# x-values
number_aa <-  c(6, 7, 8, 9, 10)
# y1-values
peptide_total <- c(62040, 57755, 50053, 45077, 39011)
# y2-values
peptide_unique <- c(56791, 54978, 47943, 43248, 37658)

# determine ymax (from y1-values)
ymax <- peptide_total[which.max(peptide_total)]
ymax

# determine xmax (from x-values)
xmax <- number_aa[which.max(number_aa)]
xmax

# assign vector of midpoint-values of first barplot (y1) to x
x <- barplot(peptide_total, names.arg = number_aa,
         xlim = c(0, xmax), ylim = c(0, ymax),
         width = 1)

# set plotting to overlay (no new plot)
par(new = TRUE)

barplot(peptide_unique, col = 'black', names.arg=x,
    xlim = c(0, xmax), ylim = c(0, ymax),
    width = 0.5,
    axisnames = FALSE)

# ----> second bar plot is not aligned on first barplot