The Pairwise view displays sequences that have been aligned pairwise. Sequence names selected in this view are simultaneously selected all other views in MegAlign Pro. Similarly, sequence names selected elsewhere will be highlighted in the Pairwise view.

To access the Pairwise view, do either of the following:

  • Perform a pairwise alignment. In this case, the Pairwise view opens automatically to display the results. To open the view at a later time, click on the Pairwise tab. If there are multiple Pairwise tabs, hover over each tab to see a tooltip showing which sequences were involved in that alignment.
  • Perform a BLAST search. In this case the Text, Table and Pairwise views are displayed together in a single popup window that is separate from the main MegAlign Pro window. To reopen the Pairwise view (and the associated views) at a later time, click on the Status link in the Jobs panel.

In the left of the header, the Align (left) drop-down menu is used to specify the target sequence, which should be the longest sequence of the two. The with (right) drop-down menu is used to specify the query sequence. Specifying a different sequence in either menu will initiate a new pairwise alignment.

Summary area:

The summary area describes the alignment engine and settings that were used to create the pairwise alignment.

Value Description
% Identity Number of matching residues divided by the sum of all residues and gap characters. The quotient is multiplied by 100 to give the similarity as a percent.
% Gaps The gap length divided by the consensus length. The quotient is multiplied by 100 to give the similarity as a percent.
Identical Number of residues that are identical in both sequences.
Gap Count Number of gaps (of any length) in either sequence of an alignment.
Gap Length Number of gap characters in an alignment.
Score The cumulative score for an alignment derived by adding the matrix-derived match scores and subtracting gap penalties.
Length Number of residues in the consensus, including gaps that match in both sequences.


Sequences area:

The sequences area consists of nucleotide or amino acid codes for each sequence on the right, and their labels on the left. The order is always “target sequence” first, and “query sequence” second. A variety of optional data tracks can be displayed in this section. The Pairwise view has a different appearance depending on the zoom level.
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Tasks pertaining to the Pairwise view:

Task How To
All Pairwise views
Customize the look and layout of the view See Customize the look and layout.
Save an image of the view Click the Export Image tool (), a shortcut to the File > Export Image subcommands. See Export an image of the view. The summary and sequences areas are both exported.
Only Pairwise views not resulting from a BLAST search
Change pairwise alignment options Click the Change alignment options in this view tool (), a shortcut to Align > Pairwise. Set options as desired and press Align.
Create a new pairwise subalignment Select a portion of the alignment, then click the Create new pairwise alignment from selection tool (). The subalignment will open in a new Pairwise view.
Export data from the view Click the Export Data tool (), a shortcut to the File > Export Data subcommands. See Export data to a file.
Make a copy of the current view Click the Clone this view tool (). This makes an exact copy of the current Pairwise view, including sequences, alignment type, settings and current selection. This is useful if you want to change one factor for comparison to the original alignment.

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