Is auto-analyze as thorough as manual analyze?

Just had an issue where a prepared query would occasionally choose a
very bad plan in production. The same data set in a different
environment consistently would choose the index scan. As would be
expected, running analyze on that table in production resolved the issue.

However, before I ran the analyze I checked pg_stat_user_tables to see
last_autoanalyze for that table. It had run today. But the problem
existed before that. I would have expected that the auto-analyze would
have corrected this (or prevented it entirely if run enough).

So that leaves me wondering: is an auto-analyze the same as manually
running analyze or is a manual analyze more thorough? This is running
version 9.6.3 on Heroku.

Thanks,

Jack