unique sequence

[mmmm]

Dear all-

following assembly of short illumina reads- have got the draft genome and when aligned with the reference using mauve- it shows high similarity among each other but the draft genome has unique sequence within the genome that is missing from the reference- when I blasted this unique sequence, it did not give good similarity with other sequence (some hypothetical proteins)- what should be the next step to find out what is this unique sequence?

(I think it might be a sequence of a bacteriophage as it is about 40kb?)

I do not think it is a plasmid since it is integrated within the bacterial genome (not at the end of the assembly)

[rhinoceros]

Does the GC% of this 40 kb stretch differ a lot from the adjacent regions? Does it have really different codon usage in the ORFs? Yes x2? It's probably a phage. But really, you should find a DNA pol, a terminase or a primase or something else phage-like from there to be more certain..

[mmmm]

unique sequence

Does the GC% of this 40 kb stretch differ a lot from the adjacent regions? Does it have really different codon usage in the ORFs? Yes x2? It's probably a phage. But really, you should find a DNA pol, a terminase or a primase or something else phage-like from there to be more certain..

thank you very much for your reply- I have annotated this sequence but not sure if these genes can make a phage??
(hypothetical proteins, replicative DNA helicase, DNA topoisomerase III, Soluble lytic murein transglycosylase, Type IV secretory pathway, VirD4 components, putative membrane protein, Flagellar basal-body rod, Protease VII (Omptin) precursor, Possible exported protein, putative Possible exported protein, putative lipoprotein, Type IV secretory pathway, VirB4 components, putative membrane protein)

[mmmm]

have found the GC% for this unique sequence as 54.5% while the surrounding sequence has 51.5%- most of the annotated proteins are hypothetical as well as DNA helicase, DNA topoisomerase III,...mentioned above

is there a way to prove it is a NEW phage???