I don't have time to dive deep into your code right now, but, at least, change this: 
      if ($start == 0)
         {
         goto NEXTLINE;
         }

[download]
to a next statement with a label: 
next NEXTLINE if $start == 0;

[download]
See also Dijkstra's famous and classical article Go to statement considered harmful: https://files.ifi.uzh.ch/rerg/arvo/courses/kvse/uebungen/Dijkstra_Goto.pdf.

In reply to Re: Finding biological palindromes by Laurent_R
in thread Finding biological palindromes by TJCooper

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