Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

it is in the reverse orientation. These orientations may change as more data is added to
the contig, unless you have used a Reference Sequence in your assembly. In this case, the
Reference Sequence determines the contig orientation. Below the fragments you will see
the coverage map and below the coverage map you will see the start and stop map. Notice
the diagram key at the base of the window.
Figure 11-1 Contig overview
Selection marquee
In the Overview you will notice a dashed rectangle. This animated marquee (sometimes
called the marching ants) highlights the section of the contig displayed when you switch
to the Bases View. You can change the location you want to view by dragging the
marquee to a new location. As you move the cursor over the marquee you will see it
change to a hand icon. You can now hold down the mouse button and drag the marquee to
the desired location.
Checking coverage in the Overview
The bar across the bottom of the overview shows various levels of sequence coverage
indicated by different graphic patterns. For instance, a wide solid green line indicates that
the sequence coverage comprises both strands. A region with no color or pattern indicates
a hole in the coverage. The full array of patterns indicating coverage are shown at the
bottom of the Overview in the figure above.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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