#!/usr/bin/perl 
use strict;
use warnings;

my $line ;
 
while (<DATA>) { 
    next unless /\A (\w+[.]\w+) \s+ (.+) \z/xms;
    print unless $line->{ $1 }++;

};


__DATA__
# Log file 13/3/2008
MA01001A1A03.f1 760 5640111 ad1
MA01001A1A03.f1 760 42572233 ubq
MA01001A1A04.f1 300 15232924 ubq
MA01001A1A04.f1 300 145334669 DNA
#
MA01001A1B22.f1 580 77745475 ra
MA01001A1B22.f1 580 30409730 ra 
MA01001A1A03.f1 760 5640111 foo
MA01001A1A04.f1 300 15232924 bar
# End of log

##</code><code>##

Output:

MA01001A1A03.f1 760 5640111 ad1
MA01001A1A04.f1 300 15232924 ubq
MA01001A1B22.f1 580 77745475 ra