Usually, there is a size selection step during library preparation, removing (reducing) fragments under a certain size. If that cutoff is above the size of your plasmid, it may have been removed. Otherwise, (reads originating from) plasmids will be part of the final dataset or assembly. Beware that the assembly process could potentially result in them being merged to another part of the genome, e.g. (one of) the chromosome(s).
Is there any computational method to check that???
I used UniVec Database For the Confirmation.. But What I think, There are limited sequences in UniVec near about 3K-4K. Now, I am looking for some computational tool which can help me regarding!