You can simply select the corresponding columns. In your case, this should be columns 1, 6, 11, ... You can get the column indices using the "seq" function:
column.5min <- seq(from = 1, to = 1440, by=5)
Now you can select the column, for instance using:
myseq5min <- myseq[, column.5min]
Here is an example using the "mvad" data set and selecting the first state of each year.
## Loading the library
library(TraMineR)
data(mvad)
## Defining sequence properties
mvad.alphabet <- c("employment", "FE", "HE", "joblessness", "school", "training")
mvad.lab <- c("employment", "further education", "higher education", "joblessness", "school", "training")
mvad.shortlab <- c("EM", "FE", "HE", "JL", "SC", "TR")
## The state sequence object.
mvad.seq <- seqdef(mvad, 17:86, alphabet = mvad.alphabet, states = mvad.shortlab, labels = mvad.lab, xtstep = 6)
## Now select the column every year (every twelve monthes)
mvad.seq.year <- mvad.seq[, seq(from=1, to=70, by=12)]
seqdplot(mvad.seq.year)