finding conserved regions of an allignment automaticallg by a software

Question

[mr.donmez.emre]

dear all. I'm trying to find the conserved regions of NS5b site of HCV genotype 2/3 in order to design primers of sequencing, I just had all the wanted sites and alligned them. my allignments are perfect but i dont wanna use my eyes to find the conserved regions, any software advice ?

Answer 1

[dago]

You can try Gblock. However, if your aim is to design primers that would be able to be as inclusive as possible I would suggest you to design degenerate primers. You can look here as a start.