I am no biologist, but I am supposing octamer motifs are just 8 particular bases (ie ATTCGTGT). You can download the whole genome (its about 135 Mb), and then run a simple program that counts the number of motifs matching yours (This is like counting the kmers for k=8).

You could do it like this in C:

#include <stdlib.h>
#include <stdio.h>

int main(){


    char myOctamer[8] = "ATTCGTGT"; // Your octamer here

    FILE * genomeFasta = fopen64("file.txt", "rt");

    char c;
    int totalFound = 0, current = 0;
    while(!feof(genomeFasta)){
        c = fgetc(genomeFasta);

        if(c != '\n'){
            if(c == myOctamer[current]){
                current++;
                if(current == 8){
                    current = 0;
                    totalFound++;
                }
            }else{
                current = 0;
            }   
        }


    }
    fprintf(stdout, "Found %d occurrences.\n", totalFound);
    return 0;
}

This works for only one octamer, but generalizing it to n octamers would not be difficult. Notice this will not work for overlapped sequences. And in case you actually use it, I recommend compiling with D_FILE_OFFSET_BITS=64 to be able to handle large sequences (over 2GB).

Hope this helps and that I am not too far from the main point, Esteban

A kmer counter like khmer or Jellyfish can be used to obtain all octamer frequencies, then filtered for the subset of interest.

compseq if EMBOSS can give you the number of times every possible octamer appears in a sequence. Can be run via galaxy. Make sure to set all frames in the parameters.

thank you very much to all of you, your response is very helpful.