my $str = '
AAGTAATCAAGTATTACAAGAAACAAAAATTCAAGTAAATAACAGATAAT
ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGC
                                                  
>YDR256C  CTA1  969666  970216
GGGAAGAACTAAGAGATGTTATGGCTCGGAGAGTTTTGAAAAGCGAAATA
GATTCGCTGCAAGTTTGTGAAGAAACCATCGACAAGAATTACAAGGTTAT
';

# and it can be more than one empty lines 

##</code><code>##

$VAR = '
AAGTAATCAAGTATTACAAGAAACAAAAATTCAAGTAAATAACAGATAAT
ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGC
>YDR256C  CTA1  969666  970216
GGGAAGAACTAAGAGATGTTATGGCTCGGAGAGTTTTGAAAAGCGAAATA
GATTCGCTGCAAGTTTGTGAAGAAACCATCGACAAGAATTACAAGGTTAT
';

##</code><code>##

use Data::Dumper;

$str =~ s/[\s]+//mgx;
print Dumper $str;