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my $ref = 'agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg';

...
}

print "$_\n" for $ref, @output;

agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg
 gctagctag tag   gctagctag         gctagctag
     gctagctag     tag tag             gctagctgac
   tag tag tagcatgctagctag           tag tag