Note that if you're using a perl as recent as perl 5.8, you can simplify your initial unpack to: 
@triplets = unpack ('(a3)*', $line);

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So long as you're sure that $line has a length that is a multiple of 3. If you don't necessarily have that, you'll get trailing crud in the last element of @triplets: 
# throw away trailing crud
pop @triplets if $triplets[-1] !~ /.../;

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This leads to this answer for your original question (very similar to what's already been posted) 
my $line      = 'atccatccctttaat';
my @triplets  = unpack( '(a3)*', $line);
my @triplets2 = unpack( 'x(a3)*', $line);
my @triplets3 = unpack( 'xx(a3)*', $line);
# throw away trailing crud
pop @triplets  if $triplets[-1]  !~ /.../;
pop @triplets2 if $triplets2[-1] !~ /.../;
pop @triplets3 if $triplets3[-1] !~ /.../;

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If you want to start reading at some arbitrary point, you can do: 
my @triplets = unpack("x${skip}(a3)*", $line);
pop @triplets if $triplets[-1]  !~ /.../;

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Of course, it might just be easier to replace $line with substr($line,$skip). 
--
@/=map{[/./g]}qw/.h_nJ Xapou cets krht ele_ r_ra/;
map{y/X_/\n /;print}map{pop@$_}@/for@/

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

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