Top CPU consuming MySQL processes
You can see which queries are slow by enabling the slow query log (SET GLOBAL slow_query_log=1; and setting a suitable value for the long query time variable to set a threshold for what you consider to be "long". (E.g. maybe SET GLOBAL long_query_time=3; - the unit is seconds). However, queries may be slow for other reasons than high CPU utilisation, e.g. due to high I/O utilisation. Still, this can be a starting point for at least identifying poor queries.

The slow log is by default written to a file in the data dir called '${HOSTNAME}-slow.log'. You can then use a tool like mysqldumpslow to analyse this file, e.g.: mysqldumpslow -s t /var/lib/mysql/localhost-slow.log. It will extract each slow query and order them from slowest to least slow. Or you can use pt-query-digest to do the same thing  

You can then enable query profiling for your session (SET profiling = 1;), execute each of the candidate queries you have identified in the slow query log, and do:

SHOW PROFILES;


This gives you a list of the recent queries and their query IDs. Use this ID to find the CPU utilisation for each query with:

SHOW PROFILE CPU FOR QUERY &lt;query id&gt;;  


This will show the various stages of the query execution, and the duration and CPU utilisation (user and system) for each of them.

Note that this isn't 100% accurate - the documentation page for SHOW PROFILE notes that:


  Profiling is only partially functional on some architectures. For
  values that depend on the getrusage() system call, NULL is returned on
  systems such as Windows that do not support the call. In addition,
  profiling is per process and not per thread. This means that activity
  on threads within the server other than your own may affect the timing
  information that you see.


Note also that the page says SHOW PROFILE is deprecated as of MySQL 5.6.7, and that the performance_schema is meant to replace it; see Query Profiling Using Performance Schema. However, there doesn't seem to be a way to extract CPU utilisation info from it, so you may just have to use SHOW PROFILE CPU ...