The footprints are dealt with here — all belonged to Rudy. Though he threw his bloody shoes away, the police found the box they came in at his apartment:
http://www.injusticeinperugia.org/footprints-01.html
The DNA on the knife was likely a bread crumb or Amanda’s:
http://www.injusticeinperugia.org/TheKnife.html
The braclasp was kicked around on the floor for 47 days before collected and when it was collected had DNA from 4 people on it. If this is so incriminating then why weren’t the other 3 people arrested and charged???
http://www.injusticeinperugia.org/TheBraClasp.html
Amanda’s DNA was found in the bathroom they all shared — why wouldn’t it be there — she lived there.
According to the site below, there also were bloody footprints that couldn’t have belonged to Guede. For example, this one matched Solecito:
http://themurderofmeredithkercher.com/The_Bathmat_Footprint
There were other footprints, but Knox claims that her DNA must’ve mixed with the victim’s because, she says, when exiting the shower, there were no towels, so she used the bloody bathmat to slide back to her room. (Does that sound credible to you?)
http://themurderofmeredithkercher.com/Luminol_Traces
Knox’s DNA was found on the knife - yes, she probably used it for cooking. But, Kercher’s DNA also was found on the knife. Solecito claimed he accidentally cut Kercher with the knife while they all were cooking dinner at his apartment, but there’s no evidence that Kercher ever went to his apartment.
The bra clasp had Solecito’s DNA on it. The defense claimed that some of that DNA could be from other people - it turns out, this claim by the defense is a stretch, but the fact that Solecito’s DNA is on the bra clasp is not disputed. More info here:
http://themurderofmeredithkercher.com/The_Bra_Clasp
Again, she might be entirely innocent, but it doesn’t look that way... I can see why she was charged and eventually found guilty.