CWEALALLAELALAAMKGSTPNGS
HHHHHHHHHHHHHHHHH-------
CWEALALLLEALMRGTTPNGG
HHHHHHHHHHHHHH-------
HHHHH is helix and ----- is loop or unknown

Like in the previous example, we know that the cysteines at the left line up. Thereafter, there cannot be a gap in a helix because if you take out a residue, for example residue 7, then residue 8 will take the place of residue 7, residue 9 the place of residue 8, etc., till we are in a loop where the precise nature of the structure becomes less important. In this particular case there is a Gly just behind each of these two helices. These Glycines allow for the flexibility needed to have different "turns" (in quotes because we don`t know if it is a turn, a turn is between things...) at the end of each of the two helices. So the alignment becomes:

CWEALALLAELALAAMKGSTPNGS
CWEALALLLEALMR---GTTPNGG

The last turn of the shorter helix is missing.

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".