in reply to Finding biological palindromes

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