in reply to substr is behaving differently with small vs large strings

It seems that your code works correctly. May be something wrong with data? Anyway I can suggest to improve you code, sub editcontig can be eliminated: 
  my $rawseq = <CONTIG>;
 
  # my $goodseq = editcontig($rawseq);
  $rawseq =~ tr/ \t\n0-9//d;

  # now use $rawseq instead of $goodseq

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