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  1. or download this
    File 1
3936 C C C C A C .....
...
Final File 

3936 3451 3607 1 1 C C C C A C .....
  2. or download this
    awk 'NR==FNR{A[$1]=$1}A[$3]{sub($3,A[$3]);print}' file2 file1 > new fi
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