It is true that these sequences are used as binding sites for sequencing primers but initially they serve as transposase recognition sequences, namely 19-bp Mosaic Ends (ME). These sequences are there in order for the oligos to bind efficiently with the transposase.

Best,

Tonis

From what I remember, the second part of the adaptor sequence is used as a spacer to make sure that you will get the sequence of ALL of your library DNA.  Also, you can use it as a way to easily trim your reads.

@Katie thx for your answer. If you are right and it's only meant to be a spacer I wonder why this sequence is identical for the Forward and reverse read. If I understand it correctly this leads to formation of hairpins within the single strands after amplification doesn't it? It should look like this:

5‘ tcgtcggcagcgtcAGATGTGTATAAGAGACAG-Targetseq-CTGTCTCTTATACACATCTccgagcccacgagac 3‘

I guess there must be a reason for that?

Dear Johannes,

this is the sequencing primer binding site.

All the best

Martin

Hi Martin,

thx for the answer, that sounds reasonable!

It is true that these sequences are used as binding sites for sequencing primers but initially they serve as transposase recognition sequences, namely 19-bp Mosaic Ends (ME). These sequences are there in order for the oligos to bind efficiently with the transposase.

Best,

Tonis