The Lowther Stakes winner finished only seventh of 11 in Saturday's Cheveley Park Stakes at Newmarket.
What makes Johnston happy to put a line through the run is that the filly who finished third at Newmarket, Roger Varian's Madeline, was some way behind Threading at York.
Johnston said: "It was very disappointing. I thought at first we were a victim of faster ground on the rail as it seemed there was a spearhead of pace there and that they were struggling out in the middle of the track but the winner has come up there just where she was.
"She was never travelling like we expected her to and she was beaten a fair way out. She has beaten the third (Madeline) two lengths last time so that is not her running.
"I know everybody else does it but if we can't see if there is anything wrong with her there is no point sticking needles in her to see if there is anything wrong with her. That won't explain why she has run like that.
"For sure I think she will still make up into a Guineas horse as that is not her form."