It depends on which penalty you owe. If it is an underpayment penalty showing on line 38 of Form 1040, then yes, it is included in you total tax due.
If you chose to "Have the IRS bill me later" in the underpayment penalty section, then no, the penalty is not included in your total.
If this doesn't fully answer your question, please respond back with more details of the type of penalty.
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