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        my @third_fragments = grep -v ($rsite3), $second_fragments[$i]
...
        $final_fragments{$final_fragment1} = $third_fragments[0];
        $final_fragments{$final_fragment2} = $third_fragments[scalar @
+third_fragments - 1];

syntax error at /Users/smithcabinets26/Desktop/RAD/Digester/Improving/
+MyTripleDigester-3.pl line 68, near "my "
Global symbol "@final_fragment1" requires explicit package name at /Us
+ers/smithcabinets26/Desktop/RAD/Digester/Improving/MyTripleDigester-3
+.pl line 68.
Global symbol "$final_fragment1" requires explicit package name at /Us
+ers/smithcabinets26/Desktop/RAD/Digester/Improving/MyTripleDigester-3
+.pl line 70.
Global symbol "$final_fragment2" requires explicit package name at /Us
+ers/smithcabinets26/Desktop/RAD/Digester/Improving/MyTripleDigester-3
+.pl line 71.
Execution of /Users/smithcabinets26/Desktop/RAD/Digester/Improving/MyT
+ripleDigester-3.pl aborted due to compilation errors.

#! /usr/bin/perl -w
# a script to get fragments of a genome based on restriction enzyme
...
    return %fasta;

}

my @third_fragments = grep !/$rsite3/, $second_fragments[$i];