It is hypothesized that transposons can rapidly move through populations and species by horizontal transfer, most likely through viruses.

Barbara McClintock named the transposons that are defective, and serve as sites of chromosomal breakage where other transposons insert (the associator, Ac) the dissociators. These were likely transposons that lacked the transposase that catalyzes their movement.

Two transposons flanking an antibiotic resistance gene can easily move between bacteria and confer new resistance. A mix of transposons and new genes such as this is called a composite transposon. Recall that bacteria exchange genetic information via conjugation, transduction, and transformation.

LTR stands for Long Terminal Repeats, which are 250-500 base pair repeats located on the ends of a transposon. These repeats encode a series of proteins, most significantly transposase. These are very likely to be early evolutionarily stages of retroviruses.

Non-LTR retrotransposons use an endonuclease that nicks thymine-rich host DNA, which eventually leads to incorporation of the transposon by host DNA repair functions. These other methods are all associated with different specializations of transposon.

The correct answer is that rRNA genes have both highly conserved and highly variable regions. Molecular typing is the process of identifying species from a microbiome by analysis of common molecules or genes. All organisms including eukaryotes, prokaryotes, and archaea, (but not viruses) have multiple rRNA genes. Given that rRNA genes have highly conserved regions, it allows researchers to identify transcripts/genes as rRNA genes in unknown species. Comparing the sequences of the variable regions of the rRNA genes allows researchers to identify the species of the organism from which it is derived. 

An orthologous gene is one that is descended from a common ancestral sequence. So, when two sequences from different species are compared, they are orthologs if they have the same evolutionary history. A paralogous gene is the case in which a similar gene sequence is derived from a genome duplication event, and do not have a evolutionary relationship. These genes often develop different functions, unlike orthologs.

Tandem arrays are used for extremely important genes, like ribosomal RNA genes that are vital for organism function. The arrays serve to allow massive parallelized encoding of these genes, because many copies are required.

The correct answer is rRNA genes and ITS have highly conserved regions and highly divergent regions. Both prokaryotes and eukaryotes have rRNA genes and ITS, making these ideal targets for molecular typing. In order to amplify, then sequence these regions for evolutionary comparisons, universal primers are designed to anneal within the highly conserved regions and amplify through the highly divergent regions. The divergent regions of rRNA genes and ITS allow for specie to specie comparison and identification. 

When two sequences have less than 20% identity, it is almost impossible to align them and identify that they are actually orthologs. This is especially the case in huge genome data sets, in which it is impossible to find matching sequences by hand.