This function calculates genetic distances between complex repeats as described in Vara (2019). This function is forked from github.com/lucaferretti/RepeatDistance/blob/master/RepeatDistance.R and adapted to work with Biostrings objects.

RepeatAlignment(
  seq1,
  seq2,
  seq1.name = "seq1",
  seq2.name = "seq2",
  gendist = NULL,
  dist.type = "hamming",
  dna.model = "K80",
  wmut = 1,
  windel = 3.5,
  wslippage = 1.75,
  exclude.pos = NULL,
  post.include = FALSE,
  show.steps = FALSE
)

Arguments

seq1

DNAStringSet

seq2

DNAStringSet

seq1.name

seq1 name [default: seq1]

seq2.name

seq2 name [default: seq2]

gendist

pairwise distance matrix of seq1 and seq2 repeats [default: NULL]

dist.type

distance calculation method if no gendist matrix is supplied [default: hamming]

dna.model

a character string specifying the evolutionary model to be used (see ape::dist.dna) [default: K80]

wmut

weight for nucleotide point mutations [default: 1]

windel

weight for unit insertions/deletions [default: 3.5]

wslippage

weight for single unit duplications [default: 1.75]

exclude.pos

positions of the repeat that will be excluded before distance calculation [default: NULL]

post.include

boolean if excluded positions should be added back for the sequence alignment after distance calculation [default: FALSE]

References

Vara C et al. (2019) PRDM9 Diveristy at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice. Molecular Biology and Evolution, 36(8), 1686-1700.

See also

Author

Kristian K Ullrich

Examples

##load example sequence data
data("mousePRDM9", package="repeatR")
myRepPattern<-"PY"
myRepLength<-84
mousePRDM9.random<-sample(mousePRDM9, 20)
mousePRDM9.random.split<-repeatR::splitRepByPattern(mousePRDM9.random,
    myRepPattern, myRepLength)
##get repeat alignment
repeatR::RepeatAlignment(mousePRDM9.random.split$cds[[1]],
    mousePRDM9.random.split$cds[[2]])
#> $gendist
#>                               AB843923.1_Mmc_MG2111_1_84
#> AB843923.1_Mmc_MG2111_1_84                             0
#> AB843923.1_Mmc_MG2111_85_168                           4
#> AB843923.1_Mmc_MG2111_169_252                          4
#> AB843923.1_Mmc_MG2111_253_336                          0
#> AB843923.1_Mmc_MG2111_337_420                          3
#> AB843923.1_Mmc_MG2111_421_504                          1
#> AB843923.1_Mmc_MG2111_505_588                          4
#> AB843923.1_Mmc_MG2111_589_672                          0
#> AB843923.1_Mmc_MG2111_673_756                          4
#> AB843923.1_Mmc_MG2111_757_840                          7
#> AB843890.1_Mmd_HS4379_1_84                             4
#> AB843890.1_Mmd_HS4379_85_168                           4
#> AB843890.1_Mmd_HS4379_169_252                          4
#> AB843890.1_Mmd_HS4379_253_336                          5
#> AB843890.1_Mmd_HS4379_337_420                          4
#> AB843890.1_Mmd_HS4379_421_504                          2
#> AB843890.1_Mmd_HS4379_505_588                          0
#> AB843890.1_Mmd_HS4379_589_672                          2
#> AB843890.1_Mmd_HS4379_673_756                          4
#> AB843890.1_Mmd_HS4379_757_840                          3
#> AB843890.1_Mmd_HS4379_841_924                          7
#>                               AB843923.1_Mmc_MG2111_85_168
#> AB843923.1_Mmc_MG2111_1_84                               4
#> AB843923.1_Mmc_MG2111_85_168                             0
#> AB843923.1_Mmc_MG2111_169_252                            2
#> AB843923.1_Mmc_MG2111_253_336                            4
#> AB843923.1_Mmc_MG2111_337_420                            4
#> AB843923.1_Mmc_MG2111_421_504                            5
#> AB843923.1_Mmc_MG2111_505_588                            3
#> AB843923.1_Mmc_MG2111_589_672                            4
#> AB843923.1_Mmc_MG2111_673_756                            4
#> AB843923.1_Mmc_MG2111_757_840                            5
#> AB843890.1_Mmd_HS4379_1_84                               3
#> AB843890.1_Mmd_HS4379_85_168                             2
#> AB843890.1_Mmd_HS4379_169_252                            2
#> AB843890.1_Mmd_HS4379_253_336                            1
#> AB843890.1_Mmd_HS4379_337_420                            2
#> AB843890.1_Mmd_HS4379_421_504                            2
#> AB843890.1_Mmd_HS4379_505_588                            4
#> AB843890.1_Mmd_HS4379_589_672                            2
#> AB843890.1_Mmd_HS4379_673_756                            3
#> AB843890.1_Mmd_HS4379_757_840                            3
#> AB843890.1_Mmd_HS4379_841_924                            5
#>                               AB843923.1_Mmc_MG2111_169_252
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              2
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             5
#> AB843923.1_Mmc_MG2111_505_588                             2
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             2
#> AB843923.1_Mmc_MG2111_757_840                             5
#> AB843890.1_Mmd_HS4379_1_84                                3
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             3
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             5
#>                               AB843923.1_Mmc_MG2111_253_336
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             4
#> AB843923.1_Mmc_MG2111_757_840                             7
#> AB843890.1_Mmd_HS4379_1_84                                4
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             5
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             2
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             2
#> AB843890.1_Mmd_HS4379_673_756                             4
#> AB843890.1_Mmd_HS4379_757_840                             3
#> AB843890.1_Mmd_HS4379_841_924                             7
#>                               AB843923.1_Mmc_MG2111_337_420
#> AB843923.1_Mmc_MG2111_1_84                                3
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             3
#> AB843923.1_Mmc_MG2111_253_336                             3
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             4
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             3
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             8
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              3
#> AB843890.1_Mmd_HS4379_169_252                             3
#> AB843890.1_Mmd_HS4379_253_336                             3
#> AB843890.1_Mmd_HS4379_337_420                             3
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             3
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             2
#> AB843890.1_Mmd_HS4379_841_924                             8
#>                               AB843923.1_Mmc_MG2111_421_504
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              5
#> AB843923.1_Mmc_MG2111_169_252                             5
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             0
#> AB843923.1_Mmc_MG2111_505_588                             5
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             6
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              5
#> AB843890.1_Mmd_HS4379_169_252                             5
#> AB843890.1_Mmd_HS4379_253_336                             6
#> AB843890.1_Mmd_HS4379_337_420                             5
#> AB843890.1_Mmd_HS4379_421_504                             3
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             3
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             4
#> AB843890.1_Mmd_HS4379_841_924                             6
#>                               AB843923.1_Mmc_MG2111_505_588
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              3
#> AB843923.1_Mmc_MG2111_169_252                             2
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             5
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             2
#> AB843923.1_Mmc_MG2111_757_840                             7
#> AB843890.1_Mmd_HS4379_1_84                                4
#> AB843890.1_Mmd_HS4379_85_168                              2
#> AB843890.1_Mmd_HS4379_169_252                             2
#> AB843890.1_Mmd_HS4379_253_336                             2
#> AB843890.1_Mmd_HS4379_337_420                             2
#> AB843890.1_Mmd_HS4379_421_504                             5
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             5
#> AB843890.1_Mmd_HS4379_673_756                             4
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             7
#>                               AB843923.1_Mmc_MG2111_589_672
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             4
#> AB843923.1_Mmc_MG2111_757_840                             7
#> AB843890.1_Mmd_HS4379_1_84                                4
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             5
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             2
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             2
#> AB843890.1_Mmd_HS4379_673_756                             4
#> AB843890.1_Mmd_HS4379_757_840                             3
#> AB843890.1_Mmd_HS4379_841_924                             7
#>                               AB843923.1_Mmc_MG2111_673_756
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             2
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             2
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             0
#> AB843923.1_Mmc_MG2111_757_840                             5
#> AB843890.1_Mmd_HS4379_1_84                                4
#> AB843890.1_Mmd_HS4379_85_168                              2
#> AB843890.1_Mmd_HS4379_169_252                             2
#> AB843890.1_Mmd_HS4379_253_336                             3
#> AB843890.1_Mmd_HS4379_337_420                             2
#> AB843890.1_Mmd_HS4379_421_504                             6
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             6
#> AB843890.1_Mmd_HS4379_673_756                             4
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             5
#>                               AB843923.1_Mmc_MG2111_757_840
#> AB843923.1_Mmc_MG2111_1_84                                7
#> AB843923.1_Mmc_MG2111_85_168                              5
#> AB843923.1_Mmc_MG2111_169_252                             5
#> AB843923.1_Mmc_MG2111_253_336                             7
#> AB843923.1_Mmc_MG2111_337_420                             8
#> AB843923.1_Mmc_MG2111_421_504                             6
#> AB843923.1_Mmc_MG2111_505_588                             7
#> AB843923.1_Mmc_MG2111_589_672                             7
#> AB843923.1_Mmc_MG2111_673_756                             5
#> AB843923.1_Mmc_MG2111_757_840                             0
#> AB843890.1_Mmd_HS4379_1_84                                6
#> AB843890.1_Mmd_HS4379_85_168                              5
#> AB843890.1_Mmd_HS4379_169_252                             5
#> AB843890.1_Mmd_HS4379_253_336                             6
#> AB843890.1_Mmd_HS4379_337_420                             5
#> AB843890.1_Mmd_HS4379_421_504                             7
#> AB843890.1_Mmd_HS4379_505_588                             7
#> AB843890.1_Mmd_HS4379_589_672                             7
#> AB843890.1_Mmd_HS4379_673_756                             6
#> AB843890.1_Mmd_HS4379_757_840                             6
#> AB843890.1_Mmd_HS4379_841_924                             0
#>                               AB843890.1_Mmd_HS4379_1_84
#> AB843923.1_Mmc_MG2111_1_84                             4
#> AB843923.1_Mmc_MG2111_85_168                           3
#> AB843923.1_Mmc_MG2111_169_252                          3
#> AB843923.1_Mmc_MG2111_253_336                          4
#> AB843923.1_Mmc_MG2111_337_420                          5
#> AB843923.1_Mmc_MG2111_421_504                          5
#> AB843923.1_Mmc_MG2111_505_588                          4
#> AB843923.1_Mmc_MG2111_589_672                          4
#> AB843923.1_Mmc_MG2111_673_756                          4
#> AB843923.1_Mmc_MG2111_757_840                          6
#> AB843890.1_Mmd_HS4379_1_84                             0
#> AB843890.1_Mmd_HS4379_85_168                           3
#> AB843890.1_Mmd_HS4379_169_252                          3
#> AB843890.1_Mmd_HS4379_253_336                          4
#> AB843890.1_Mmd_HS4379_337_420                          3
#> AB843890.1_Mmd_HS4379_421_504                          5
#> AB843890.1_Mmd_HS4379_505_588                          4
#> AB843890.1_Mmd_HS4379_589_672                          5
#> AB843890.1_Mmd_HS4379_673_756                          0
#> AB843890.1_Mmd_HS4379_757_840                          3
#> AB843890.1_Mmd_HS4379_841_924                          6
#>                               AB843890.1_Mmd_HS4379_85_168
#> AB843923.1_Mmc_MG2111_1_84                               4
#> AB843923.1_Mmc_MG2111_85_168                             2
#> AB843923.1_Mmc_MG2111_169_252                            0
#> AB843923.1_Mmc_MG2111_253_336                            4
#> AB843923.1_Mmc_MG2111_337_420                            3
#> AB843923.1_Mmc_MG2111_421_504                            5
#> AB843923.1_Mmc_MG2111_505_588                            2
#> AB843923.1_Mmc_MG2111_589_672                            4
#> AB843923.1_Mmc_MG2111_673_756                            2
#> AB843923.1_Mmc_MG2111_757_840                            5
#> AB843890.1_Mmd_HS4379_1_84                               3
#> AB843890.1_Mmd_HS4379_85_168                             0
#> AB843890.1_Mmd_HS4379_169_252                            0
#> AB843890.1_Mmd_HS4379_253_336                            1
#> AB843890.1_Mmd_HS4379_337_420                            0
#> AB843890.1_Mmd_HS4379_421_504                            4
#> AB843890.1_Mmd_HS4379_505_588                            4
#> AB843890.1_Mmd_HS4379_589_672                            4
#> AB843890.1_Mmd_HS4379_673_756                            3
#> AB843890.1_Mmd_HS4379_757_840                            1
#> AB843890.1_Mmd_HS4379_841_924                            5
#>                               AB843890.1_Mmd_HS4379_169_252
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              2
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             5
#> AB843923.1_Mmc_MG2111_505_588                             2
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             2
#> AB843923.1_Mmc_MG2111_757_840                             5
#> AB843890.1_Mmd_HS4379_1_84                                3
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             3
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             5
#>                               AB843890.1_Mmd_HS4379_253_336
#> AB843923.1_Mmc_MG2111_1_84                                5
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             5
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             6
#> AB843923.1_Mmc_MG2111_505_588                             2
#> AB843923.1_Mmc_MG2111_589_672                             5
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             6
#> AB843890.1_Mmd_HS4379_1_84                                4
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             3
#> AB843890.1_Mmd_HS4379_505_588                             5
#> AB843890.1_Mmd_HS4379_589_672                             3
#> AB843890.1_Mmd_HS4379_673_756                             4
#> AB843890.1_Mmd_HS4379_757_840                             2
#> AB843890.1_Mmd_HS4379_841_924                             6
#>                               AB843890.1_Mmd_HS4379_337_420
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              2
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             5
#> AB843923.1_Mmc_MG2111_505_588                             2
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             2
#> AB843923.1_Mmc_MG2111_757_840                             5
#> AB843890.1_Mmd_HS4379_1_84                                3
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             3
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             5
#>                               AB843890.1_Mmd_HS4379_421_504
#> AB843923.1_Mmc_MG2111_1_84                                2
#> AB843923.1_Mmc_MG2111_85_168                              2
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             2
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             5
#> AB843923.1_Mmc_MG2111_589_672                             2
#> AB843923.1_Mmc_MG2111_673_756                             6
#> AB843923.1_Mmc_MG2111_757_840                             7
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             3
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             2
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             5
#> AB843890.1_Mmd_HS4379_841_924                             7
#>                               AB843890.1_Mmd_HS4379_505_588
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             3
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             4
#> AB843923.1_Mmc_MG2111_757_840                             7
#> AB843890.1_Mmd_HS4379_1_84                                4
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             5
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             2
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             2
#> AB843890.1_Mmd_HS4379_673_756                             4
#> AB843890.1_Mmd_HS4379_757_840                             3
#> AB843890.1_Mmd_HS4379_841_924                             7
#>                               AB843890.1_Mmd_HS4379_589_672
#> AB843923.1_Mmc_MG2111_1_84                                2
#> AB843923.1_Mmc_MG2111_85_168                              2
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             2
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             5
#> AB843923.1_Mmc_MG2111_589_672                             2
#> AB843923.1_Mmc_MG2111_673_756                             6
#> AB843923.1_Mmc_MG2111_757_840                             7
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             3
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             2
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             5
#> AB843890.1_Mmd_HS4379_841_924                             7
#>                               AB843890.1_Mmd_HS4379_673_756
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              3
#> AB843923.1_Mmc_MG2111_169_252                             3
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             5
#> AB843923.1_Mmc_MG2111_421_504                             5
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             4
#> AB843923.1_Mmc_MG2111_757_840                             6
#> AB843890.1_Mmd_HS4379_1_84                                0
#> AB843890.1_Mmd_HS4379_85_168                              3
#> AB843890.1_Mmd_HS4379_169_252                             3
#> AB843890.1_Mmd_HS4379_253_336                             4
#> AB843890.1_Mmd_HS4379_337_420                             3
#> AB843890.1_Mmd_HS4379_421_504                             5
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             5
#> AB843890.1_Mmd_HS4379_673_756                             0
#> AB843890.1_Mmd_HS4379_757_840                             3
#> AB843890.1_Mmd_HS4379_841_924                             6
#>                               AB843890.1_Mmd_HS4379_757_840
#> AB843923.1_Mmc_MG2111_1_84                                3
#> AB843923.1_Mmc_MG2111_85_168                              3
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             3
#> AB843923.1_Mmc_MG2111_337_420                             2
#> AB843923.1_Mmc_MG2111_421_504                             4
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             3
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             6
#> AB843890.1_Mmd_HS4379_1_84                                3
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             2
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             5
#> AB843890.1_Mmd_HS4379_505_588                             3
#> AB843890.1_Mmd_HS4379_589_672                             5
#> AB843890.1_Mmd_HS4379_673_756                             3
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             6
#>                               AB843890.1_Mmd_HS4379_841_924
#> AB843923.1_Mmc_MG2111_1_84                                7
#> AB843923.1_Mmc_MG2111_85_168                              5
#> AB843923.1_Mmc_MG2111_169_252                             5
#> AB843923.1_Mmc_MG2111_253_336                             7
#> AB843923.1_Mmc_MG2111_337_420                             8
#> AB843923.1_Mmc_MG2111_421_504                             6
#> AB843923.1_Mmc_MG2111_505_588                             7
#> AB843923.1_Mmc_MG2111_589_672                             7
#> AB843923.1_Mmc_MG2111_673_756                             5
#> AB843923.1_Mmc_MG2111_757_840                             0
#> AB843890.1_Mmd_HS4379_1_84                                6
#> AB843890.1_Mmd_HS4379_85_168                              5
#> AB843890.1_Mmd_HS4379_169_252                             5
#> AB843890.1_Mmd_HS4379_253_336                             6
#> AB843890.1_Mmd_HS4379_337_420                             5
#> AB843890.1_Mmd_HS4379_421_504                             7
#> AB843890.1_Mmd_HS4379_505_588                             7
#> AB843890.1_Mmd_HS4379_589_672                             7
#> AB843890.1_Mmd_HS4379_673_756                             6
#> AB843890.1_Mmd_HS4379_757_840                             6
#> AB843890.1_Mmd_HS4379_841_924                             0
#> 
#> $distance
#> [1] 26.75
#> 
#> $order
#>        [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> order1    0    1    0    2    3    4    5    6    7     8     9    10
#> order2    1    2    3    4    5    6    0    7    8     9    10    11
#> 
#> $sequence
#> DNAStringSet object of length 2:
#>     width seq                                               names               
#> [1]  1008 -----------------------...AGAGGACACATACAAGAGAGAAG seq1
#> [2]  1008 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG seq2
#> 
#> $sequence.dist
#>      seq1
#> seq2   18
#> 
##get repeat alignment and exclude highly variable sites for the distance
##calculation
repeatR::RepeatAlignment(mousePRDM9.random.split$cds[[1]],
    mousePRDM9.random.split$cds[[2]],
    exclude.pos = c(37:39, 46:48, 55:57))
#> $gendist
#>                               AB843923.1_Mmc_MG2111_1_84
#> AB843923.1_Mmc_MG2111_1_84                             0
#> AB843923.1_Mmc_MG2111_85_168                           0
#> AB843923.1_Mmc_MG2111_169_252                          0
#> AB843923.1_Mmc_MG2111_253_336                          0
#> AB843923.1_Mmc_MG2111_337_420                          0
#> AB843923.1_Mmc_MG2111_421_504                          1
#> AB843923.1_Mmc_MG2111_505_588                          0
#> AB843923.1_Mmc_MG2111_589_672                          0
#> AB843923.1_Mmc_MG2111_673_756                          1
#> AB843923.1_Mmc_MG2111_757_840                          4
#> AB843890.1_Mmd_HS4379_1_84                             1
#> AB843890.1_Mmd_HS4379_85_168                           0
#> AB843890.1_Mmd_HS4379_169_252                          0
#> AB843890.1_Mmd_HS4379_253_336                          0
#> AB843890.1_Mmd_HS4379_337_420                          0
#> AB843890.1_Mmd_HS4379_421_504                          0
#> AB843890.1_Mmd_HS4379_505_588                          0
#> AB843890.1_Mmd_HS4379_589_672                          0
#> AB843890.1_Mmd_HS4379_673_756                          1
#> AB843890.1_Mmd_HS4379_757_840                          0
#> AB843890.1_Mmd_HS4379_841_924                          4
#>                               AB843923.1_Mmc_MG2111_85_168
#> AB843923.1_Mmc_MG2111_1_84                               0
#> AB843923.1_Mmc_MG2111_85_168                             0
#> AB843923.1_Mmc_MG2111_169_252                            0
#> AB843923.1_Mmc_MG2111_253_336                            0
#> AB843923.1_Mmc_MG2111_337_420                            0
#> AB843923.1_Mmc_MG2111_421_504                            1
#> AB843923.1_Mmc_MG2111_505_588                            0
#> AB843923.1_Mmc_MG2111_589_672                            0
#> AB843923.1_Mmc_MG2111_673_756                            1
#> AB843923.1_Mmc_MG2111_757_840                            4
#> AB843890.1_Mmd_HS4379_1_84                               1
#> AB843890.1_Mmd_HS4379_85_168                             0
#> AB843890.1_Mmd_HS4379_169_252                            0
#> AB843890.1_Mmd_HS4379_253_336                            0
#> AB843890.1_Mmd_HS4379_337_420                            0
#> AB843890.1_Mmd_HS4379_421_504                            0
#> AB843890.1_Mmd_HS4379_505_588                            0
#> AB843890.1_Mmd_HS4379_589_672                            0
#> AB843890.1_Mmd_HS4379_673_756                            1
#> AB843890.1_Mmd_HS4379_757_840                            0
#> AB843890.1_Mmd_HS4379_841_924                            4
#>                               AB843923.1_Mmc_MG2111_169_252
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_253_336
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_337_420
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_421_504
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             0
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             0
#> AB843923.1_Mmc_MG2111_757_840                             3
#> AB843890.1_Mmd_HS4379_1_84                                2
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             1
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             1
#> AB843890.1_Mmd_HS4379_673_756                             2
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             3
#>                               AB843923.1_Mmc_MG2111_505_588
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_589_672
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_673_756
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             0
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             0
#> AB843923.1_Mmc_MG2111_757_840                             3
#> AB843890.1_Mmd_HS4379_1_84                                2
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             1
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             1
#> AB843890.1_Mmd_HS4379_673_756                             2
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             3
#>                               AB843923.1_Mmc_MG2111_757_840
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             0
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             4
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             4
#> AB843890.1_Mmd_HS4379_841_924                             0
#>                               AB843890.1_Mmd_HS4379_1_84
#> AB843923.1_Mmc_MG2111_1_84                             1
#> AB843923.1_Mmc_MG2111_85_168                           1
#> AB843923.1_Mmc_MG2111_169_252                          1
#> AB843923.1_Mmc_MG2111_253_336                          1
#> AB843923.1_Mmc_MG2111_337_420                          1
#> AB843923.1_Mmc_MG2111_421_504                          2
#> AB843923.1_Mmc_MG2111_505_588                          1
#> AB843923.1_Mmc_MG2111_589_672                          1
#> AB843923.1_Mmc_MG2111_673_756                          2
#> AB843923.1_Mmc_MG2111_757_840                          5
#> AB843890.1_Mmd_HS4379_1_84                             0
#> AB843890.1_Mmd_HS4379_85_168                           1
#> AB843890.1_Mmd_HS4379_169_252                          1
#> AB843890.1_Mmd_HS4379_253_336                          1
#> AB843890.1_Mmd_HS4379_337_420                          1
#> AB843890.1_Mmd_HS4379_421_504                          1
#> AB843890.1_Mmd_HS4379_505_588                          1
#> AB843890.1_Mmd_HS4379_589_672                          1
#> AB843890.1_Mmd_HS4379_673_756                          0
#> AB843890.1_Mmd_HS4379_757_840                          1
#> AB843890.1_Mmd_HS4379_841_924                          5
#>                               AB843890.1_Mmd_HS4379_85_168
#> AB843923.1_Mmc_MG2111_1_84                               0
#> AB843923.1_Mmc_MG2111_85_168                             0
#> AB843923.1_Mmc_MG2111_169_252                            0
#> AB843923.1_Mmc_MG2111_253_336                            0
#> AB843923.1_Mmc_MG2111_337_420                            0
#> AB843923.1_Mmc_MG2111_421_504                            1
#> AB843923.1_Mmc_MG2111_505_588                            0
#> AB843923.1_Mmc_MG2111_589_672                            0
#> AB843923.1_Mmc_MG2111_673_756                            1
#> AB843923.1_Mmc_MG2111_757_840                            4
#> AB843890.1_Mmd_HS4379_1_84                               1
#> AB843890.1_Mmd_HS4379_85_168                             0
#> AB843890.1_Mmd_HS4379_169_252                            0
#> AB843890.1_Mmd_HS4379_253_336                            0
#> AB843890.1_Mmd_HS4379_337_420                            0
#> AB843890.1_Mmd_HS4379_421_504                            0
#> AB843890.1_Mmd_HS4379_505_588                            0
#> AB843890.1_Mmd_HS4379_589_672                            0
#> AB843890.1_Mmd_HS4379_673_756                            1
#> AB843890.1_Mmd_HS4379_757_840                            0
#> AB843890.1_Mmd_HS4379_841_924                            4
#>                               AB843890.1_Mmd_HS4379_169_252
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_253_336
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_337_420
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_421_504
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_505_588
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_589_672
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_673_756
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             2
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             2
#> AB843923.1_Mmc_MG2111_757_840                             5
#> AB843890.1_Mmd_HS4379_1_84                                0
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             1
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             1
#> AB843890.1_Mmd_HS4379_673_756                             0
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             5
#>                               AB843890.1_Mmd_HS4379_757_840
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_841_924
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             0
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             4
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             4
#> AB843890.1_Mmd_HS4379_841_924                             0
#> 
#> $distance
#> [1] 5.75
#> 
#> $order
#>        [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
#> order1    1    2    3    4    5    6    0    7    8     9    10
#> order2    1    2    3    4    5    6    7    8    9    10    11
#> 
#> $sequence
#> DNAStringSet object of length 2:
#>     width seq                                               names               
#> [1]   825 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG seq1
#> [2]   825 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG seq2
#> 
#> $sequence.dist
#>      seq1
#> seq2    4
#> 
##get repeat alignment, exclude highly variable sites for the distance
##calculation and add them back afterwards
repeatR::RepeatAlignment(mousePRDM9.random.split$cds[[1]],
    mousePRDM9.random.split$cds[[2]],
    exclude.pos = c(37:39, 46:48, 55:57),
    post.include = TRUE)
#> $gendist
#>                               AB843923.1_Mmc_MG2111_1_84
#> AB843923.1_Mmc_MG2111_1_84                             0
#> AB843923.1_Mmc_MG2111_85_168                           0
#> AB843923.1_Mmc_MG2111_169_252                          0
#> AB843923.1_Mmc_MG2111_253_336                          0
#> AB843923.1_Mmc_MG2111_337_420                          0
#> AB843923.1_Mmc_MG2111_421_504                          1
#> AB843923.1_Mmc_MG2111_505_588                          0
#> AB843923.1_Mmc_MG2111_589_672                          0
#> AB843923.1_Mmc_MG2111_673_756                          1
#> AB843923.1_Mmc_MG2111_757_840                          4
#> AB843890.1_Mmd_HS4379_1_84                             1
#> AB843890.1_Mmd_HS4379_85_168                           0
#> AB843890.1_Mmd_HS4379_169_252                          0
#> AB843890.1_Mmd_HS4379_253_336                          0
#> AB843890.1_Mmd_HS4379_337_420                          0
#> AB843890.1_Mmd_HS4379_421_504                          0
#> AB843890.1_Mmd_HS4379_505_588                          0
#> AB843890.1_Mmd_HS4379_589_672                          0
#> AB843890.1_Mmd_HS4379_673_756                          1
#> AB843890.1_Mmd_HS4379_757_840                          0
#> AB843890.1_Mmd_HS4379_841_924                          4
#>                               AB843923.1_Mmc_MG2111_85_168
#> AB843923.1_Mmc_MG2111_1_84                               0
#> AB843923.1_Mmc_MG2111_85_168                             0
#> AB843923.1_Mmc_MG2111_169_252                            0
#> AB843923.1_Mmc_MG2111_253_336                            0
#> AB843923.1_Mmc_MG2111_337_420                            0
#> AB843923.1_Mmc_MG2111_421_504                            1
#> AB843923.1_Mmc_MG2111_505_588                            0
#> AB843923.1_Mmc_MG2111_589_672                            0
#> AB843923.1_Mmc_MG2111_673_756                            1
#> AB843923.1_Mmc_MG2111_757_840                            4
#> AB843890.1_Mmd_HS4379_1_84                               1
#> AB843890.1_Mmd_HS4379_85_168                             0
#> AB843890.1_Mmd_HS4379_169_252                            0
#> AB843890.1_Mmd_HS4379_253_336                            0
#> AB843890.1_Mmd_HS4379_337_420                            0
#> AB843890.1_Mmd_HS4379_421_504                            0
#> AB843890.1_Mmd_HS4379_505_588                            0
#> AB843890.1_Mmd_HS4379_589_672                            0
#> AB843890.1_Mmd_HS4379_673_756                            1
#> AB843890.1_Mmd_HS4379_757_840                            0
#> AB843890.1_Mmd_HS4379_841_924                            4
#>                               AB843923.1_Mmc_MG2111_169_252
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_253_336
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_337_420
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_421_504
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             0
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             0
#> AB843923.1_Mmc_MG2111_757_840                             3
#> AB843890.1_Mmd_HS4379_1_84                                2
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             1
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             1
#> AB843890.1_Mmd_HS4379_673_756                             2
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             3
#>                               AB843923.1_Mmc_MG2111_505_588
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_589_672
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843923.1_Mmc_MG2111_673_756
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             0
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             0
#> AB843923.1_Mmc_MG2111_757_840                             3
#> AB843890.1_Mmd_HS4379_1_84                                2
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             1
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             1
#> AB843890.1_Mmd_HS4379_673_756                             2
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             3
#>                               AB843923.1_Mmc_MG2111_757_840
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             0
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             4
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             4
#> AB843890.1_Mmd_HS4379_841_924                             0
#>                               AB843890.1_Mmd_HS4379_1_84
#> AB843923.1_Mmc_MG2111_1_84                             1
#> AB843923.1_Mmc_MG2111_85_168                           1
#> AB843923.1_Mmc_MG2111_169_252                          1
#> AB843923.1_Mmc_MG2111_253_336                          1
#> AB843923.1_Mmc_MG2111_337_420                          1
#> AB843923.1_Mmc_MG2111_421_504                          2
#> AB843923.1_Mmc_MG2111_505_588                          1
#> AB843923.1_Mmc_MG2111_589_672                          1
#> AB843923.1_Mmc_MG2111_673_756                          2
#> AB843923.1_Mmc_MG2111_757_840                          5
#> AB843890.1_Mmd_HS4379_1_84                             0
#> AB843890.1_Mmd_HS4379_85_168                           1
#> AB843890.1_Mmd_HS4379_169_252                          1
#> AB843890.1_Mmd_HS4379_253_336                          1
#> AB843890.1_Mmd_HS4379_337_420                          1
#> AB843890.1_Mmd_HS4379_421_504                          1
#> AB843890.1_Mmd_HS4379_505_588                          1
#> AB843890.1_Mmd_HS4379_589_672                          1
#> AB843890.1_Mmd_HS4379_673_756                          0
#> AB843890.1_Mmd_HS4379_757_840                          1
#> AB843890.1_Mmd_HS4379_841_924                          5
#>                               AB843890.1_Mmd_HS4379_85_168
#> AB843923.1_Mmc_MG2111_1_84                               0
#> AB843923.1_Mmc_MG2111_85_168                             0
#> AB843923.1_Mmc_MG2111_169_252                            0
#> AB843923.1_Mmc_MG2111_253_336                            0
#> AB843923.1_Mmc_MG2111_337_420                            0
#> AB843923.1_Mmc_MG2111_421_504                            1
#> AB843923.1_Mmc_MG2111_505_588                            0
#> AB843923.1_Mmc_MG2111_589_672                            0
#> AB843923.1_Mmc_MG2111_673_756                            1
#> AB843923.1_Mmc_MG2111_757_840                            4
#> AB843890.1_Mmd_HS4379_1_84                               1
#> AB843890.1_Mmd_HS4379_85_168                             0
#> AB843890.1_Mmd_HS4379_169_252                            0
#> AB843890.1_Mmd_HS4379_253_336                            0
#> AB843890.1_Mmd_HS4379_337_420                            0
#> AB843890.1_Mmd_HS4379_421_504                            0
#> AB843890.1_Mmd_HS4379_505_588                            0
#> AB843890.1_Mmd_HS4379_589_672                            0
#> AB843890.1_Mmd_HS4379_673_756                            1
#> AB843890.1_Mmd_HS4379_757_840                            0
#> AB843890.1_Mmd_HS4379_841_924                            4
#>                               AB843890.1_Mmd_HS4379_169_252
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_253_336
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_337_420
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_421_504
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_505_588
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_589_672
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_673_756
#> AB843923.1_Mmc_MG2111_1_84                                1
#> AB843923.1_Mmc_MG2111_85_168                              1
#> AB843923.1_Mmc_MG2111_169_252                             1
#> AB843923.1_Mmc_MG2111_253_336                             1
#> AB843923.1_Mmc_MG2111_337_420                             1
#> AB843923.1_Mmc_MG2111_421_504                             2
#> AB843923.1_Mmc_MG2111_505_588                             1
#> AB843923.1_Mmc_MG2111_589_672                             1
#> AB843923.1_Mmc_MG2111_673_756                             2
#> AB843923.1_Mmc_MG2111_757_840                             5
#> AB843890.1_Mmd_HS4379_1_84                                0
#> AB843890.1_Mmd_HS4379_85_168                              1
#> AB843890.1_Mmd_HS4379_169_252                             1
#> AB843890.1_Mmd_HS4379_253_336                             1
#> AB843890.1_Mmd_HS4379_337_420                             1
#> AB843890.1_Mmd_HS4379_421_504                             1
#> AB843890.1_Mmd_HS4379_505_588                             1
#> AB843890.1_Mmd_HS4379_589_672                             1
#> AB843890.1_Mmd_HS4379_673_756                             0
#> AB843890.1_Mmd_HS4379_757_840                             1
#> AB843890.1_Mmd_HS4379_841_924                             5
#>                               AB843890.1_Mmd_HS4379_757_840
#> AB843923.1_Mmc_MG2111_1_84                                0
#> AB843923.1_Mmc_MG2111_85_168                              0
#> AB843923.1_Mmc_MG2111_169_252                             0
#> AB843923.1_Mmc_MG2111_253_336                             0
#> AB843923.1_Mmc_MG2111_337_420                             0
#> AB843923.1_Mmc_MG2111_421_504                             1
#> AB843923.1_Mmc_MG2111_505_588                             0
#> AB843923.1_Mmc_MG2111_589_672                             0
#> AB843923.1_Mmc_MG2111_673_756                             1
#> AB843923.1_Mmc_MG2111_757_840                             4
#> AB843890.1_Mmd_HS4379_1_84                                1
#> AB843890.1_Mmd_HS4379_85_168                              0
#> AB843890.1_Mmd_HS4379_169_252                             0
#> AB843890.1_Mmd_HS4379_253_336                             0
#> AB843890.1_Mmd_HS4379_337_420                             0
#> AB843890.1_Mmd_HS4379_421_504                             0
#> AB843890.1_Mmd_HS4379_505_588                             0
#> AB843890.1_Mmd_HS4379_589_672                             0
#> AB843890.1_Mmd_HS4379_673_756                             1
#> AB843890.1_Mmd_HS4379_757_840                             0
#> AB843890.1_Mmd_HS4379_841_924                             4
#>                               AB843890.1_Mmd_HS4379_841_924
#> AB843923.1_Mmc_MG2111_1_84                                4
#> AB843923.1_Mmc_MG2111_85_168                              4
#> AB843923.1_Mmc_MG2111_169_252                             4
#> AB843923.1_Mmc_MG2111_253_336                             4
#> AB843923.1_Mmc_MG2111_337_420                             4
#> AB843923.1_Mmc_MG2111_421_504                             3
#> AB843923.1_Mmc_MG2111_505_588                             4
#> AB843923.1_Mmc_MG2111_589_672                             4
#> AB843923.1_Mmc_MG2111_673_756                             3
#> AB843923.1_Mmc_MG2111_757_840                             0
#> AB843890.1_Mmd_HS4379_1_84                                5
#> AB843890.1_Mmd_HS4379_85_168                              4
#> AB843890.1_Mmd_HS4379_169_252                             4
#> AB843890.1_Mmd_HS4379_253_336                             4
#> AB843890.1_Mmd_HS4379_337_420                             4
#> AB843890.1_Mmd_HS4379_421_504                             4
#> AB843890.1_Mmd_HS4379_505_588                             4
#> AB843890.1_Mmd_HS4379_589_672                             4
#> AB843890.1_Mmd_HS4379_673_756                             5
#> AB843890.1_Mmd_HS4379_757_840                             4
#> AB843890.1_Mmd_HS4379_841_924                             0
#> 
#> $distance
#> [1] 5.75
#> 
#> $order
#>        [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
#> order1    1    2    3    4    5    6    7    8    0     9    10
#> order2    1    2    3    4    5    6    7    8    9    10    11
#> 
#> $sequence
#> DNAStringSet object of length 2:
#>     width seq                                               names               
#> [1]   924 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG seq1
#> [2]   924 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG seq2
#> 
#> $sequence.dist
#>      seq1
#> seq2   24
#>