Spoiler Alert: Tom Mccallister is Red John.
The Red John Story: He grew up with an abusive father living with his family in a rural area, surrounded with wildlife. Became fascinated with hunting animals as an outlet for the pain who his Father was inflicting on him at home. He became involved with Visualize during his later years (17-22) and soon furthered his connections to people who were obsessed with pain, like himself. His first public murder came at the Visualize farm when he was about 24 or 25 which is where he adopted the red smiley face. He then began partnering with other troubled people which he connected with through his time at visualize. His first accomplice was Orville Tanner someone that had a similar background as him, growing up in a small rural town. (similar to the town in Season 3 Episode 9 "Red Moon", also the character Todd Johnson's childhood was very similar to Red John and Orville Tanner.) After Orville Tanner was arrested, Mcallister thought out a position of power in order to disguise his new identity and help prevent him from meeting the same fate as his partner. Sheriff was the perfect position for him because it kept him in a rural area somewhere he is very familiar with. This way he can hide in the shadows while committing high-scale murders between long intervals of time. He became even more obsessed with the famous character that had become which is around the time he killed Jane's family after hearing Jane mock in on television.
I believe his identity still remains unknown to both members of visualize and the tyger tyger group however both of these people know that Red John was once or is currently associated with their group.
Similarities-
Red John and Tom Mcalister are both left handed, but shoot their gun with their right hand. (Red John is a very good marksman much like Mcalister, which is due to his hunting background.... He began killing people with knives, his weapon of choice and developed his gun skills from shooting animals)
They both enjoy drinking tea and wear the same pointed cowboy boots.
They both have phobias (heights and partridges) Partridges are especially important because they are used as symbolism in the first 3 episodes of season 3.
In the season 2 finale Red John saves Jane's life by shooting the copycat killers and in episode 3 of season six Tom Mcallister does the same thing by shooting the man taking Jane hostage. This similarity was used by Bruno Heller on purpose to subtly built Jane and Red John's relationship as protagonist and antagonist.
AND IF YOU STILL DONT BELIEVE ME GO AND WATCH THE PROMO TO SEASON 6 EPISODE 6 AND PAUSE IT WHEN YOU SEE THE SUSPECTS REACTIONS TO JANE POINTING HIS GUN AND TELLING THEM THAT ONE OF THEM IS RED JOHN. Everyone is on the edge on their seat with looks of confusion and surprise while Tom Mcallister is completely comfortable in the same power stance seen in season 6 episode 2 when Jane tell Bertram, Reede Smith and Mcallister that Red John has made a mistake. (His hat is in his hand, legs crossed, head tilted).
