I think that what you want to do is "frequent pattern mining". It is a classical problem in data mining, where you have many lines which contains items (numbers). Then we try to find these sets of items that appears in many lines.
To do that, you can try the FPGrowth algorithm offered in SPMF
It will let you specify a minimum support threshold as parameter. This indicates the minimum frequency for the patterns that you want to find. For example, if you set that parameter to 0.4, the algorithm will find all the sets of items appearing in at least 40 % of the lines in your file.
Besides, the FPGrowth implementation in SPMF allows you to specify a maximum length. Thus if you set that to 5, for example, then you will only find sets containing 5 items or less. Then you could sort this by size if you need to.
So I think that you should check this out. I think this is exactly what you need.