How can I make a faster search algorithm

[pianistseb]

Thank you very much! I started learn python some months ago, but I haven't problems with speed because I didn't deal with big data. Now as my job is in dna sequences, the data structures are very big. In dna science is important to find some motif effects. Erdos motifs are some new mathematical motifs. I change into the binary alphabet because the first research in erdos motifs was in binary alphabet. I want to generalize this research in four-letters alphabet. The erdos_motif, where is also in this program, is a mathematical pattern that has the minimum repeats in it's elements. I have found some effects of this model in an hypothetical dna and now I want to found this motif in a natural dna. This is the reason why I put errors. It's impossible to find this motif in dna except if I put errors. My goal is to search this motif with errors and see if these effects that I have found are valid. Thank you very much guys! Your help is very important to me!
There is the site you can download any fasta file you want!
https://www.ebi.ac.uk/genomes/eukaryota.html
Now I am learning numpy to make my codes faster! I feel very relieved because using this package I will find a solution to my problem.