If you use strict and warnings, you will see these warnings:

Argument "A" isn't numeric in numeric eq (==)
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You need to use string equality. Change == to eq

use warnings;
use strict;

$_ = 'AAGCTT';
while (/(.)/g) {
    my $letter = uc $1;
    print $letter;
    my $len = length($letter);

    my $sub = "";
    if    ( $letter eq "A" ) { $sub = "T"; }
    elsif ( $letter eq "T" ) { $sub = "A"; }
    elsif ( $letter eq "G" ) { $sub = "C"; }
    elsif ( $letter eq "C" ) { $sub = "G"; }
    print "  $len\t$sub\n";
}    # close while

__END__

A  1    T
A  1    T
G  1    C
C  1    G
T  1    A
T  1    A
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Another way to do it is with a hash:

my %conv = (
    A => 'T',
    T => 'A',
    G => 'C',
    C => 'G',
);

$_ = 'AAGCTT';
while (/(.)/g) {
    my $letter = uc $1;
    print $letter;
    my $len = length($letter);
    print "  $len\t$conv{$letter}\n";
}
[download]