Unfortunately my data doesn't give simple answers, and that is my fault completely for not being more careful with how I constructed the test data. My results are:

0 :: 1  ATGGAGAACATCACATCA and GACTCCTAGGACCCCTTC
0 :: 2  TCACATCAGGACTCCTAGGACC
0 :: 3  ACATCAC
1 :: 2  GACTCCTAGGACC
1 :: 3  ACATCAC
2 :: 3  CAGGA and ACAGG
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