The default JRE store is in:
<JRE>\lib\security\cacerts
Add a certificate with keytool:
<JRE>\bin\keytool.exe -importcert -file my-cert.cer -alias 'My cert' -keystore <JRE>\lib\security\cacerts
Alias is a name by which the certificate can be, for instance, removed from the store.
Default password for cacerts
is:
changeit
TeamCity has a private JRE in:
<TeamCity>\jre\