if ( $file_no1 gt $file_no2 )
[download]

You are using text comparison on numbers which will not work correctly:

$ perl -le'print "$ARGV[0] is ", $ARGV[0] gt $ARGV[1] ? "" : "NOT ", "
+greater than $ARGV[1]"'  12 18
12 is NOT greater than 18
$ perl -le'print "$ARGV[0] is ", $ARGV[0] gt $ARGV[1] ? "" : "NOT ", "
+greater than $ARGV[1]"'  12 10
12 is greater than 10
$ perl -le'print "$ARGV[0] is ", $ARGV[0] gt $ARGV[1] ? "" : "NOT ", "
+greater than $ARGV[1]"'  7 10
7 is greater than 10
[download]

Also wrong on these lines:

        if ( $file_no1 eq 0 )
                if ( $mkey eq $k )
                    if ($k eq $file_no1-1 )
            if ( $count1 eq $count2 )
    if ( $flag eq 1 )
[download]

            $indexed= "\(";
            foreach my $index (@array)
            {
                $temp=$index+0;
                $indexed="$indexed $temp";
                $indexed="$indexed,";
            }
            $indexed ="$indexed \)";
[download]

Or just:

            $indexed = "(" . join ", ", @array, ")";
[download]

            $hashref2 = @$VAR2[$k];
[download]

That is correctly written as:

            $hashref2 = $VAR2->[$k];
[download]

                my $srt;
                for (my $s=0;$s<@array; $s++)
                {
                    for (my $r=0;$r<@array;$r++)
                    {
                        if ($s ne $r)
                        {
                            if($array[$s]<$array[$r])
                            {
                                $srt=$array[$s];
                                $array[$s]=$array[$r];
                                $array[$r]=$srt;
                            }
                        }
                    }
                }
[download]

That is usually written as:

                for my $s ( 0 .. $#array )
                {
                    for my $r ( 0 .. $#array )
                    {
                        if ( $s != $r && $array[ $s ] < $array[ $r ] )
                        {
                            @array[ $r, $s ] = @array[ $s, $r ];
                        }
                    }
                }
[download]

Or as:

                @array = sort { $a <=> $b } @array;
[download]

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