Keep the longest chains

[SheeppOSU]

Try this

L1=[]
L2=[]
L3=[]
L4=[]
with open ("C:/Users/lveillat/Desktop/Données stage/Fichiers tests/test_retrait_chaines_intermediaire.txt","r") as f1:
 
    for lignes in f1:
        lignes=lignes.rstrip('\n')
        L1.append (lignes)
        L2.append (lignes)
 
    for i in L1:
        if i not in L4:
         
            L4.append(i)
            L3.append(i)
        else:
            continue
 
        for j in L2:
            if i in j or j in i:
                if i != j:
                    L4.append(j)
                    L3.append(j)
            i = j
 
        print(L3)
        L3.clear()

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Hope this works