Do you really need to specify a max? Can't you just replace {1,9} with +?

The last \s+ needs to be \s* (or needs to be removed) for regexp to match what you provided.

(\n\w+) should be (?:\n\w+) (speeds things up a little), or maybe even (?:\n[ACGT]+) (for conciseness).

$ssh[0] = <<'__EOI__';
>MWG869551-C3277-T7
CCCATCCAGTTTATGAGATCGCGCATTGATCGCCCGAGGCGGTCTA
GCCGCCACACCACTAATGTATCGCCGGCGCGCAATTGCTCTTTAATTTTCTCAAGCCCCG
GCCGCGCAGTGACAACGCCAGAGACCTTATCAGTGATGACCTTTTCGCAGCCCGCCGCCC
GTAAAGCGTCGGTTTGAAGATCCAAATTTTGTTCGATGGTCGAGACCCGCGCATAGCCAA
TCTTCATACGAGCAGTGCCCGGCCATTGAGAAAAGGAAGAAAACTCATGTTATCCTGAAA
TTCATTGCCCTAGTTTTCTTTACCGAGTAGATTTACCGGCATTCGGTAGAATTGGCAACG
TGTTGGAGATCGCGTGACCATTACC
>...
__EOI__


if ($ssh[0] =~ /^\s*>(\w+)\-(\w+)\-(\w+)\s*((?:\n[ACGT]+)+)/)  {
   print "$1 $2 $3 \n $4\n";
}

__END__
output
======
MWG869551 C3277 T7

CCCATCCAGTTTATGAGATCGCGCATTGATCGCCCGAGGCGGTCTA
GCCGCCACACCACTAATGTATCGCCGGCGCGCAATTGCTCTTTAATTTTCTCAAGCCCCG
GCCGCGCAGTGACAACGCCAGAGACCTTATCAGTGATGACCTTTTCGCAGCCCGCCGCCC
GTAAAGCGTCGGTTTGAAGATCCAAATTTTGTTCGATGGTCGAGACCCGCGCATAGCCAA
TCTTCATACGAGCAGTGCCCGGCCATTGAGAAAAGGAAGAAAACTCATGTTATCCTGAAA
TTCATTGCCCTAGTTTTCTTTACCGAGTAGATTTACCGGCATTCGGTAGAATTGGCAACG
TGTTGGAGATCGCGTGACCATTACC
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