I am trying to align multi fasta files containing HLA allele sequence data. My goal is to match the MAFFT alignment with the IMGT/HLA database alignment. After alignment, the number of gaps remain the same but the assignment of gap positions is varying by 1 or 2 nucleotides.

For example:

        GCCCT_ _ _ _ _ _ GACCC
     CCCTG _ _ _ _ _ _TGACCC

Can anyone give me some pointers on how I can match these alignments?

I tried reversing the sequencing before alignment and then reversing the alignment output again before visualising.