Hi, I am trying to find the best match of the primer sequence which is 20bp long from a multi fasta file consisting 3 sequences in python3. 10 % mismatch is allowed. I tried to match complement bases of primer and found 1 match but there are supposed to be 2 more but I am struggling with it. Can anyone help me please?

The code I wrote to find the match of complement bases of primer are:

1)

def complement(bases):  ### returning complement bases
    List=[]
    seq_dict={"A":"T","T":"A","G":"C","C":"G"}
    for x in bases:
        if x in seq_dict:
            List.append(seq_dict[x])
    return ''.join(List)

complement(Primer)

2)

with open(multi_fasta,"r")as f_in:   ### extracting the sequence in which there is a primer(complement) match in it
    for lines in f_in:
        if lines.startswith(">"):
            headers=lines.strip()
        else:
            seq=lines.strip()
            if complement(Primer) in lines:
                print(headers+ "\n" + lines)

3) applying re.search to find the location of the match

import re
with open(multi_fasta, "r")as f_in:   
    for lines in f_in:
        if not lines.startswith(">"):
            seq=lines
            r1=re.search(comp_primer, seq)
            print (r1)