It's possible to search for a query not the length used to create the index (for example a query >n or a multiple of n) without recreating the whole hashtable?

This program does it.

Update: Changed program so it finds matches in while loop - no need to store data. Process it as you read it.

#!/usr/bin/perl
use strict;
use warnings;

# 'shift' removes items from @ARGV
my $nomefile = shift;
open my $fh, '<', $nomefile or die "Unable to open $nomefile. $!";

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

my $sequenza;
chomp(my $id = <$fh>); # reads first line ('should' be ID)

print "\nResults for $nomefile\n\n";

while (my $line = <$fh>) {
    chomp $line;
    
    if (substr($line, 0, 1) eq '>') {        
        find_matches($id, $sequenza, $query);
        
        $sequenza = '';
        $id = $line;
    }
    else {
        $sequenza .= uc $line;    
    }
    
    find_matches($id, $sequenza, $query) if eof;
}

close $fh or die "Unable to close $nomefile. $!";


sub find_matches {
    my ($id, $sequenza, $query) = @_;
    my @pos;
    
    while ($sequenza =~ /(?=$query)/g) {
        push @pos, $-[0] + 1;    
    }
    
    if (@pos) {
        printf "%s compare %d volte in posizione @pos with ID %s\n",
            $query, scalar @pos, $id;
    }
    else {
        print "$query does not appear in the sequence with ID $id\n";
    }
}
[download]

For 3 runs of the program (using the same data file I used in my first post).

C:\Old_Data\perlp>perl t33.pl fasta.txt
Insert query:
ttag

Results for fasta.txt

TTAG compare 1 volte in posizione 108 with ID >chr1
TTAG does not appear in the sequence with ID >chrM

C:\Old_Data\perlp>perl t33.pl fasta.txt
Insert query:
aaaaa

Results for fasta.txt

AAAAA compare 3 volte in posizione 59 130 131 with ID >chr1
AAAAA does not appear in the sequence with ID >chrM

C:\Old_Data\perlp>perl t33.pl fasta.txt
Insert query:
tagcgat

Results for fasta.txt

TAGCGAT does not appear in the sequence with ID >chr1
TAGCGAT does not appear in the sequence with ID >chrM
[download]

 

And it seems that the position of the oligos found in the sequence are shifted by one, i know that we count from zero but i can't figure out how to change it

This code push @pos, $-[0] + 1; will give the position as though counting from 1 (instead of 0). It adds 1 to the offset of the beginning of the pattern match.

The @- special variable can be found here Variables related to regular expressions. Scroll down to •@LAST_MATCH_START.

It says

$-[0] is the offset of the start of the last successful match. $-[n] is the offset of the start of the substring matched by n-th subpattern, or undef if the subpattern did not match.

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