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A little advice please.

As I have mentioned before I am a noob and know little about growing peppers. After a few failed attempts at growing super hots I decided to try some scotch bonnets. These two plants are doing the best but I have some concerns. Now I know I need to get them out of the clear cups. Anywho the first pic the leaves seem to have started growing in an upward direction.
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The next two pics are the second plant that started growing really tall and leggy it was gangster leanin sideways. So I added some soil but now it has developed some light spots on the bigger leaves.
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any input is greatly appreciated.
 
The clear cups really don't make a difference, though some swear they do. Likely you're going to move them into larger pots that aren't clear before it makes any difference. Hard to say what's going on with those pics, but here are a few thoughts:
 
- Leaning over can be from a couple things. First is the plant leaning towards a light source. Yes, you have artificial lights on them, but is the sun coming in a window for part of the day? That could simply be it. The other most common cause of leaning is the damping off fungus. It usually arrives at the soil of the surface, and if you can't tell by looking at the soil, look at the base of the plant at the soil line - a weak/watery section of the stem at the base tells you it's damping off. You've put more soil there to boost the plant up, so I can't tell if you have that or not.
 
-  Do you have several holes in the bottom of those cups? If not, make some - the soil should be allowed to drain. 
 
- Have you put a fan (gently) blowing on them for at least part of the day? If not, get one. Point it towards the wall to allow the wind to reflect if it's too hard when direct. 
 
- If you don't already have one, get a jeweler's loupe of at least 30x and check for mites. Some aren't visible to the naked eye, so you must get a loupe to see them. 
 
Geeme gave good advise. One thing you mentioned was a plant growing tall and leggy. That's a plant needing to be closer to the light source. Either lower the lights and put the seedlings on something to get them closer to the light.
 
The plants are under 100 percent artificial light right now. I do have a fan on them at first it was direct but I thought it may be too strong so now it is blowing aginst the wall and I still see a little flutter so I think thats under control. I hope its not damping off I experienced that with my first attempts and have been bottom watering ever since about once every 10-12 days. As they grew taller and the first leaves grew bigger they started leaning so I figured maybe they were top heavy? That is the reason for adding more soil.
Geeme gave good advise. One thing you mentioned was a plant growing tall and leggy. That's a plant needing to be closer to the light source. Either lower the lights and put the seedlings on something to get them closer to the light.

Thats what I was thinking getting them closer to the light. I dont have the greatest lights (im working on that part) right now I have a couple cfls that claim 1800 lumens each. Ill try moving them closer which bring me to another question how close is too close right now the temp in that room is about 82 degrees by the end of the day and drops to around 70-72 over night. Do I have to worry about burning the plants?
 
thirdcoasttx said:
Thats what I was thinking getting them closer to the light. I dont have the greatest lights (im working on that part) right now I have a couple cfls that claim 1800 lumens each. Ill try moving them closer which bring me to another question how close is too close right now the temp in that room is about 82 degrees by the end of the day and drops to around 70-72 over night. Do I have to worry about burning the plants?
I start most plants and cuttings under 2 bulb 48 in 6500k daylight bulbs. With peppers, I start them 12 inches below the light, when the first set of true leaves develop, I move them to within six inches of the light, after a few more leaves I move them within 3-4 inches. At 82 degrees they should fine that close. If they seem to be getting heat stressed then move them down a few inches.

Once my peppers are 5-6 inches they go into my greenhouse so I can't help you on artificial lighting after that.
 
It's not the room temperature that's at issue as much as the temperature at the top of the plant, if you haven't measured it there then that is a good idea.  It should stay below 95F and ideally in the 80's.
 
However if you have even a modest amount of fan forced airflow it's very hard to have them get too hot from 1800 lumen CFLs in an 82F room unless the leaves are physically touching the light, or the entire setup is fully enclosed so there's nowhere for heated air to go.  Otherwise you can put those lights as close as your willingness to continually raise them as the plants grow, allows for.
 
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