Beckman Coulter CEQ 8000, User Manual

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Analyzing Sequence Data
User’s Guide 161
Advanced Alignment Parameters
When the
Perform Alignment
checkbox is selected, the
Advanced Alignment
Parameters
button becomes active. Click the
Advanced Alignment
Parameters
button to access the feature described below.
Figure 97: Advanced Alignmant Parameters
The information on this tab is used to define the parameters used to perform
alignments with the active sequence. The system uses a scoring matrix to perform the
alignment. The alignment that produces the highest total score is the one that will be
displayed. In general, matches should be given higher scores than non-matches. The
definitions of the scoring values are described below. Clicking the
Alignment
Parameters
tab will provide the options described below.
The
Match
text box is used for the value of a match between a base position of the
sequence and the alignment sequence. The range is -1000.0 to 1000.0. A value of 1.0
is the default value.
The
Mismatch
text box is used for the value of a mismatch between a base position
of the sequence and the alignment sequence. The range is -1000.0 to 1000.0. A value
of -2.0 is the default value.
The
Insert start
text box is used for the value of an insertion of a base in the
sequence that does not exist in the alignment sequence. The range is -1000.0 to
1000.0. A value of -4.0 is the default value.
The
Insert extend
text box is used for the value of a consecutive insertion of a base
in the sequence that does not exist in the alignment sequence. The range is -1000.0 to
1000.0. A value of -3.0 is the default value.
The
Delete start
text box is used for the value of a deletion of a base in the sequence
that does not correspond to the alignment sequence. The range is -1000.0 to 1000.0. A
value of -4.0 is the default value.
The
Delete extend
text box is used for the value of a consecutive deletion of a base
in the sequence that does not exist in the alignment sequence. The range is -1000.0 to
1000.0. A value of -3.0 is the default value.