Using the regex
module:
import regex
sequence = 'aaaaaaaaaaaabbbbbbbbbbbbcccccccccccc' #being searched
query = 'aaabbbbbbbbbbbbccc' #100% coverage
query_1 = 'aaaabbbbbbbbcbbbcccc' #95% coverage
query_2 = 'aaabbbbcbbbbbcbccc' #90% coverage
threshold = 0.97
queries = (query, query_1, query_2)
for q in queries:
error = int(len(q) - (len(q)*threshold))
m = regex.search(r'(%s){e<=%d}'%(q,error), sequence)
print 'match' if m else 'nomatch'