G'day azheid,

You can just use the glob function: there's no need to use the shell.

#!/usr/bin/env perl -l

use strict;
use warnings;

my @x = glob '{CAT,CAC}TGG{GTT,GTC,GTA,GTG}{CCT,CCC,CCA,CCG}';
print "@x";
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Output:

CATTGGGTTCCT CATTGGGTTCCC CATTGGGTTCCA CATTGGGTTCCG CATTGGGTCCCT CATTG
+GGTCCCC CATTGGGTCCCA CATTGGGTCCCG CATTGGGTACCT CATTGGGTACCC CATTGGGTA
+CCA CATTGGGTACCG CATTGGGTGCCT CATTGGGTGCCC CATTGGGTGCCA CATTGGGTGCCG 
+CACTGGGTTCCT CACTGGGTTCCC CACTGGGTTCCA CACTGGGTTCCG CACTGGGTCCCT CACT
+GGGTCCCC CACTGGGTCCCA CACTGGGTCCCG CACTGGGTACCT CACTGGGTACCC CACTGGGT
+ACCA CACTGGGTACCG CACTGGGTGCCT CACTGGGTGCCC CACTGGGTGCCA CACTGGGTGCCG
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Be aware that there's a system-dependent limit on the size of the result. See GLOB_LIMIT, in File::Glob, for details.