All NCI Shows say your wrong,wrong,Wrong When Sasuke defeated Deira Karin took His shirt and rub Her face in it getting Her DNA in it. It tells you that She had a habit collecting things that belong to Sasuke and rubbing it on Her thus getting Her DNA on it too. Why do you think the police always takes the bed shits at a murder site? Too know they might have had *** with someone before the murder DNA. Parental test today have a 98% proof in a court of Law.
Naruto isn't known for its scientific accuracy.
Nor are most entertainment productions, for that matter.
Assuming Kishimoto sat down and did some research, he would know that the best means of determining maternal lineage is through mitochondrial DNA, since all of our mitochondria come from our mothers. Thus, direct maternal lineage can be obtained through an analysis of mitochondrial DNA. Determining paternity of a female is not as simple and has a much higher margin of error since one has to look at nucleic DNA and infer how many markers were likely inherited from the father. Generally, paternity tests of females is best done to eliminate potential candidates. Paternity of males is easy to establish since the y chromosome is inherited directly from the father and is, actually, a very short chromosome that is easy to track mutagenic changes through.
Anyway - if Suigetsu's machine works off of mitochondrial DNA (which is stable enough to perform an analysis after several years and can be obtained from hair other than the root), then the only scenario in which there could be a match between Sasuke and Sarada is if Sasuke's mother is from the same direct maternal lineage as Sarada's mother. IE - Sarada's mother would have to be the daughter of a sister or maternally-linked cousin to Sasuke's mother.
If this is how his machine works, and this is how Kishimoto envisioned it, then it is most likely the case that Karin is the only logical match. Granted, the cited time of 1000 years is not great enough to produce substantial mutations in the mitochondrial DNA - so in theory, if the Uzumaki do not predate Kaguya (I suspect they do, and that the Sage's father was an Uzumaki), then it is logical to assume that women of Uzumaki, Senju, Uchiha, and Hyuuga are still part of the same maternal tribe and would all appear as very similar matches. Thus - if Sakura traces her maternal lineage back to Senju, Uzumaki, Uchiha, or Hyuuga, then she could theoretically appear very similar to Karin from a mitochondrial standpoint.
Further, Sasuke would appear very similar to Karin under such a context, as well, assuming both have a direct maternal lineage tracing back to Kaguya.
The only other way a match could be obtained from Sasuke is if one is going off of nucleic DNA. It is not possible to get this from strands of hair that do not include the root, and it is difficult to get quality samples. While flakes of skin, sweat, and saliva can contain DNA, getting clean samples from these sources for analysis is problematic. Rarely do you get large portions of the genetic code, and you often have to introduce various polymerase strategies that are known to be the source of errors when identifying strains of viral infection (often inducting other strands of code from the host's destroyed cells into the chain).
Contamination from various other DNA sources is, therefor, an issue with these types of samples. If rubbing one person's face on a shirt is enough to leave behind DNA that can be sampled - then the person who was wearing it first also left behind substantial traces. This is why these types of samples are generally used only as a last resort and must be given a wide margin of error even in the case of using them to positively identify an individual - much less use them to infer maternity.
But, we're dealing with Naruto, here.
The only thing we can assume for the moment is that the machine is accurate in its analysis - whatever sample was placed in it has correctly identified a match to Sarada as being from her mother (the machine is not mistaken or flawed).
This leaves two possible scenarios for this to point to something other than the direct interpretation:
As the OP states, that the sample is somehow not from Karin and is, instead, from Sasuke (thus, the machine has identified a match to the father).
Or that Sakura and Karin have a very strong or close common ancestry.
I suppose a third option does exist where Sarada is some kind of experiment from Orochimaru who Sakura opted to take care of. Or maybe an experiment from Karin...
Or... perhaps Sakura is Karin in disguise...
The real Sakura is out there, somewhere (though one would think that Naruto and others would have noticed the difference... but...).