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

print $str;
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    AAGTAATCAAGTATTACAAGAAACAAAAATTCAAGTAAATAACAGATAAT
ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGC
>YDR256C  CTA1  969666  970216
GGGAAGAACTAAGAGATGTTATGGCTCGGAGAGTTTTGAAAAGCGAAATA
GATTCGCTGCAAGTTTGTGAAGAAACCATCGACAAGAATTACAAGGTTAT