Unfortunately, the answers are not simple and that's my fault for not being more careful with the test data I created. The correct answers are:

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