Firtly, reshape your data to the long format with one value per row.
library(reshape2)
covM <- melt(cov, id.var = "seq")
This returns the following data frame:
seq variable value
1 1 fileA 8429.262
2 2 fileA 8766.138
3 3 fileA 9081.893
4 4 fileA 9342.380
5 5 fileA 9480.860
6 6 fileA 9581.437
7 1 fileB 8606.623
8 2 fileB 9066.361
9 3 fileB 9456.915
10 4 fileB 9784.373
11 5 fileB 10067.121
12 6 fileB 10312.253
Once you have the new object, it's easy to plot:
library(ggplot2)
ggplot(covM, aes(seq, value)) +
stat_smooth(aes(color = variable))