What does the cryptic crossword clue "Wanting independence, instructs naughty pets in parts of church (9)" mean?

The definition is "parts of church". The wordplay uses anagram+deletion. TRA (synonym="TRA") + NS (synonym="‘instructs’") + EPTS (synonym="EPTS") = TRANSEPTS; definition: "parts of church" The answer is TRANSEPTS.

Wanting independence, instructs naughty pets in parts of church (9)

Guardian Cryptic #29042 | 5 Down | 2023-04-12 flower

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