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 the two contigs from here. Please send your answers to indicating “gap1” as subject.