I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome.

For example, in the paper AFLP fingerprinting of the human genome, Human Genetics, 108(1):59-65, Table 1 reports 100's of location of each primer pair:

Now the MseI primer is GATGAGTCCTGAGTAA. So the M-CAA primer should be GATGAGTCCTGAGTAACAA. When I blast this on the reference human genome at NCBI, the results show the best alignment only covers 6-21 of the query:

    Homo sapiens chromosome 7, GRCh38.p2 Primary Assembly
    Query  6          TGAGTCCTGAGTAACA  21
                      ||||||||||||||||
    Sbjct  148723256  TGAGTCCTGAGTAACA  148723241

However, there should be close to a thousand matches for MseI-CAA across the genome according to the table. Does AFLP not require the whole primer to be matched?

According to the original AFLP paper, AFLP: a new technique for DNA fingerprinting, NAR 1995, the figure 1, the whole primer is being aligned.

Cross-posted to Biology.SE