From a sequences generate 4 possible changes

isomirs_combinations

mir = "CCCGGGGGGGGGGGGGGGGGGGGGCCC"
# generate different length +/-3 at both size
lapply(c(1,2,3,4,5,6,7), function(x){
    lapply(c(0,1,2,3,4,5,6,7), function(y){
        substr(mir, x, nchar(mir)-y)
    }) %>% unlist()
}) %>% unlist() -> trim

# add non-tempaltes 3' A or U up to 3
trim_add = expand.grid(trim, c("A","AA", "AAA", "U", "UU", "UUU", "")) %>% 
    apply(., 1, paste0, collapse = "")

# add non-template 5' A
trim_add_both = expand.grid(c("A", ""), trim_add) %>% 
    apply(., 1, paste0, collapse = "")

# add nucleotides changes at each position, different from the current nt
all = sapply(trim_add_both, function(x){ # move through all calculated sequences
    lapply(1:nchar(x), function(y){ # move through the sequence
        lapply(setdiff(c("A", "T", "C", "G"), substr(x, y, y)), function(n){
            t = x # copy the sequence
            substr(t, y, y) <- n #change the new sequence nt at that position
            t # return value
        }) %>% unlist()
    }) %>% unlist %>% c(x, .) # add the unchanged sequence to the list
}) %>% unlist

length(all)