In the UCSC genome tracks, I come across many blocks of nucleotide positions that have no conservation data corresponding to them. But if I enter this range of positions for which there is no data on conservation, I get the nucleotide sequence ( using view -> DNA ) from the genome browser. For eg, for the position 550000-560000 on the GL172799 (which contains hoxd genes in Xenopus tropicalis) do not have any PhastCons conservation data, but I can get the nucleotide sequence for this region in FASTA format. Could this be because this region isnt present in other taxa against whom conservation is calculated and hence, talking about conservation in such locations doesnt make sense ? What could be other possible reasons this could happen ?
Note - Wherever I mention conservation, I mean the 9way PhastCons conservation scores for Xenopus tropicalis.