Are you trying to say that you want to remove all spaces (including newlines) and then ensure that there's a newline after every 59th character?
my $input = do { local $/ = undef; <DATA> };
$input =~ s/\s//mg; # Remove all whitespace.
$input =~ s/(.{59})/$1\n/g; # Place a \n after every 59th character.
print "$input\n";
__DATA__
GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAAC
GCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATTCG
AAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAG
GTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG
CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG
AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCA
AGAAAATTCGTGAAGCCAGGGGTTACTCTTACATG
GACATTTGTGATGTGTGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTC
TTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG
GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGG
GCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTACGTTGGATAGTGACAACTACA
TCAAG
GCAATGCGTCTATTTGTGGGTGAGCCTGTCTGGACACCATACAATCGTCCGCATGACCAT
CTCCCGGCTAG
...produces...
GAGGGTGCAATCTACAAGAGTGCGGGTTCGCGTTCAGTCCAAGCTGAACATAAACGCAA
CGCAAGGCCCCTCGACGCAGATACCGCGCTCAGGAGCATTCGAGAAGCCGAAGAAAATT
CGAAGACGAGGACCAGCTACACTGCGGACGGACTTCGGGCATGGAGGGCCAGTTCCAGG
TTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGG
CTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGAACTAGG
AATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAA
TTCGTGAAGCCAGGGGTTACTCTTACATGGACATTTGTGATGTGTGCCCAGAGAAGTTG
CCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGA
GATACGATATTGCCTTGAGGGTAGCGGCTACTTTGATGTGAGGGACCAAGATGATCAGT
GGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAATGTATCAT
CGCTTTACGTTGGATAGTGACAACTACATCAAGGCAATGCGTCTATTTGTGGGTGAGCC
TGTCTGGACACCATACAATCGTCCGCATGACCATCTCCCGGCTAG
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