Evaluation of the contribution of the most common CDR3 motifs vs less common motifs to the TCR repertoire relatedness and structural similarity of intergroup reconstitution. Each panel represents the result for an individual recipient group for 1 representative experiment. The mean Hellinger distance for comparisons of individual mice within each recipient group is shown for the complete TCR repertoire (blue). Decreasing values indicate that the repertoire is more similar. The mean Hellinger distance was recalculated by using a subset of the TCR repertoire for each individual mouse in which only clones with the top 10 CDR3 clonal motifs identified in each group were preserved, and the mean Hellinger distance is shown (yellow). Finally, the mean Hellinger distance was recalculated by using a subset of the TCR repertoire for each individual mouse in which clones with the top 10 CDR3 clonal motifs were removed (gray). Using this analysis, the donor C57BL/6 GI repertoire showed an increase in the Hellinger distance when analysis was restricted to the top 10 motifs vs without these motifs, in which the Hellinger distance is decreased. The same trend is present for the C57BL/6 syngeneic recipient group but not for the allogeneic recipient groups. This suggests that the structure of reproducible TCR repertoire reconstitution is less sensitive to intragroup shared common CDR3 clonal motifs in allogeneic recipients and more dependent on rarer clones and a more polyclonal response. n ≥ 10 per group; ANOVA statistical analysis; P value as shown.