One thing to consider is age, CDR3 length will increase with age (Rechavi, E. et al. Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Sci. Transl. Med. 7, 276ra25–276ra25 (2015); Hall, M. A., Reid, J. L. & Lanchbury, J. S. The distribution of human TCR junctional region lengths shifts with age in both CD4 and CD8 T cells. Int. Immunol. 10, 1407–1419 (1998).). If your controls are older, this might be a reason. However, this should co-incide with more N-insertions.