1) It was thought that he was tall
= He was thought to be tall (OK) 2) It is thought that he was tall= He is thought to have been tall (OK) 3) It was thought that he is tall (??)= He was thought to be tall (??)"It was thought that he is tall" is a slightly awkward mixture of tenses.
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"It was thought that he is tall" is a slightly awkward mixture of tenses.