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File 1:
one
...
B
C
D

one[tab]A
two[tab]B
three[tab]C
four[tab]D

while (my $col1 = <FILE1>) {
    chomp $col1;
    my $col2 = <FILE2>;
    print "$col1\t$col2";
}

until(eof(ONE) and eof (TWO)) 
{
...
    chomp($two);
    print "$one\t$two\n";
}