I have to go run an errand, so I don't have time to analyze your code.

But to make things easier for others, I've re-indented it.

Once I get back, if no one else has figured this out, I'll take a look during the F1 race.

my %file1=();
while(<INPUT1>){
    (my $id, my $number) = split("\t", $_);

    if ($id=~ m/^(CLS_S3_Contig[0-9]+)([-]?)([0-9]+)([_]?)([0-9]+)$/i)
+ {
        my $matched_id=$id; # breaks the CLS_Contig1000_200-202 to its
+ componenents
        for (my $i=$3-8;$i<$5+9;$i++){
            push (@{$file1{$1}}, $i); # This makes a hash of names and
+ each position 
                                      # plus/minus 8 - this is the has
+h with each key
                                      # have multiple values. 
        }
    }#end for if
    else {my $mismatch_id=$id;
        # print "$mismatch_id does not match with CLS_S3_Contigs!\n";
    } # end for else
} # end for while

#reading the file 2 with several columns. columns 2, 5 make a hash of 
+multiple
#value and $mismatch column is the one that need to meet the condition

while(<INPUT2>){
    my ($serial_no ,$contig_id, $position_with_gap, $gap,
     $position_corrected, $ATGCN, $depth,
     $consensus, $mismatch, $star, $geno_A, $geno_B) = split("\t", $_)
+;

    push (@{$file2{$contig_id}}, $position_corrected); #Make a hash of
+ contig ID
                                                       #and base posit
+ion one key
                                                       #multiple value
+s
    push (@{$file2_2{$position_corrected}}, $mismatch);

} #end for while


# Here we are going to have access each element of hash of hash
my $rHoH = foo();my %hash_1;

my( $contig_id, $position_corrected, $mismatch );

for my $serial_no ( keys %$rHoH ) {

    $contig_id = $rHoH->{ $serial_no }->{ 'contigID' };
    $position_corrected = $rHoH->{ $serial_no}->{ 'position_corrected'
+ };
    $mismatch = $rHoH->{ $serial_no }->{ 'mismatch' };
# Now we want to know how many of contigs contain more than three mism
+atch

#Hash_1 here
    if ($mismatch >= 3) {
        #$hash_1{$contig_id} = $position_corrected; 
        ## this will result a hash with name of contig and only one va
+lue per contig
        # that is why it is commented here
        push (@{$hash_1{$contig_id}}, $position_corrected); # This mak
+e a hash
                                                            # with one
+ key with
                                                            # multiple
+ values
        #print RESULTS "$contig_id\t$position_corrected\t$mismatch\n";
+ # This prints all contige that have more than 3 mismatch.
    }
}


# here is where I messed up for the query. I cannot control this loop.
# it finds the things but fails to print them only once. 

foreach $1 (sort keys %file1){
    foreach my $position1 (@{$file1{$1}}){
        $found =0;
        foreach $contig_id(sort keys %hash_1){
            foreach my $position (@{$hash_1{$contig_id}}){
                $found = 1 if $1 =~ /^$contig_id/ && $contig_id=~ /^$1
+/ && $position1==$position;
                print RESULTS "$position1\t$1\n" if $found;

                print "not matched\n" if !$found;
            }
        }
    }
}




##############################################################
sub foo
{
    my ( $serial_no ,$contig_id, $position_with_gap, $gap,
         $position_corrected, $ATGCN, $depth, $consensus,
         $mismatch, $star, $geno_A, $geno_B);

    my %HoH = ();
    open(INPUT2,$ARGV[1]) || die "Cannot open file \"$ARGV[1]\""; # MA
+P file
    while( <INPUT2> ) {
        ( $serial_no ,$contig_id, $position_with_gap, $gap, $position_
+corrected,
           $ATGCN, $depth, $consensus, $mismatch, $star, $geno_A, $gen
+o_B) = split("\t", $_);

        $HoH{$serial_no} {'contigID'} = $contig_id;
        $HoH{$serial_no} {'position_corrected'} = $position_corrected;
        $HoH{$serial_no} {'mismatch'} = $mismatch;
    }

    return \%HoH;
}
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