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Hello. Unfortunately Primer-Blast is not supported by UGENE yet. We have planned this feature and it will be implemented in one of some future releases (not the
nearest one).

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As I understood your task, you want to BLAST the gene's sequence in your BLAST database (created from one genome). And you are not interested in the found regions (BLAST results), but you are interested in regions (several nucleotides) located out of the BLAST results (left and right regions). And you don't know how to get these regions using UGENE. Am I right?

If yes: Is it true that this task can be solved using a simple find operation? You can open the genome sequence with UGENE and find the subsequence (the gene's sequence) in the genome. The regions on the left and right sides of the found result are the solution of the task.

Sorry, but I don't understand your task. Could you describe it in more details?
Your input data are:
1) Genome sequence [G].
2) Gene sequence [g].
What is your goal?

As I understood, you try to do the following steps:
1) Create the BLAST database [DB] from G.
2) Search g in G using the find pattern functionality (CTRL+F in the sequence view). It gives the gene region [gr].
3) Pick primers for gr. It gives the primers regions [pr].
So, now you have pr - the regions (annotations) of primers in the source genome.

What do you want to do next? You want to BLAST something (g, or the sequence of gr, or the sequences of pr) in DB and get E-values.