Haven't used BioEdit in ages but perhaps the program is simply using the IUPAC codes for degenerate bases? W=A/T S=C/G, M=A/C, K=G/T, R=A/G, Y=C/T

Hope it helps!

Hi Izzah,

As Alejandro said, these are the Wobbles (degenerate bases).

So you can act as below:

The universal codes for specifying a wobble are: R = A/G, Y = C/T, M = A/C, K = G/T, S = C/G, W = A/T, B = C/G/T, D = A/G/T, H = A/C/T, V = A/C/G, and N = A/C/G/T.

Good luck

Thank you so much Amir and Martin, got it now!!

Can anyone tell what 'X' depicts in multiple sequence alignment using bioedit?

Monu Karki A gap that occurs within a codon (in frame 1) will cause the translation to see an “X” rather than a valid amino acid. You can refer to page 65 in the attached document.