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I found this sentence below in a test passage:

Less well known at the time was the fact that Freud had found out, almost by accident, how helpful his pet dog Jofi was to his patients.

Why is "Jofi was" used instead of "Jofi had been" when the tense of the main clause is "had found out"?

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Clauses within a sentence do not have to agree in tense in English. The present perfect and the simple past (preterite) indicate past-in-present (i.e., in the past from the time of speaking), while past perfect indicates past-in-past (i.e., in the past from the main time of the sentence). However, the past-ness of the preterite is more general than the perfect forms. It can be used to make general statements in the same way as the present tense, but to indicate that they were generally true in the past.

At some time before the main time of this sentence (which can usually be inferred from context if it is not stated), Freud found out about Jofi being helpful. The statement about Jofi being helpful is in the past from the time of speaking (or, in this case, writing - 'speaking' is used as a catch-all for that), and it might just mean that Jofi was helpful at some time in the past from the time of speaking - obviously including the time that Freud found it out. It more likely, however, is making a general statement, that Jofi was helpful to Freud's parents.

Don't get too hung up on tense changes in an English sentence. There's no requirement for general agreement. It's the semantics you need to make sure make sense.

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