The purple strips on the stem are anthocyanin, due to the growth under blue-green spectrum fluorescent lighting.
In flowers, bright reds and purples are adaptive for attracting pollinators. In fruits, the colorful skins also attract the attention of animals, which may eat the fruits and disperse the seeds. In photosynthetic tissues (such as leaves and sometimes stems), anthocyanins have been shown to act as a "sunscreen", protecting cells from high-light damage by absorbing blue-green and UV light, thereby protecting the tissues from photoinhibition, or high-light stress.
POTAWIE said:Not just seedlings, it can happen to stems, leaves, and pods indoors or out. Some varieties show more than others. I frequently get purple tinted jalapenos(and many other types) when theres lots of sun but they eventually ripen to red
RichardK said:It's quite normal, probably a bit of suntan...
Heres some stem suntan
Leaf with Suntan
nailed itPOTAWIE said:I have purpling stems,leaves, and pods all the time and for me its definitely not a deficiency, it seems to only occur indoors with certain types of lighting(likely blue/green spectrum), and outdoors only during the hottest/sunniest periods. Certain varieties, like many jalapenotypes, are usually more susceptible to having purpling pods than others