You can map syntenic regions using the R package DECIPHER. I will assume that your goal is to find the start and endpoints of each scaffold on a (closely related) reference genome. The process would look something like this:

library(DECIPHER)

# connect to an in-memory database
db <- dbConnect(SQLite(), ":memory:")

# load the sequences from each FASTA file
Seqs2DB("<<PATH TO SCAFFOLDS>>", "FASTA", db, "Scaffolds")
Seqs2DB("<<PATH TO REFERENCE GENOME>>", "FASTA", db, "Ref")

# find the syntenic regions w/o using 6-frame translations
synteny <- FindSynteny(db, useFrames = FALSE)

# look at the start and end on the reference:
synteny[2, 1][[1]][, c("start2", "end2")]

# count breakpoints in each bin
h <- hist(synteny[2, 1][[1]][, c("start2", "end2")],
          breaks = seq(from = 0,
                       to = max(synteny[1, 1][[1]],
                                synteny[2, 2][[1]]) + 1e4,
                       by = 1e4))
h$counts # number of endpoints per 10k nucleotides

dbDisconnect(db)

This will display the number of start and endpoints on the reference genome per 10k nucleotides. Hope that helps!