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["This worksheet contains a macro Karlin(MinMismatchScore as integer,MaximumMatchScore as integer,GetLambda as boolean,GetK as boolean,GetH as boolean)"]
["Example of calling the function: Karlin(-3, 1, True,True,True)"]
["You will provide the probabilities corresponding to the match-mismatch scores:"]
["Score","Prob"]
[-3,0.75]
[-2,0]
[-1,0]
[0,0]
[1,0.25]
[]
["The above is based on equal nucleotide frequencies so that"]
[null,"A","G","C","T"]
[null,0.25,0.25,0.25,0.25]
["A",1,-3,-3,-3]
["G",-3,1,-3,-3]
["C",-3,-3,1,-3]
["T",-3,-3,-3,1]
[]
["The probability that we have nucletide pairs AA, GG, CC, and TT is the same, i.e., 0.25*0.25 = 0.0625"]
["So the probability corresponding to score 1 is simply 4*0.0625 = 0.25"]
["All other nucleotide pairs would get a score of -3 and corresponding to a total probability of 0.75 ( = 1 - 0.25)"]