[Genome] Unable to re-map sequence to reference assembly

[Tan Hui Hui Jenny]

Hi,

I retrieved the sequence corresponding to these hg18 coordinates chrY:
2,714,760-2,978,360 and designed primers. Then I attempted to do an in
silico PCR to ensure that the primer pairs are giving unique hits. 

Strangely, a couple of primer pairs failed to be re-mapped to hg18.
Eg. primer pair CTGAGTAGCTGGGATTATAGGCA    TGAGGTCCACAATGAATTTCTCT

Then I blat one of these primer sequences, CTGAGTAGCTGGGATTATAGGCA, and
still could not find any hit to hg18.  This is quite puzzling because
doing a simple "find" of the primer sequence within the reference
sequence  (chrY: 2,714,760-2,978,360) confirms that the query sequence
is present.

Could someone explain the apparent discrepancy?

Thanks...

Jenny Tan
Genome Institute of Singapore