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my $input = do { local $/ = undef; <DATA> };
$input =~ s/\s//mg;          # Remove all whitespace.
...
GCAATGCGTCTATTTGTGGGTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCAT
CTCCCGGCTAG

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GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAA
CGCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATT
...
GGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAATGTATCAT
CGCTTTACGTTGGATAGTGACAACTACATCAAGGCAATGCGTCTATTTGTGGGTGAGCC
TGTCTGGACACCATACAATCGTCCGCATGACCATCTCCCGGCTAG