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

(see Figure 13-5). It is possible for a sequence to have partial coverage, a pink header and
footer, but not have any pink X’s in the column.
Note: When comparing multiple consensus sequences, the View menu’s Display Base
Confidences option is not relevant, because confidence values exist only in fragments
and not in consensus sequences.
Figure 13-5 Compare Consensus to Reference Variance Table
For more information about Assemble by Name and Reference Sequences, see Chapter
10 “Assemble by Name” and Chapter 7 “The Reference Sequence”.
Translated Variance Table for sequences in the same contig
When you are ready to begin creating your Translated Variance Table, either select
individual sequences from within a contig or go to the Project Window and select a
contig by clicking on its icon. This will select all of the contig’s sequences.
Then go to the Sequence menu and choose Compare Translation To and either
Consensus, Reference Sequence or Top Sequence from the submenu. The Translated
Variance Table appears in a new window (see Figure 13-6).
The Translated Variance Table header summarizes the table’s contents including a
Description, the Base Positions and the Amino Acid Positions. If a sequence in the
Table does not extend the full length of the Comparison Range, its column header will be
shaded in pink. The pink X’s mark cells that are not covered by sequence data, indicating
that the status of the base at that position is unknown.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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