You'll note that you're only testing against the length of your 0th string, and not the longest one. What you need to do is figure out which is the longest, and test against that. 
my $line_length = 60;
my @strings = ($genome1, $mismatches, $genome2);

# Determine the longest string of the group
my $length = (reverse sort { $a <=> $b } map { length } @strings)[0];

# Then iterate through
for (my $x = 0; $x < $length; $x += $line_length)
{
     print substr ($strings[$_], $x, $line_length),$/ for (0..2);
}

[download]
It's not clear what your join/map combination was doing.

In reply to Re: Wrapping Strings by tadman
in thread wrapping a pair of lines; what if different lengths? by Anonymous Monk

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