Primer Design

1. Gene Runner
2. Oligo 6
3. Primer 3(on line)
4. Manual
 Gene Runner
1.Sequence Insertion
Oligo 6
 Manual
1. Reference sequence & other sequences (NCBI)
2. Alignment (Mega 4)
3. Sequence selection (In selected gene)
4. Blast (NCBI)
5. TM (oligo analyzer, oligo6, gene runner)
6. Secondary structures (loop, hairpin,…)
7. False priming (oligo 6)
Genome HCV
Alignment
 Current oligo length

Position number
Non specific band
- Length
-Miss match
*5-7nt from 3’ end