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

Basic Reference Sequence properties
When you assemble sequences, which include a Reference Sequence, the base numbering
of a contig will be the same as the base numbering of the Reference Sequence (see Figure
7-1).
Figure 7-1 Contig showing base numbering set by Reference Sequence
When a contig is built that includes a Reference Sequence, the contig will always remain
in the same orientation relative to that Reference. This way you can keep the contig from
flipping as more fragments are added. Because of this, there can only be one Reference
Sequence in a contig. You can easily spot the Reference Sequence in a contig editor
because it is highlighted along its entire length with a gray border.
When you assemble sequences that include a Reference Sequence you will notice that
gaps in the Reference Sequence are given decimal numbers, thereby preserving the
absolute numbering of base positions.
The Reference Sequence does not contribute to the calculation of the consensus line
of a contig. For example, if a ‘T’ in the Reference Sequence overlaps a ‘G’ in another
fragment, the consensus line will show a ‘G’.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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