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#!/usr/bin/perl -w

...
close (INPUT1);
close (RESULTS);
close (DIR);

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THE FIRST FILE 
...
3121652 A209.EF064284   95      9       0.447002        -30.8   A     
+  3121652 491.059 104.1
4911506 A209.EF064284   97      9       0.371932        -30.2   S     
+  4911506 99.0901 24.5
4389484 A209.EF064284   99      10      0.48621 -32.2   A       438948
+4 123.912 47.2