After the Jobs panel shows the Status of a BLAST search or Entrez search is Done, pressing the “Done” hyperlink opens the search results simultaneously in the Text, Table, and Pairwise views. All three views are contained in a large pop-up window that is separate from the main SeqMan Ultra window. The Pairwise view consists of three areas: toolbar, summary, and sequences.


Toolbar area:

This area consists of two drop-down menus and one tool. The Align drop-down menu is used to specify the target sequence, which should be the longest sequence of the two. The *with*drop-down menu is used to specify the query sequence. Specifying a different sequence in either menu will initiate a new pairwise alignment.

The Export image* tool (), located on the right of the header, lets you export the summary and sequences areas.


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.

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