open(INPUT1, "file1");

my ($havar1, $havar2i, $Genename);

while (<INPUT1>) {
        my $startvar;
        if ($_ =~ /([^-]+)-(.*)/) {
                $Genename = $1;
                my @sparr = split('_', $2);
                open(INPUT2, "file2");
                while(<INPUT2>) {
                        if ($_ =~ /([^-]+)-(.*)/) {
                                my @sparr1 = split('_', $2);
                                if (($Genename eq $1) && ($sparr[0] < $sparr1[0]) && ($sparr[1] > $sparr1[0])) {
                                        print "$Genename\t$sparr[0]\t$sparr[1]\t$1\t$sparr1[0]\t$sparr1[1]\n";
                                }
                        }
                }
                close(INPUT2);
        }
}
close(INPUT1);