Duplicating character strings in R - r

Question

I am simulating some random DNA strings (sequences) in R. These sequences are composed of the letters A, C, G and T.
In a dataset of such sequences, some may be identical (duplicates).
Suppose I have 100 such sequences, which can be grouped in 5 unique sets.
Working code that I now have (shown below) will output something like
Unique groups: 1 2 3 4 5
Number of Sequences: 96 1 1 1 1
However, I would like the distribution to be something like
Unique groups: 1 2 3 4 5
Number of Sequences: 56 24 10 5 5
This can be accomplished through randomly allocating some sequences from group 1 (96 sequences) to all other groups containing only a single sequence.
My sequences are stored in a variable called 'res'.
The below code doesn't quite do what I would like.
res <- res[sample(unique(nrow(res)), size = nrow(res), replace = TRUE), ]
In the above code, 'size' is the number of DNA sequences in the dataset.
How can the above code be altered to accomplish what I am needing?
Note: one does not know the number of unique sets that will be generated a priori, so using the 'probs' argument in sample will not suffice.
Reproducible example:
library(pegas)
num.seqs <- 100 # number of DNA sequences to generate
length.seqs <- 500 # length of DNA sequences
mu.rate <- 1e-4 # mutation rate
set.seed(1234) # for reproducibility
nucl <- as.DNAbin(c('a','c','g','t')) # DNA alphabet
res <- sample(nucl, size = length.seqs, replace = TRUE, prob = rep(0.25, 4)) # generate a random DNA sequence
mu.set <- list('a' = as.DNAbin('c'),
'a' = as.DNAbin('g'),
'a' = as.DNAbin('t'),
'c' = as.DNAbin('a'),
'c' = as.DNAbin('g'),
'c' = as.DNAbin('t'),
'g' = as.DNAbin('a'),
'g' = as.DNAbin('c'),
'g' = as.DNAbin('t'),
't' = as.DNAbin('a'),
't' = as.DNAbin('c'),
't' = as.DNAbin('g'))
muts <- function(res) {
unlist(mu.set[as.character(res)])
}
duplicate.seq <- function(res) { # duplicate sequrnce
num.muts <- rbinom(n = 1, size = length.seqs, prob = mu.rate) # add random mutations
if (num.muts > 0) {
idx <- sample(length.seqs, size = num.muts, replace = FALSE)
res[idx] <- muts(res[idx])
}
res
}
res <- matrix(replicate(num.seqs, duplicate.seq(res)), byrow = TRUE, nrow = num.seqs) # generate num.seqs sequences
class(res) <- "DNAbin"
h <- sort(haplotype(res), decreasing = TRUE, what = "frequencies") # distribution of unique groups
rownames(h) <- 1:nrow(h)
h # print distribution
A simpler example (sans R package)
num.seqs <- 10
length.seqs <- 10
lets <- letters[c(1, 3, 7, 20)] # DNA alphabet
lets
res <- t(replicate(num.seqs, sample(lets, length.seqs, replace = TRUE))) # generate sequences
res <- res[sample(nrow(res), size = nrow(res), replace = TRUE), ] # duplicate some sequences