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data.txt

...
+
/66AE     3

data1.txt
...
+
#66AE     5

@gi
AGATC
...
ACCTA
+
/66AE     8

@gi
AGATC
...
+
#66AE     5

my %compare;
...
        print join( "\t", $key, $tot, @{ $compare{$key} } ), "\n\n";
    }
}