Reads aligned into contigs Barry et al. Figure S1 A. Step 1: Degenerate primers designed to DBLa conserved amino acid blocks D and H [26] D H B. Step 5: Remove vector contamination and edit raw sequence data (“reads”) Individual reads Forward primer Reverse primer Step 2: PCR of P. falciparum genomic DNA with degenerate primers results in a pool of PCR products containing distinct sequences from different genes Step 6: Align reads with a 96% DNA sequence identity cutoff Reads aligned into contigs Pooled PCR products Step 3: Ligate PCR products with Topo-TA vector (Invitrogen) and clone to separate distinct sequences Step 7: Remove redundancy by generating consensus “sequences” (together they form a “repertoire”) Repertoire Colonies Clones Sequences E.coli transformation Step 8: Alignment of sequences with a 96% DNA sequence identity cutoff defines distinct sequences (“types”) in the population. Step 4: Culture 96 E. coli colonies in 1ml L-broth plus Kanamycin. Extract plasmid DNA and sequence using M13 Universal primers Types (1-7) A B C D 96 well plate Repertoires