> Most recently, a transposon jumped from E.coli into my backbone, and I picked it up during sequence. 6kbp added instantly.

Can you explain this more? Are you referring to your actual backbone? How did ecoli meet your backbone and why were you sequencing your backbone?

Backbone refers to the cloning plasmid.

Plasmids are grown inside of bacteria which have their own genome with all sorts of oddities like transposons.

Transposons are 'jumping' bits of dna that can insert themselves (given the right criteria is met).

So a transposon(s) from the E. coli genome inserted itself into the plasmid.

This causes all sorts of problems for people who use them to clone (insert) dna into them.

Apologies, sometimes I forget that I am on a computing forum. Backbone == plasmid backbone. greazy had a good explanation. I'm trying to clone synthetic DNA into plasmids, so all the junk that is necessary for replication and selection is commonly referred to as the "backbone" or "vector", whereas your insert is usually just called the "insert".

Thanks for the explanation that’s very interesting.