library(Matrix)
dat = data.frame(t(replicate(5,
  sample(as.character(1:3),100,replace=T))))
tmp_m = combn(1:nrow(dat), 2)
m = matrix(NA, nrow(dat), nrow(dat))
m[t(tmp_m)] = rowSums(dat[tmp_m[1,],] == dat[tmp_m[2,],])
m[lower.tri(m)] = m[upper.tri(m)]
apply(out, 2, function(x) match(1:2, order(x)))