Section II: Troubleshooting a CEQ System Problem
Sequence Analysis Troubleshooting Guide
15
In the following examples (Figure 9 and Figure 10), the template is the same, but two
different primers have been used. Primer 1 has a T
m
of 43.5°C, a 31.6% GC content
and is 19 bases long. Primer 2 has a T
m
of 79.8°C, a 62.5% GC content and is 24 bases
long. The effect on the data obtained from the CEQ is clear. With a less than efficient
reaction, the signal level is low and the base calling accuracy is not optimal.
Figure 9:
Primer 1
Figure 10: Primer 2
