Against whose DNA does Cisco match?

It takes a few steps to know this.

First, we know that Eobard Thawne, the Reverse Flash traveled back in time to kill the 11 year old Barry Allen. During that event, he fought with 2024's Flash, and both of their blood got splattered on the walls of the Allen house. DNA comparison tests were made using the Central City PD DNA database, which only carries the DNA of criminals who are alive.* Joe West asked Cisco to specifically test the samples against Dr. Wells.

Getting a DNA sample of the present Dr. Wells would be trivial, as all that is needed a single hair, some spit on a water bottle, or even the oil from a fingerprint. Cisco had plenty of access. Incidentally, the scoobies have Barry's DNA on file, as they run extensive tests on him, as well as all the other meta-humans they routinely analyze in order to determine how their powers work.

The blood sample shows two DNA patterns, one "wasn't identified", the other matching an adult Barry (based on protein p16 levels). This was Episode 13 "The Nuclear Man".

A few episodes later, in "Tricksters", we see that Eobard Thawne looks nothing like Wells when he pulled off the mask. But later in the episode we see that he has stalked and followed the real Harrison Wells, and stabs him with a device after the car crash. This device drains Wells and allows Eobard to look like him. From an interview:

"That's future tech. We're calling it genetic camouflage," executive producer Andrew Kreisberg told E! News and a small group of reporters after screening the episode early. "He basically stole his body. He rewrote his DNA to match Wells".

This is basically how the meta-human "Everyman" works, which is the main antagonist from episode 19, "Who Is Harrison Wells?". The theme of the episode, DNA based cloning, is giving you the clue to answer the question in-universe. Eobard-Wells has the DNA of the real Wells. Cisco and Joe already doubt Eobard-Wells. Having found a corpse at the scene of a fatal car crash Wells said he was in, they put two and two together, and decided the logical test would be to compare Wells' DNA to the corpse. They use the sample of the Real Wells to confirm the corpse is the Real Harrison Wells. The scoobies are smart enough to know that two people should not have the same DNA, and all evidence points to the current Dr. Wells as being a fraud. They can't prove it 100%, but the evidence is enough for everyone, even Caitlin to question Eobard-Wells' actions.

* _{This is fairly inaccurate, as US police practice tends to be collecting and keeping DNA samples of anyone processed by the police, indefinitely, even if they are acquitted or never charged, alive or dead. Removing the dead would prevent past crimes from being linked, or showing that someone assumed to be dead really isn't. Sometimes they have police DNA on file to exclude them from crime scene samples. We know the CCPD database doesn't have dead criminals based on The Mist/Kyle Nimbus being removed when he was executed.}

There must have been a DNA of the old Dr Wells stored or it is possible that Eobard Thawne himself became the new Dr Well because he used a device to change himself into Dr Wells and got his DNA.

On Imdb they say this is a plot hole. They say that there was no way that Cisco could get a DNA sample from the real Dr wells to match with the dead body.