Rudy Guede's conviction was based on his being one of multiple attackers who murdered MK. Pathologist have testified that Meredith must have been attacked by multiple attackers, due to the size and nature of her injuries, and the lack of defensive marks.
AK's DNA was found mixed with Merdith's blood in numerous places at the cottage, including the washbasin, the bidet and Philomena's room (the one with the staged burglary). Funnily enough, none of her DNA was found in her own room.
There was evidence of a clean-up at the cottage. Bloody footprints corresponding to AK's feet and RS's feet were revealed only by luminol. A woman's bloody shoe print, not corresponding to Meredith's size, but coprresponding to AK's, was found on the pillow underneath Meredith's body. AK and RS were found outside the cottage with a mop and bucket by the postal police, before they had actually called the police. (The police turned up to return one of Merdith's phones which had been discared in the garden of a nearby house, almost certainly by her attacker(s)). Phone records show that they called the police after the police had already arrived.
The washing machine was still warm when the police arrived, and contained both Meredith's clothes and AK's - all of which had been washed in bleach.
AK knew where Mereith's body was found, and how she had died before the police had revealed this information.
That's not counting the constantly changing alibis, non-matching alibis.
And the clincher? For me, it was the picture of the bathroom where AK noticed a "few spots of blood", but was supposedly unconcerned enough to take a shower nevertheless. (And bear in mind that AK had already returned to the cottage, she claimed, and found the front door unlocked).