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Appendix S1 Additional material.

Figure S1 Map positions of selected intra-MHC microsatellites in the horse.

Figure S2 The 2 × 2 contingency tables for microsatellite allele association using alleles of the A2 and A3a microsatellite haplotypes as examples.

Figure S3 The 2 × 2 contingency tables for correlation coefficient (r) analysis in 218 serotyped and microsatellite (msat) typed horses.

Table S1 Microsatellite allele size and number of animals positive for each allele in a sample population of 320 horses and 33 unknown breed ponies.

Table S2 Correlation between MHC microsatellite (msat) haplotypes and serological (sero) ELA haplotypes in 218 serotyped and msat-typed horses.

Table S3 Equine MHC microsatellite haplotype frequencies across breeds.

Table S4 Equine MHC microsatellite primer sequences.

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