open (TEXT, "sample.txt")||die"Cannot";
...
NEXTLINE: while ($count < 1000)
    {
    $line = <TEXT> ;
    $count++;
    foreach my $value (@regexes)
       {
       ...
       while ($line =~ /$value/g)
          {
          ...
          }
       ...          
       }
    }
...
[download]

If the file you're reading has fewer than $count-limit lines, the loop will continue to operate on an undefined value of  $line until  $count reaches its limit. (I tried the code on a file with the single DNA sequence included in the OP with interesting results.) I suggest adding a test after the file read:
    $line = <TEXT>;
    last NEXTLINE unless defined $line;

Use of warnings would have allowed Perl to alert you to what was happening. Use of strict is also highly recommended, but would necessitate several further changes to the code.

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