use Data::Dumper;

my %hash    = (
 'mus09r' => [ '0,-464,AAACCATCTTGAAAC',
               '0,-350,GGTTCAGGATGGTTT',
               '0,-75,AAAACATCGTGACAC' ],
);

my $string;
while (my ($file,$val) = each %hash) {
      $string.=">dataset\n".
               "$file\n".
               ">instances\n".
               join("\n",@{$val}).
               "\n";
}
print Dumper $string;