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
)
DNAStringSet
DNAStringSet
seq1 name [default: seq1]
seq2 name [default: seq2]
pairwise distance matrix of seq1 and seq2 repeats [default: NULL]
distance calculation method if no gendist matrix is supplied [default: hamming]
a character string specifying the evolutionary model to be
used (see ape::dist.dna
) [default: K80]
weight for nucleotide point mutations [default: 1]
weight for unit insertions/deletions [default: 3.5]
weight for single unit duplications [default: 1.75]
positions of the repeat that will be excluded before distance calculation [default: NULL]
boolean if excluded positions should be added back for the sequence alignment after distance calculation [default: FALSE]
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.
##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
#>