High. I used the RNAmmer site to search for rRNA genes in a draft prokaryotic genome. RNAmmer found rRNA genes, but curiously they are not in a operon. The software found three 5s genes distributed in three different contigs and another 16S rRNA in another contig. This makes no sense as there must be an operon. Have you ever seen something like this and is there another tool that can be used to search for rRNA genes? ( tRNAs were already succesfully predicted with ARAGORN)
You can fetch relevant CMs from Rfam and use them with infernal. However, consider the assembly process. Assemblies tend to break in repetitive regions, no? Since there are multiple rRNAs in prokaryote genomes, they can be considered repetitive regions, no? IMO it's only natural that you'll find partial rRNAs from the ends of multiple contigs..