finding conserved regions of an allignment automaticallg by a software

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 ?

alignment conserved regions not eyes

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updated 9.7 years ago by dago

• written 9.7 years ago by mr.donmez.emre •

1 answer

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.

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written 9.7 years ago by dago

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