...in $matches{>scaffold_446}{0}[1]
$sets{>scaffold_446}[1] is:
$VAR1 = '0';
$VAR2 = [
          0,        #  These 2 array elements should not BOTH 
          0         #  be 0!!!  What did I do wrong?
        ];
...in $matches{>scaffold_446}{1}[0]
...in $matches{>scaffold_446}{2}[0]
...in $matches{>scaffold_446}{0}[0]
...in $matches{>scaffold_446}{0}[1]
...in $matches{>scaffold_446}{1}[0]
$sets{>scaffold_446}[2] is:
$VAR1 = '1';     #  For each of these different  '...in $matches..."
$VAR2 = [        #  There should be 6 $VAR variables.  corresponding 
          40048    #  to 3 key/value pairs, but I am doing something wrong
        ];              #  in my code, such that sometimes there are 3 pairs, but
$VAR3 = '0';     #  often not.  Any thoughts?
$VAR4 = undef;
...in $matches{>scaffold_446}{2}[0]
...in $matches{>scaffold_446}{0}[0]
...in $matches{>scaffold_446}{0}[1]
...in $matches{>scaffold_446}{1}[0]
...in $matches{>scaffold_446}{2}[0]
$sets{>scaffold_446}[3] is:
$VAR1 = '1';
$VAR2 = undef;
$VAR3 = '0';
$VAR4 = undef;
$VAR5 = '2';
$VAR6 = [
          5468
        ];
...in $matches{>scaffold_3198}{0}[0]
$sets{>scaffold_3198}[0] is:
$VAR1 = '0';
$VAR2 = [
          1829
        ];