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Catching up on some very old posts:
greenthumbs - no, your peppers that look like chillies are peppers. If there has been cross-pollination, the results of the cross wouldn't appear until you saved seed from the crossed fruit and planted it next year.
flungmonkey - yes, you can plant toms and chillies together.
justbegining - no, you don't need to remove the side shoots of chillies. They don't develop anything like the amount of foliage that toms do.
sonia1 - you grow peppers exactly as you do toms. Start them at the same time - in fact, if possible, start them earlier than toms. Like chillies, they can take longer to germinate and develop than toms do. So it's too late this year. The plants won't grow to the same size as, say, an indeterminate tomato plant. Mine usually grow to about 4' so you still need a decent size pot.
I'm growing chillies for the first time and the flowers are just starting to develop. I'm a bit concerned as there is some dark discolouration on the stalks at some higher leaf axils. Is something wrong?