Question: Ambiguity In Repeat Masked File In Ucsc
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gravatar for figo
7.3 years ago by
figo200
figo200 wrote:

Hi All

I extracted the sequences from chromosome for a repeat element from UCSC which is around 6000 in length which is LINE/L1. Now when I put this sequences in the repeat masker web version to just check it what I find that this sequence has now 3 LINE/L1 which are different types of LINE/L1. So now the length of the repeat element got down and in place I have 3 repeats . Can some one help me to understand this .what should be the length of this element?

Best regards

ucsc • 1.6k views
ADD COMMENTlink modified 7.3 years ago by KCC4.0k • written 7.3 years ago by figo200
0
gravatar for KCC
7.3 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

I would get the consensus sequence for the LINE repeat either from here: http://www.girinst.org/ (You will need to sign up.)

Or you can get consensus sequence from here: http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html

This should give you the size of your LINE/L1 repeat unit.

ADD COMMENTlink written 7.3 years ago by KCC4.0k
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