral sequence are listed on the blue bar. For example, a blue bar labelled Hsap, Ptro, Mmul shows an ancestor of the Homo sapiens, Pan troglodytes, and Macaca mulatta genomes.

Customise the view by adding variations, gene sets, and other features using the configure this page link at the left.

To export alignments do so from the genomic alignments link, and click on export data from that page.

The image above shows a pairwise alignment between human and mouse. The mouse alignment was clicked on to show a pop-up box with information about that aligned region (on mouse chromosome 5).