Why is NNN sequence at the end of chromosomes

Question

[cammm988]

I was looking at genome.ucsc.edu for chromosome 1 and realized that it was marked as "NNNNNN" sequences for the end of chromosome.

Why isn't it repeating as "TTAGGG" for these telomeric regions? Isn't N defined as undefined or error regions?

Thank you

[lieven.sterck]

yes it is.

perhaps they have been 'repeat masked' (hard-masking) ?

Answer 1

[GenoMax]

See: Why Does The Chr1.Fa Fasta File Have A Bunch Of Ns And Why Is Some Of The Dna In Lower Case Vs. The Rest In Upper Case?

Truly complete sequence of human genome was just pre-published last month. https://www.biorxiv.org/content/10.1101/2021.05.26.445798v1 It will take a while before official genome build gets to that level of resolution.

[cammm988]

Thank you very much. I'll take a close look!