I have never heard of Jcoda, but your values are all over the place from 0.18 to 1.8 or so which does not make a lot of sense to me.  For most genes, the majority of codons are under negative selection to maintain function of the protein even if some sites are positively selected for change.  For example most of the HIV-1 polymerase gene is quite conserved but some sites evolve rapidly to evade drug selection pressure.  The envelope gene from the same virus isolates is under quite a variety of host immune selection pressures  (antibodies and CTL responses) but there are still many invariant sites.

I would recommend trying some other selection pressure tools such as the DataMonkey tools and SNAP to see if the results generally agree with JCoda.

http://www.datamonkey.org/

http://www.hiv.lanl.gov/content/sequence/SNAP/SNAP.html