[EMBOSS] Question about showalign program

[Jean Mao]

Hi,

A user of ours have a question regarding showaling. When running 
showalign with the input file (attached), the consensus (and parental) 
residue is Lysine (K) and one of her mutants residue is Glutamic acid 
(E). Lysine is basic and Glutamic acid is basic, which are opposites and 
shouldn't be similar. She was using all default setting which supposed 
to show (E) in the alignment output. But instead, it shows (e) which 
indicate similarity between Lysine and Glutamic acid. Can someone help?

Thank you

Jean Mao

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