R Under development (unstable) (2025-09-02 r88773 ucrt) -- "Unsuffered Consequences"
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> library(SVAlignR)
> data(longreads)
> seqs <- longreads$connection[1:15]
> pad <- c(rep("0", 9), rep("", 6))
> names(seqs) <- paste("LR", pad, 1:length(seqs), sep = "")
> seqs <- seqs[!duplicated(seqs)]
> 
> alfa <- Cipher(seqs)
> seqclust <- SequenceCluster(seqs, NC = 5)
> plot(seqclust)
> coded <- encode(alfa, seqclust@rawSequences)
> kmers <- lapply(1:11, function(N) {countWords(coded, N)})
> #motifNodes <- lapply(kmers, function(x) x[names(x) %in% names(motifs)])
> #save(alfa, motifs, kmers, motifNodes, decomp,
> #     file = file.path(paths$scratch, "motifNodes.Rda"))
> 
> proc.time()
   user  system elapsed 
   2.53    0.32    2.79