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use strict;
use warnings;
...
    say $consensus if length $consensus;
    $consensus = q{};
}

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at
gctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaat
+cctgcggacgacccctctcgtggtcg
ttggggctct
ccgccctcttctccgcctgccgttc
ggc