You need to use semicolon after the end of your statement in your program. It should be

my $dna1 ="AACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAA
+AACAATCACAATCGCGGGTTTCATAGAAAATGGTTGGGAAGGAATGGTGGATGGTTGGTACGGTTT;
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Also, your regular expression doesn't makes sense to me. I think you need to use if loop rather than while for looking is you are looking for a space in your string. Also, I really don't understand the use of {} in you regex as you are substituting it with the space. Also there is no command called pos.