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while (my $line =<FILE>) {
    my ($one,$two,$three,$four,$five) = split "\t",$line;
    if ($three eq $checkthree) {
...
        last;
    }
}

my $matched;
while (my $line = <FILE>) {
    my ($one,$two,$three,$four,$five) = split "\t",$line;
...
unless ($matched) { # this is like the else
    print "<p>If I put the else statement in it ignores the fact that 
+the parameters match - and comes here!  (But I don't know why).</p>";
}