I have a list of epitope sequences from the pathogen causing human infection. I am planning to align these sequences to its corresponding antigenic protein seq coming from different populations to detect the polymorphisms present in epitope seq. My question is does it makes any sense to conduct this analysis? Since most of the epitope seq are belong to the repetitive region. A suggestion would be appreciated.

Epitope seq

DRAAGQPAGDRAAGQPAGDRA
DRAAGQPAGDRAAGQPAGDRC
DRAAGQPAGDRADGQPAGDR
DRAAGQPAGNGAGGQAAGGN
DRADGQPAGDRAAGQPAGDR
DRADGQPAGDRADGQPAGDR
EDGAGNQPGANGAGNQPG