To display the Match Bar track:

The Match Bar track is used to show similarities and differences between the query and target sequences. This track is available in the Pairwise view only after performing a pairwise alignment.

The visibility of this track in the Pairwise view is dependent on:

  • Whether or not tracks are visible in the Pairwise view. To display tracks, click on the plus sign next to the sequence of interest.
  • Whether or not the Match Bar box is checked in the Tracks panel. This box is only visible after performing a pairwise alignment.

To learn how to access the options section for this track, see Tracks.

  • Use the Show identity as drop-down menu to choose how to show the connection between the query and the target. Choosing Residues in target case or Residues in query case cause the connection to appear as a copy of the residue from the target or query sequence. Choosing Vertical bars causes the connection to appear as a symbol, depending on the match status.
Symbol Interpretation Weight table value
Vertical line Match 1
Colon Favorable mismatch (0,1)
Period Neutral mismatch 0
Space Unfavorable mismatch < 0
  • To add a background color behind each residue, check the Color background check box and use the adjacent drop-down menu to choose between Same as query and Same as target.

Click if you wish to return to the default values.

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