Hello, Thank you for your kind response! I worked on it and this program does everything i need

use strict;

my @bases;
my @list;
my @List;
my %oligo = ();
my %pos = ();
my $base;
my $list;
my $f;
my $nomefile;
my $line;
my $piece;
my $query;
my $len;
my $sequenza;
my $i;
my $j;
my $rev;
my $revcomp;
my $oligo;
my $length = length($sequenza);
my $piececomp;


print("Insert query:\n");
$query = <STDIN>;

chomp($query);

$len = length($query);

$query = uc $query;


@bases = qw(A G C T); #bases
@list = qw(A G C T);  #seed


for ($i = 0; $i < ($len - 1); $i++) 
{
    foreach $base (@bases)
    {
         foreach $list (@list)
         {
            $oligo{$base.$list} = 1;
         }
         
    @List = keys %oligo; 
    
    }
    
  @list = keys %oligo;
  
  %oligo = ();
  
    #print "@list   xxx \n";             
} 

%oligo = ();
@List = sort @List;



$nomefile = $ARGV[0];

open $f, "< $nomefile" or die "cannot open $nomefile: $!";

$line = <$f>;
chomp($line);

if(substr($line,0,1) ne ">")
{
 print STDERR ("Input file $nomefile not in FASTA format\n");
 exit;
 }



$sequenza = <$f>;


while($line = <$f>)
{
    chomp($line);    
    
    if(substr($line, 0, 1) ne ">")
    {
        $sequenza = $sequenza.$line;
    }
    
     
}

$sequenza = uc $sequenza;



for($i = 0; $i < length($sequenza) - ($len - 1); $i++) # nell'ultimo f
+rame di lettura non deve contare la len intera se no va 'fuori sequen
+za' e non trova l'oligo corrispondente
{

 $piece = substr($sequenza, $i, $len);

 if(exists $oligo{$piece})
  {
     $oligo{$piece} = $oligo{$piece} + 1;
     push(@{$pos{$piece}} , $i );
  }
 else
  {
    $oligo{$piece} = 1;
    push(@{$pos{$piece}} , $i );
    
  }
  
}


foreach $piece (sort keys %oligo)
{
 print("$piece\t$oligo{$piece}\t@{$pos{$piece}}\n\n");
}


$rev= reverse $query;
$rev=~ tr/ACTG/TGAC/;
$revcomp = $rev;


for($j = $length; $j < $length - $len; $j--) 
{    

    $revcomp = substr($sequenza, $j, $len);
 

    if(exists $oligo{$revcomp})
    {
        push(@{$pos{$revcomp}} , ($length - $j) - ($len - 1));
      }
 
}
  

if(exists $oligo{$query} && !exists $oligo{$revcomp}) 
 {
    print("$query\t compare $oligo{$query} volte\t in posizione @{$pos
+{$query}} solo sul filamento positivo\n");
 }
 else
 {        
    if(exists $oligo{$query} && exists $oligo{$revcomp})
    {
        print("$query\t compare $oligo{$query} volte\t in posizione @{
+$pos{$query}} sul filamento positivo\n\ne compare $oligo{$revcomp} vo
+lte\t in posizione @{$pos{$revcomp}}\t  sul filamento negativo\n");
    }
    else
    {    
        if(!exists $oligo{$query} && exists $oligo{$revcomp})
        {
            print("$query compare $oligo{$revcomp} volte\t in posizion
+e @{$pos{$revcomp}}\t sul filamento negativo\n");
        }
        else
        {
            print("$query non compare nella sequenza\n");
        }
    }
 }
[download]

It tells me if an oligo appears only in positive strand, in positive and negative and only in negative strand by searching in an hash table i created using the length of the query written from keyboard. I'm searching an oligo on the negative strand by searching its reverse complementary on the positive strand. The sequence i'm working on begins with GATCAC and end with ACGATG. The program works fine with these sequence, but when i search their reverse complementary, the position on the negative strand are wrong (if i search the reverse complementary of the first oligo in the positive strand, it should be in the last position of the negative strand, instead the program tells me that it is in the first one). This is the problem! However you've done a great work, and it should help me with my problem!