Prediction of SSU, LSU, and ITS regions from genome assembly that related together

Question

[ALI Hkz]

Hi,

I would like to find SSU, LSU, and ITS regions from a genome assembly. however, I used metaxa2 and ITSx software for that, but i want to find which of these regions are related together. These regions will be later for creating a curated database. do i use the right tools for this purpose? That's important that they be in the right direction (belonging to main strand or complementary).

Thanks in advance for your help.