Number of sequences and clusters

The table below shows a summary of the generated Multiple Sequence Alignments (MSAs). Paired MSAs have fewer sequences than the alignments they are made of due to restrictions when pairing sequences of the same Taxa. Not all taxa contained in one MSA may be available in other MSAs to be paired with.

The Cluster id column, shows how many "groups" or clusters of sequences more than 62% identical can be found on that MSA. This gives an idea of the diversity of the sequences in that MSA. If the numbers of clusters is low, it means there is little diversity in the MSA should be interpreted with caution

MSA	Number of sequences	Cluster id: 62	Cluster id: 70
ATP synthase epsilon chain & ATP synthase gamma chain	17452	493	804
ATP synthase gamma chain	19225	489	795
ATP synthase epsilon chain	19022	1144	3442

Download individual alignments

Download paired alignments

Download covariation raw data

Covariation Circos

Select a protein pair and then choose any combination of methods to view. Only the pairs present in all the selected methods are shown. If you don't see any pairs in the beginning, try using the slider. This will select the top X scoring pairs for each method, and get the intersection of those lists of top scoring pairs. These are the final pairs drawn in the circos.

You can draw up to two circos using left and right panels. Don't forget to hit the "Draw Circos" button! If you need more then use the "Add new Circos panel" below. This is useful for looking at different pairs of proteins with different combinations of methods!

You can select the subsets of residue pairs to be displayed (intra, inter or intra + inter-protein). A table is shown with information about the number and type of the displayed links.

Density plots

You can view the distribution of covariation scores as kernel density plots.

Choose one plot from the dropdown list with all available plots.

Covariation Matrix

Results can be visualized in a matrix context. Each side of the matrix represents the concatenated proteins depicted in green and purple. Points indicate that those residues covariate for the selected method. Different colors represent pairs in the Top 100, 500 and 2500 best scoring pairs.