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Y- STRs are Short Tandem Repeats (STRs, refer to the STR page for more details) found on the male-specific Y Chromosome. The coding genes, mostly found on the short arm of the Y Chromosome, are vital to male sex determination, spermatogenesis and other male related functions. The Y-STRs are polymorphic among unrelated males and are inherited through the paternal line with little change through generations.

Y-STRs have been used by forensic laboratories to examine sexual assault evidence. In a sexual assault case, evidence such as vaginal swabs will contain both female and male DNA. Differential extraction is often used to separate the male component from the female component. More often, however, the male and female components cannot be separated completely. As a result, the female component could exist prominently even in the male component after separation. When the "male DNA sample" undergoes the PCR amplification process, the female DNA component is amplified as well, sometimes masking the male DNA, which makes analysis difficult.

Masking does not occur when Y-STRs are examined. Since there is no Y-STR in the female evidence, the only contribution of Y-STR can only come from the assailant(s) in a sexual assault case. The male component will be easily detected, since only this part of DNA will be amplified. The Y-STR system is especially helpful when there are more than one assailant. The mixed pattern in the evidence can help to identify those males responsible for the assault.

Y-STR is also used for non-sexual assault cases where mixed samples are collected from evidence. Sometimes, regular STR will cause the masking effect if there is a very small quantity of male DNA in the mixed sample. Performing Y-STR testing can help to identify all males who have contributed to the evidence.