Here is just a small snippet that you can use inside your main program.

#!/usr/bin/perl -w
use strict;
my $base = 'ATCGGTAC';
print "base is $base\n";
my @pairs = SplitPairs($base);
print "pairs are @pairs\n";

sub SplitPairs {
  my $base = shift;
  my $baselen = (length $base) - 2;
  my @pairs;
  for my $i (0 .. $baselen) {
    $pairs[$i] = substr $base, $i, 2;
  }
  return @pairs;
}
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This snippet outputs:

base is ATCGGTAC
pairs are AT TC CG GG GT TA AC
[download]

Updated: Put the code snippet into a subroutine.