import pandas as pd

df = pd.read_csv('TypeII_REs.tsv', delimiter='\t')
sites = pd.read_csv('out_2.tsv', delimiter='\t')['Site'].to_list()
result = df[(df['Putative'] == 'no') & (df['Recognition site'].isin(sites))]
result.to_csv('result.tsv', sep='\t')