[Genome] question about repeats in hg16

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lise andrieux

Mar 8, 2011, 12:31:29 PM3/8/11
to gen...@soe.ucsc.edu

I couldnt find the answer therefore I am contacting you:

I have downloaded data for chromosome 1 of hg16 from the downloads page, at

It is written there:

- chr*.fa.zip: compressed FASTA sequence of each chromosome.
Each chromosome is in a separate file in a zipped Fasta format.
Repeats -- which are shown in lower case -- are annotated by
RepeatMasker run at the sensitive setting and Tandem Repeats Finder

(repeats of period 12 or less).

Repeats are in lower case, however in my data there are lower-case
letter but also N, and as usually N is used to annotate repeats,

I am now wondering what are the lowercase letters, if they really are
repeats, or introns, and if they are repeats, what are the N ?

Thanks for your help,

Best regards,

Lise Andrieux

Lise Andrieux, PhD
Life Sciences DPT
Barcelona Supercomputing Center

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Vanessa Kirkup Swing

Mar 8, 2011, 7:40:48 PM3/8/11
to lise andrieux, gen...@soe.ucsc.edu
Dear Lise,

The N's are gaps. You can open up a gap track in the the Genome Browser to visually see these.

Hope this helps. If you have further questions, please contact the mailing list.

Vanessa Kirkup Swing
UCSC Genome Bioinformatics Group
Genome maillist - Gen...@soe.ucsc.edu
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