Nevermind all, I figured out a way with a bit more tinkering. I just made variables using substrings that took the first 100 base pairs from both the forward and reverse. The foreach loop is now a for loop that looks like this:

for (my $i = 0; $i < scalar(@mainseq); ++$i)
{
$rvscomp = reverse $mainseq[$i][1];
$rvscomp =~ tr/ACGT/TGCA/; 
$fwd100 = substr($mainseq[$i][1],0,100);
$rvs100 = substr($rvscomp,0,100);
print "$mainseq[$i][0]_forward_first_100\n$fwd100\n$mainseq[$i][0]_rev
+ersecomp_first_100\n$rvs100\n";
}
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