Initializing nucleic acids...done.
Applying constraints...Warning: Invalid nucleobase positions in SHAPE file Pipeline_SINEC_Cf_80_amplicon.shape: [81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155]. (Sequence length is 80.)
done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 25% [=============                                     ] /                     
 31% [================                                  ] -                     
 37% [===================                               ] \                     
 43% [======================                            ] |                     
 50% [==========================                        ] /                     
 56% [=============================                     ] -                     
 62% [================================                  ] \                     
 68% [===================================               ] |                     
 75% [======================================            ] /                     
 81% [=========================================         ] -                     
 87% [============================================      ] \                     
 93% [===============================================   ] |                     done.
Writing output ct file...done.
Single strand folding complete.