Ok im tired of alot of people ignorance first things first brett partridge is dead!! some are saying brett partridge was the only one in the house with lisbon in S6e1 The desert rose (wrong) pay close attention when lisbon walks towards the bathroom to open it the door is closed then she hears a noise from the closet brett partridge says tiger tiger The bathroom door squeaks open then lisbon gets grabbed!! lets rewind before partridge's death a room full of 7 pigeons 1 flew out remaining 6 pigeon's 3 Pigeons where together that's the clue i think bruno heller was talking about . in the next episode S6E2 Black winged redbird You'll see these 3 together Gale Bertram ' Sheriff Thomas McAllister & Reede Smith ' When Jane and lisbon are in the park talking about rj you'll see a close up of someone feeding pigeons Sophie miller says jay roth (alias of rj) suffers from acrophobia (fear of heights) which was a lie to gain her trust but he does have some sort of phobia issues that are real ..S6E3 Wedding in red Sheriff McAllister Acts like he's afraid of height's until he saves jane from the roof top...now when jane and lisbon kept trying to get him to go near height''s he must of figured they knew something so he saves jane from the roof ' when he leaves a group of pigeons are on him and he says got i hate those things.. he has a fear of pigeons (ornithophobia) & in S6E4 there are no pigeons seen at all.... Bruno Heller in the other writers on the show do alot of twist and turns to lead us in the wrong direction that's what makes things interesting your going to notice something strange watch this ...Lets look at the five remaining suspects In order of season appearance
1 Bret Stiles S2 (Red All Over)
2 Gale Bertram S3 (Red Sky At Night)
3 Ray Haffner S4 (Little Red Book)
4 Reede Smith S5 (The Red Glass Beed)
5 Sheriff Thomas McAllister S1 E2 (Red Hair & Silver Tape)

The list is in season order until you get to mcallister thats why partridge & kirkland got killed early 
Sheriff Thomas McAllister Is Red John if red john is actually on the list (bruno heller said people will be disappointed when rj is revealed