Answer for question in bioinformatics course

Answer:

Aligning them by hand gives the red situation as shown above the question on the course website

You have two sequences TCTVTSNSITCT and TCTVSTCT. Predict their structures. The two structures, schematically, look like:

T-C-T-V-T-S
          |
T-C-T-I-S-N
T-C-T-V
      |
T-C-T-S

So, given that the two cysteine bridges MUST be aligned, and given that an alignment should reflect which residues are at the same position in space, we see that the purple TCTV aligns with the purple TCTV and the orange TCTI with the orange TCTS. So, in the alignment, we need to have the S from TCTS under the I from TCTI.

If this all is still looking difficult, then you can look at a series of videos that are found on the seminars page under "Aligning video page".