Try to close a gap

Here you are a simple homework to practice with Primer3 and our genome finishing goal.

Using the information stored in mate-paired reads, we see that the 5′-end of “contig05189” is linked to 3′-end of “contig01316”. Please note the 3′ and 5′ ends are indicated in gray boxes for each connection.

You can see that the path to the 3′ is a little bit more complex.

So your task now is to design – using Primer3 – a couple of primers to verify that contig01316 is linked to contig05189 in the direction suggested by the scheme.

You can download the sequence of ┬áthe two contigs from here. Please send your answers to indicating “gap1” as subject.


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