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Each cell in the matrix shows the number of correspondences (and maps) between each pair. A correspondence is any relationship between two features.

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Matrix returns

Reference Set Genetic Reference Set
Raphanus sativus
  Budahn et al 2009  
  a b c d e f g h i  
Genetic Raphanus sativus
Budahn et al 2009
g - - - - - - N/A - - g Raphanus sativus
Budahn et al 2009
Genetic
  a b c d e f g h i  
  Budahn et al 2009  
Legend: Correspondences (Corresponding Maps)