Gap Fraction track

To display the Gap Fraction track:

Gap Fraction is a graph track with a scale of 0-1 that shows the proportion of gapped positions in a sliding window centered on each position.

The availability of a Gap Fraction track in the Sequences view or Pairwise view is available only for aligned sequences, and is dependent on:

• Whether or not tracks are visible in the views. To display tracks, click on the plus sign next to the sequence of interest.

• Whether or not the Gap Fraction box is checked in the Tracks panel. This box is only visible after alignment has taken place.

To change Gap Fraction options:

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

• Calculations are performed in a sliding window. Type a number in the Window size box to specify the number of consecutive residues to use in the gap fraction calculation. The window size may be any integer from 1-50,000, and the default is 7 residues. The window shifts along sequences one position at a time, and will therefore overlap for widths greater than 1.

*Note: The gap fraction value at each position is computed using a window centered over the position in the gapped sequence. An even window width causes the window to be slightly off-center. As the window approaches either end of the sequence, one side will stop moving, and the window will shrink.

• By default, the Gap Fraction graph is shown in gold. To choose another color, click on the color box to the right of Line Color.

Click if you wish to return to the default values.