Critical parameters in the classification tree are illustrated with respect to their average values for alternative start sites and non-alternative start sites. Differences among these values facilitated the effective classification of mRNAs with aTIS. The number of AUGs is a count of the number of AUGs in the 5'-UTR. Consensus sequences matches against a C in the -7 position from the start site and a G or C in the -6 position. The sequences are also scanned for the IRES secondary structure and the ratio of Guanine and Cytosine in the 5' UTR is also measured. Although the G/C ratio was the least important variable, it resulted in a split in the classification tree and is, therefore, listed as an parameter required for the final classification results.