1. Open these 2 tutorials for your reference:
Be sure that you have installed Java jdk 8.0 and Java JRE 8.0 and you have defined your environment variables correctly.
Note that jarsigner is part of the JDK, and resides inside this folder: C:\Program Files\Java\jdk1.8.0_71\bin
2. Build your app on Cocoon.io without signing it there and download it on your PC.
3. Run this command to sign your app:
jarsigner -verbose -sigalg SHA1withDSA -digestalg SHA1 -keystore PATH/TO/YOUR_RELEASE_KEY.keystore PATH/TO/YOUR_UNSIGNED_PROJECT.apk YOUR_ALIAS_NAME
It will ask for password, write your keystore password (I use same pass for storepass and keypass).
If you have different storepass and keypass passwords, then the above command should look like this:
jarsigner -verbose -sigalg SHA1withDSA -digestalg SHA -keystore PATH/TO/YOUR_RELEASE_KEY.keystore -storepass YOUR_STORE_PASS -keypass YOUR_KEY_PASS PATH/TO/YOUR_UNSIGNED_PROJECT.apk YOUR_ALIAS_NAME
Ok your app is signed.
* If you have 2 versions of your app (x86 and armv7) run the above command for both .apks.
4. Now we align the apps:
zipalign -v 4 PATH/TO/YOUR_SIGNED_PROJECT.apk PATH/TO/YOUR_SIGNED_AND_ALIGNED_PROJECT.apk
5. Upload your apk to Play Store. It worked for me fine.