./targetscan_70.pl miR_Family_info_sample.txt UTR_Sequences_sample.txt targetscan_70_output.txt

I do get the same error if I try to run this as Perl code. This is not Perl.

You're supposed to run this command using your shell (you do know how to use bash and Terminal.app, right?). cd to where you downloaded the files and then type in something like perl targetscan_70.pl miR_Family_info_sample.txt UTR_Sequences_sample.txt targetscan_70_output.txt. Otherwise (if you require Padre to work with the script for some reason), open targetscan_70.pl itself in Padre and find a way to change directory from within Padre and pass the opened script some command line arguments.