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It's probably / certainly going to rain in minutes.

It'll probably / certainly rain in minutes.

Is the 1st one based on something we can see now and the 2nd one based on our personal opinion or knowledge?

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  • Or, you can simplify things by saying, "I think it's going to rain today," or "I think it'll rain today." – rhetorician Oct 2 '13 at 17:54
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Yes, be + going to can be used to refer to a future event for which there is present evidence. Will often describes an intention or, in this case, an opinion, formed more or less at the time of speaking.

That, at least, is the theory, but a native speaker is unlikely to say either of those two. More often a native speaker will say something like It looks as if it’s going to rain soon or It looks as if it’ll rain soon without much difference in meaning between them.

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