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Alignment Graphic Display

The alignment can be viewed as an x-y plot graphic (the default) or as a linear graphic. Both graphics show precisely how the bases in the two sequences match up. The color key (BLAST only) is the same for both versions.

x-y Plot Graphic

The default view on this page is the x-y Plot Graphic.

In this graphic, base positions along the scaffold are marked by numbers on the vertical (y) axis, and base positions along the hit sequence are marked by numbers on the horizontal (x) axis. The alignment is represented by one or more plotted segments, each representing a high-scoring pair (HSP), colored according to the alignment score color key (shown directly above the plot).

You can customize the display by setting the base ranges for each sequence in the text boxes at the top and clicking Rescale.

xstart Sets the first base of the hit sequence to be shown.
xend Sets the last base of the hit sequence to be shown.
ystart Sets the first base of the scaffold sequence to be shown.
yend Sets the last base of the scaffold sequence to be shown.
Reset Redraws the graphic with the original ranges.

Quick Tip

To jump to an Alignment Hit Report for one of the HSPs, click the segment representing it.

Linear Graphic

To view the alignment in a linear display, click Linear Graphic.

This graphic displays base numbers for the scaffold along the top and base numbers for the hit sequence along the bottom. Each high-scoring pair (HSP) is represented by a filled-in region between the two axes that is color coded by alignment score. To jump to an alignment hit report for one of the HSPs, click the colored trapezoid representing it.

Quick Tips

In some cases, the hit sequence is on the minus strand (the opposite strand from the scaffold), and the linear graphic appears twisted. To untwist an alignment, click Flip Scaffold. A red minus sign will appear to the left of the scaffold to indicate that it has been flipped.
By default, both sequences are displayed as large as possible. If one of the sequences is much shorter than the other you may want to change the scale. To toggle between viewing with both sequences at full width and viewing with a one-to-one scale, click Scale.