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 Biostars.
Update: One needs to use the digestion enzyme recognition site to map the AFLP markers. Example: http://insilico.ehu.es/AFLP/info.html