But it could have been worse after they moved a point nearer to Carlisle United after their defeat, with Cobblers also having a game in hand.
Salford City are just two points further back after securing back-to-back wins as a three horse race begins to develop for the third automatic promotion place.
Here is who is going up according to the latest supercomputer predictions.
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1. Stevenage - 88pts (+29)
Win the league: 42%
Promotion chances: 86%
Play-off chances: 16% Photo: Pete Norton
2. Leyton Orient - 88pts (+27)
Win the league: 39%
Promotion chances: 87%
Play-off chances: 14% Photo: Pete Norton:
3. Northampton Town - 81pts (+23)
Win the league: 10%
Promotion chances: 59%
Play-off chances: 41% Photo: Pete Norton
4. Carlisle United - 77pts (+24)
Win the league: 4%
Promotion chances: 59%
Play-off chances: 41% Photo: Stu Forster