Figure 3.

Positions of footprint 5-mers. (A) Frequency distribution of all footprint 5-mers out of total unique sequences (n = 42,221) plotted against the normalized CDR3 position. The CDR3 is herein defined to begin at the conserved CAR amino acid sequence (TGT GCG AGA nucleotide sequence) within the 3′ end of VH and end at the conserved W (TGG nucleotide sequence) that is immediately upstream of the first conserved glycine, GGC nucleotide sequence) within the JH. “TGGAG” is excluded as it is found in many alleles of all DH genes. The position of the footprint is defined by where the footprint starts within the CDR3. For example, if a footprint occupies nucleotides 12–16 of the CDR3, it will be plotted at position 12. CDR3 lengths were normalized to a scale of 1–100 using p1 = p/(L × 100); where p is the position of the 5-mer in the real CDR3 sequence, L is the length of the CDR3 sequence, and p1 is the normalized position. Normalized positions are rounded to the nearest integer. (B) Frequency distribution of all footprint 5-mers plotted against the normalized CDR3 position, corrected for footprint 5-mers in the germline JH6 gene. “ATGGA,” “TACGG,” and “CATGG” were excluded when found in the 3′ end of the CDR3 within the JH6 gene, as these 5-mers are found in the germline JH6 sequence. Footprint 5-mers found in other JHs (see Table 2) are not counted in either (A) or (B) because they are all located outside CDR3 region of JH.