Exploring repeats
You want to look at some repeat regions in zebrafish 11:23080000-23135000. Go to that region in Ensembl
(a) Turn on the LTR repeat track. How many LTR repeat sites can you see in this locus?
(b) How long is the longest LTR? What is its name?
(c) Mark the region of the longest LTR. Do you notice anything about the density of any other tracks in this region? Why do you think this is?
(a) Go to the Ensembl homepage (http://www.ensembl.org/).
Select Search: zebrafish and type 11:23080000-23135000 in the text box (or alternatively leave the Search drop-down list like it is and type zebrafish 11:23080000-23135000 in the text box). Click Go.
Click Configure this page.
Click on Repeats regions in the left hand menu. Select LTR (repeats (Zebrafish)) in Expanded. There are nine LTR sites in this region.
(b) Click on the longest repeat to get a pop-up. It is 3814 bp long and is called Gypsy107-I_Dr.
(c) Click and drag a box around the site, then select Mark region. There are no SNPs found in this region. This is likely down to the difficulty of calling SNPs in repeat regions which are longer than NGS sequence reads.
