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string1 (C)C(T)A 
string2 T(A)GG(A)GGG(G)

string1 1 C A 
string1 3 T C 
string1 20 A T  /* This is out of range, and has to be omitted*/
...
string2 9 G A 
string2 30 A C /* This is out of range, and has to be omitted*/
string3 9 G A /* This string is not there in the main file.. so has to
+ be omitted */