Ah right. Because you had "probe" in the metric name I thought you were
using blackbox_exporter. That isn't going to help you here, because each
probe only make one request. To make 500 requests in 5 minutes, you would
need to be scraping nearly two times per second!
It sounds like rather what you want to do is read your webserver log files
and turn them into statistics. You'll need to look at tools like mtail or
grok_exporter to do that.
In order to answer "how many queries took more than 3 seconds to respond?"
you will need to generate histogram buckets at whatever intervals are of
interest, e.g.
http_request_duration_seconds_sum{le="0.5"}
http_request_duration_seconds_sum{le="1.0"}
http_request_duration_seconds_sum{le="3.0"}
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