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

Variance Table
The Variance Table preferences control how ambiguous matches and large gaps will
be treated. If you wish to include ambiguous matches in your table, click the Include
Ambiguous Matches checkbox. If you wish to exclude large gaps from your table, click
the Exclude Large Gaps checkbox.
When you generate a Variance Table you would expect to have blank cells where the
base at that position matches the exemplar. If you would like to see all bases across the
comparison range whether they match or are different to the exemplar then click the
Populate All Cells checkbox (see Figure 21-18).
Figure 21-18 Variance Table preference settings
Input/Output
File Import
File Import preferences control how Sequencher applies the automatic trim function to
imported files.
Use the checkboxes grouped under Add Imported Sequences To Trim Window to
specify which sequences Sequencher should examine for poor quality ends and then trim.
You can also specify how you want to resolve conflicts between the names of imported
files and names stored with particular sequences. If you click the Prefer File Names To
Data Names checkbox, Sequencher uses the file name.
Clicking the Review Trim Parameters button displays the Ends Trimming dialog box,
in which you can set trim criteria. (See Chapter 6, “Preparing your Data for Assembly,”
for details.)
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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