$str =~ s/(^|\n)[\n\s]*/$1/g;

print $str;

##</code><code>##

AAGTAATCAAGTATTACAAGAAACAAAAATTCAAGTAAATAACAGATAAT
ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGC
>YDR256C  CTA1  969666  970216
GGGAAGAACTAAGAGATGTTATGGCTCGGAGAGTTTTGAAAAGCGAAATA
GATTCGCTGCAAGTTTGTGAAGAAACCATCGACAAGAATTACAAGGTTAT