[Biodevelopers] Scoring matrixes, negative values for Y==Y?

[Theodore H. Smith]

Is it possible for a matrix to contain a positive match for Y to Y?  
Where Y could be any DNA letter or protein? Y could be A or B or C...  
etc etc.

Normally, scores range from 0 and up, correct?

Are there matrixes in use that can have negative values for an exact  
identity match?

What if a matrix had something like B to B had a score of -1, but W  
to W had a score of 6.

Would such a matrix have any use?

I am just asking, because I'm writing some hobbyist bio-informatics  
software, and... I'm basically learning as I go along, and I'd like  
to eliminate this possibility if possible, because assuming it's not  
possible would make it possible for me to write some simpler code.

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