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Y 39 1jpeA
Y 40 1jpeA
...
L 76 1gtiA
etc ...1jpe,0,TYR,A,42

1jpe,0,CYS,A,109
1jpe,0,CYS,A,103
...
1jpe,0,TYR,A,71
1jpe,0,PHE,A,70
etc ...

1jpeA 42

Y 42 1jpeA (from file 1)
1jpe,0,TYR,A,42 (from file 2)

#!/usr/local/bin/perl

...
   }
    
}