Since you had repeating code, my preference is to put it in a loop. I'd also use length instead of /.../, it's computationally less expensive which I assume is important if you're parsing lots of sequences. 
my $line = 'atccatccctttaat';
my %triplets;
for (0 .. 2) {
    @{$triplets{$_}} = unpack(('x' x $_).'(a3)*',$line);
    pop @{$triplets{$_}} if length($triplets{$_}->[-1]) != 3;
    print "Offset $_: @{$triplets{$_}}\n";
}

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In reply to Re^2: variation on splitting a string into elements of an array by bageler
in thread splitting a sequence using unpack by Rashmun

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