The dark genome refers to the portions of DNA that do not encode for traditional proteins. These non-coding regions are primarily composed of repetitive elements, also known as repeats.

Repetitive elements are sequences of DNA that occur in multiple copies throughout the genome. They can vary in length, ranging from a few base pairs to several thousand base pairs. Repetitive elements can be classified into two main types: tandem repeats and interspersed repeats.

Tandem repeats: These repeats are characterized by sequences of DNA that are repeated one after another in a head-to-tail fashion. One example of tandem repeats is microsatellites or short tandem repeats (STRs). These consist of short sequences, usually 1-6 base pairs in length, that are repeated in tandem. For instance, the DNA sequence "ACGACGACG" repeated multiple times forms a tandem repeat.

Interspersed repeats: These repeats are scattered throughout the genome and can be further divided into two subtypes: transposable elements and satellite DNA.

Transposable elements: These are DNA sequences that have the ability to move or transpose themselves within the genome. They can be classified into two main classes: DNA transposons and retrotransposons. DNA transposons move via a "cut and paste" mechanism, while retrotransposons use an RNA intermediate to "copy and paste" themselves into new genomic locations. One well-known example of a retrotransposon is the Alu element, which is around 300 base pairs long and is estimated to have over one million copies in the human genome.

Satellite DNA: Satellite DNA consists of highly repetitive sequences that are often found in centromeres and telomeres, the specialized regions of chromosomes. These repetitive sequences play important roles in chromosome structure and function. One example of satellite DNA is the human telomeric repeat sequence (TTAGGG), which is repeated hundreds to thousands of times at the ends of chromosomes.

The presence of repetitive elements in the dark genome has raised questions about their functional significance. While some repetitive elements have been associated with genetic disorders and diseases, many of them are thought to have regulatory roles in gene expression, chromatin structure, and genome stability.

References:

1. De Koning, A. P., Gu, W., & Castoe, T. A. (2011). Repetitive elements may comprise over two-thirds of the human genome. PLoS genetics, 7(12), e1002384.
2. Feschotte, C. (2008). Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics, 9(5), 397-405.
3. Rudd, M. K., & Wray, G. A. (2015). The evolutionary dynamics of repetitive DNA in eukaryotes. Nature, 16(2), 109-120.