Ambiguity In Repeat Masked File In Ucsc

Question

[figo]

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

Answer 1

[KCC]

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.