This function splits a repeat containing DNAStringSet, into sequences (repeat units) given a repeat start pattern and repeat length.

splitRepByPattern(x, p, l, threads = 1)

Arguments

x

DNAStringSet

p

repeat pattern

l

repeat length in nucleotides

threads

number of parallel threads [default: 1]

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)
mousePRDM9.random.split$cds
#> $AB843934.1_Mmc_HI276
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843934.1_Mmc_HI...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843934.1_Mmc_HI...
#> 
#> $AB843987.1_Mmm_MG3054
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [2]    84 CCCTATGTTTGCAGGGGGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...AAGGACACACACAGGGGAGAAG AB843987.1_Mmm_MG...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843987.1_Mmm_MG...
#> 
#> $MK848114.1_cds_QCI31692.1_1
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848114.1_cds_QC...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG MK848114.1_cds_QC...
#> 
#> $AB843883.1_Mmd_MG382
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843883.1_Mmd_MG...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843883.1_Mmd_MG...
#> 
#> $AB843979.1_Mmm_MG3065
#> DNAStringSet object of length 9:
#>     width seq                                               names               
#> [1]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [2]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [3]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [4]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [5]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [6]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [7]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [8]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG AB843979.1_Mmm_MG...
#> [9]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB843979.1_Mmm_MG...
#> 
#> $KF462407.1_cds_AHA80503.1_1
#> DNAStringSet object of length 9:
#>     width seq                                               names               
#> [1]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [2]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [3]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [4]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [5]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [6]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [7]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [8]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462407.1_cds_AH...
#> [9]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG KF462407.1_cds_AH...
#> 
#> $`AB843898.1_Mmd_P/J`
#> DNAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#>  ...   ... ...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843898.1_Mmd_P/...
#> [12]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843898.1_Mmd_P/...
#> 
#> $KF462414.1_cds_AHA80510.1_1
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462414.1_cds_AH...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG KF462414.1_cds_AH...
#> 
#> $KF462460.1_cds_AHA80556.1_1
#> DNAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#>  ...   ... ...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462460.1_cds_AH...
#> [12]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG KF462460.1_cds_AH...
#> 
#> $KF462446.1_cds_AHA80542.1_1
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462446.1_cds_AH...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG KF462446.1_cds_AH...
#> 
#> $KF462457.1_cds_AHA80553.1_1
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462457.1_cds_AH...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG KF462457.1_cds_AH...
#> 
#> $AB843952.1_Mmm_MG80
#> DNAStringSet object of length 14:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#>  ...   ... ...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#> [12]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#> [13]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843952.1_Mmm_MG...
#> [14]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843952.1_Mmm_MG...
#> 
#> $KF462467.1_cds_AHA80563.1_1
#> DNAStringSet object of length 7:
#>     width seq                                               names               
#> [1]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> [2]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> [3]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> [4]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> [5]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> [6]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> [7]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462467.1_cds_AH...
#> 
#> $KF462458.1_cds_AHA80554.1_1
#> DNAStringSet object of length 11:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  ...   ... ...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG KF462458.1_cds_AH...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG KF462458.1_cds_AH...
#> 
#> $MK848147.1_cds_QCI31725.1_1
#> DNAStringSet object of length 15:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#>  ...   ... ...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#> [12]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#> [13]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#> [14]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG MK848147.1_cds_QC...
#> [15]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG MK848147.1_cds_QC...
#> 
#> $KF462403.1_cds_AHA80499.1_1
#> DNAStringSet object of length 9:
#>     width seq                                               names               
#> [1]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [2]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [3]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [4]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [5]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [6]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [7]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [8]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACACACAGGGGAGAAG KF462403.1_cds_AH...
#> [9]    84 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG KF462403.1_cds_AH...
#> 
#> $AB843917.1_Mmc_MG503
#> DNAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#>  ...   ... ...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843917.1_Mmc_MG...
#> [12]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843917.1_Mmc_MG...
#> 
#> $`AB844112.1_Mmd_PGN2/Ms`
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB844112.1_Mmd_PG...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB844112.1_Mmd_PG...
#> 
#> $`AB843908.1_Mmd_BFM/2Ms`
#> DNAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [6]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [7]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843908.1_Mmd_BF...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843908.1_Mmd_BF...
#> 
#> $AB843947.1_Mmc_HI159
#> DNAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#>  [2]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#>  [3]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#>  [4]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#>  [5]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#>  ...   ... ...
#>  [8]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#>  [9]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#> [10]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGAGAAG AB843947.1_Mmc_HI...
#> [11]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACACACAGGGGGGAAG AB843947.1_Mmc_HI...
#> [12]    84 CCCTATGTTTGCAGGGAGTGTGG...GAGGACACATACAAGAGAGAAG AB843947.1_Mmc_HI...
#> 
mousePRDM9.random.split$aa
#> $AB843934.1_Mmc_HI276
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [2]    28 PYVCRECGRGFTQKSVLIQHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [4]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [5]    28 PYVCRECGRGFTEKSSLIKHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [6]    28 PYVCRECGWGFTAKSNLIQHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [7]    28 PYVCRECGRGFTQKSSLIKHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [8]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843934.1_Mmc_HI...
#>  [9]    28 PYVCRECGWGFTQKSNLIKHQRTHTGEK                     AB843934.1_Mmc_HI...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB843934.1_Mmc_HI...
#> 
#> $AB843987.1_Mmm_MG3054
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTAKSSLVQHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [2]    28 PYVCRGCGRGFTAKSSLIQHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [3]    28 PYVCRECGRGFTQNSHLIKHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [4]    28 PYVCRECGRGFIAKSNLIQHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [5]    28 PYVCRECGRGFTTKSDLIKHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [6]    28 PYVCRECGRGFTQNSHLIKHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [7]    28 PYVCRECGRGFIAKSNLIQHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [8]    28 PYVCRECGRGFTTKSDLIKHQRTHTGEK                     AB843987.1_Mmm_MG...
#>  [9]    28 PYVCRECGRGFTQNSHLIKHQRTHTGEK                     AB843987.1_Mmm_MG...
#> [10]    28 PYVCRECGRGFTQKSDLIQHQRTHTREK                     AB843987.1_Mmm_MG...
#> 
#> $MK848114.1_cds_QCI31692.1_1
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTAKSSLVQHQRTHTGEK                     MK848114.1_cds_QC...
#>  [2]    28 PYVCRECGRGFTAKSNLIKHQRTHTGEK                     MK848114.1_cds_QC...
#>  [3]    28 PYVCRECGRGFTQNSHLIKHQRTHTGEK                     MK848114.1_cds_QC...
#>  [4]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     MK848114.1_cds_QC...
#>  [5]    28 PYVCRECGRGFTAKSDLIKHQRTHTGEK                     MK848114.1_cds_QC...
#>  [6]    28 PYVCRECGRGFTQKSHLIKHQRTHTGEK                     MK848114.1_cds_QC...
#>  [7]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     MK848114.1_cds_QC...
#>  [8]    28 PYVCRECGRGFTTKSDLIKHQRTHTGEK                     MK848114.1_cds_QC...
#>  [9]    28 PYVCRECGRGFTQNSHLIKHQRTHTGEK                     MK848114.1_cds_QC...
#> [10]    28 PYVCRECGRGFTQKSDLIQHQRTHTREK                     MK848114.1_cds_QC...
#> 
#> $AB843883.1_Mmd_MG382
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [3]    28 PYVCRECGRGFTVKSVLIKHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [4]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [5]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [6]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [7]    28 PYVCRECGRGFTQKSDLIQHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [8]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843883.1_Mmd_MG...
#>  [9]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     AB843883.1_Mmd_MG...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB843883.1_Mmd_MG...
#> 
#> $AB843979.1_Mmm_MG3065
#> AAStringSet object of length 9:
#>     width seq                                               names               
#> [1]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [2]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [3]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [4]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [5]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [6]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [7]    28 PYVCRECGRGFTAKSNLIKHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [8]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                      AB843979.1_Mmm_MG...
#> [9]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                      AB843979.1_Mmm_MG...
#> 
#> $KF462407.1_cds_AHA80503.1_1
#> AAStringSet object of length 9:
#>     width seq                                               names               
#> [1]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                      KF462407.1_cds_AH...
#> [2]    28 PYVCRECGRGFTEKSSLIKHQRTHTGEK                      KF462407.1_cds_AH...
#> [3]    28 PYVCRECGRGFTAKSDLIKHQRTHTGEK                      KF462407.1_cds_AH...
#> [4]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                      KF462407.1_cds_AH...
#> [5]    28 PYVCRECGRGFTAKSDLIKHQRTHTGEK                      KF462407.1_cds_AH...
#> [6]    28 PYVCRECGRGFTQKSSLIKHQRTHTGEK                      KF462407.1_cds_AH...
#> [7]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                      KF462407.1_cds_AH...
#> [8]    28 PYVCRECGWGFTQKSNLIKHQRTHTGEK                      KF462407.1_cds_AH...
#> [9]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                      KF462407.1_cds_AH...
#> 
#> $`AB843898.1_Mmd_P/J`
#> AAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     AB843898.1_Mmd_P/...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843898.1_Mmd_P/...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843898.1_Mmd_P/...
#>  [4]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     AB843898.1_Mmd_P/...
#>  [5]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     AB843898.1_Mmd_P/...
#>  ...   ... ...
#>  [8]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     AB843898.1_Mmd_P/...
#>  [9]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     AB843898.1_Mmd_P/...
#> [10]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     AB843898.1_Mmd_P/...
#> [11]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     AB843898.1_Mmd_P/...
#> [12]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB843898.1_Mmd_P/...
#> 
#> $KF462414.1_cds_AHA80510.1_1
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     KF462414.1_cds_AH...
#>  [2]    28 PYVCRECGRGFTQKSVLIQHQRTHTGEK                     KF462414.1_cds_AH...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462414.1_cds_AH...
#>  [4]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     KF462414.1_cds_AH...
#>  [5]    28 PYVCRECGRGFTEKSSLIKHQRTHTGEK                     KF462414.1_cds_AH...
#>  [6]    28 PYVCRECGWGFTAKSNLIQHQRTHTGEK                     KF462414.1_cds_AH...
#>  [7]    28 PYVCRECGRGFTQKSSLIKHQRTHTGEK                     KF462414.1_cds_AH...
#>  [8]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     KF462414.1_cds_AH...
#>  [9]    28 PYVCRECGWGFTQKSNLIKHQRTHTGEK                     KF462414.1_cds_AH...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     KF462414.1_cds_AH...
#> 
#> $KF462460.1_cds_AHA80556.1_1
#> AAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462460.1_cds_AH...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462460.1_cds_AH...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462460.1_cds_AH...
#>  [4]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     KF462460.1_cds_AH...
#>  [5]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     KF462460.1_cds_AH...
#>  ...   ... ...
#>  [8]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     KF462460.1_cds_AH...
#>  [9]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     KF462460.1_cds_AH...
#> [10]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     KF462460.1_cds_AH...
#> [11]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     KF462460.1_cds_AH...
#> [12]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     KF462460.1_cds_AH...
#> 
#> $KF462446.1_cds_AHA80542.1_1
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462446.1_cds_AH...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462446.1_cds_AH...
#>  [3]    28 PYVCRECGRGFTVKSVLIKHQRTHTGEK                     KF462446.1_cds_AH...
#>  [4]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462446.1_cds_AH...
#>  [5]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     KF462446.1_cds_AH...
#>  [6]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462446.1_cds_AH...
#>  [7]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462446.1_cds_AH...
#>  [8]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     KF462446.1_cds_AH...
#>  [9]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     KF462446.1_cds_AH...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     KF462446.1_cds_AH...
#> 
#> $KF462457.1_cds_AHA80553.1_1
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462457.1_cds_AH...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462457.1_cds_AH...
#>  [3]    28 PYVCRECGRGFTVKSVLIKHQRTHTGEK                     KF462457.1_cds_AH...
#>  [4]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462457.1_cds_AH...
#>  [5]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     KF462457.1_cds_AH...
#>  [6]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462457.1_cds_AH...
#>  [7]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462457.1_cds_AH...
#>  [8]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     KF462457.1_cds_AH...
#>  [9]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     KF462457.1_cds_AH...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     KF462457.1_cds_AH...
#> 
#> $AB843952.1_Mmm_MG80
#> AAStringSet object of length 14:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQKSDLIQHQRTHTGEK                     AB843952.1_Mmm_MG...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843952.1_Mmm_MG...
#>  [3]    28 PYVCRECGRGFTQKSVLIQHQRTHTGEK                     AB843952.1_Mmm_MG...
#>  [4]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843952.1_Mmm_MG...
#>  [5]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843952.1_Mmm_MG...
#>  ...   ... ...
#> [10]    28 PYVCRECGRGFTAKSNLIKHQRTHTGEK                     AB843952.1_Mmm_MG...
#> [11]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     AB843952.1_Mmm_MG...
#> [12]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     AB843952.1_Mmm_MG...
#> [13]    28 PYVCRECGWGFTQKSNLIKHQRTHTGEK                     AB843952.1_Mmm_MG...
#> [14]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB843952.1_Mmm_MG...
#> 
#> $KF462467.1_cds_AHA80563.1_1
#> AAStringSet object of length 7:
#>     width seq                                               names               
#> [1]    28 PYVCRECGRGFTQKSHLIKHQRTHTGEK                      KF462467.1_cds_AH...
#> [2]    28 PYVCRECGRGFTQKSNLIQHQRTHTGEK                      KF462467.1_cds_AH...
#> [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                      KF462467.1_cds_AH...
#> [4]    28 PYVCRECGRGFTAKSHLIKHQRTHTGEK                      KF462467.1_cds_AH...
#> [5]    28 PYVCRECGRGFTQKSNLIQHQRTHTGEK                      KF462467.1_cds_AH...
#> [6]    28 PYVCRECGRGFTAKSNLIKHQRTHTGEK                      KF462467.1_cds_AH...
#> [7]    28 PYVCRECGRGFTQNSHLTQHQRTHTGEK                      KF462467.1_cds_AH...
#> 
#> $KF462458.1_cds_AHA80554.1_1
#> AAStringSet object of length 11:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462458.1_cds_AH...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462458.1_cds_AH...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462458.1_cds_AH...
#>  [4]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     KF462458.1_cds_AH...
#>  [5]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     KF462458.1_cds_AH...
#>  ...   ... ...
#>  [7]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     KF462458.1_cds_AH...
#>  [8]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     KF462458.1_cds_AH...
#>  [9]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     KF462458.1_cds_AH...
#> [10]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     KF462458.1_cds_AH...
#> [11]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     KF462458.1_cds_AH...
#> 
#> $MK848147.1_cds_QCI31725.1_1
#> AAStringSet object of length 15:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     MK848147.1_cds_QC...
#>  [2]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     MK848147.1_cds_QC...
#>  [3]    28 PYVCRECGRGFTVKSDLIKHQRTHTGEK                     MK848147.1_cds_QC...
#>  [4]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     MK848147.1_cds_QC...
#>  [5]    28 PYVCRECGRGFTAKSVLIQHQRTHTGEK                     MK848147.1_cds_QC...
#>  ...   ... ...
#> [11]    28 PYVCRECGRGFTQKSVLIKHQRTHTGEK                     MK848147.1_cds_QC...
#> [12]    28 PYVCRECGRGFTQNSHLIQHQRTHTGEK                     MK848147.1_cds_QC...
#> [13]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     MK848147.1_cds_QC...
#> [14]    28 PYVCRECGRGFTQKSNLIKHQRTHTGEK                     MK848147.1_cds_QC...
#> [15]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     MK848147.1_cds_QC...
#> 
#> $KF462403.1_cds_AHA80499.1_1
#> AAStringSet object of length 9:
#>     width seq                                               names               
#> [1]    28 PYVCRECGRGFTQKSDLIQHQRTHTGEK                      KF462403.1_cds_AH...
#> [2]    28 PYVCRECGRGFTAKSSLIKHQRTHTGEK                      KF462403.1_cds_AH...
#> [3]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                      KF462403.1_cds_AH...
#> [4]    28 PYVCRECGRGFTEKSSLIKHQRTHTGEK                      KF462403.1_cds_AH...
#> [5]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                      KF462403.1_cds_AH...
#> [6]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                      KF462403.1_cds_AH...
#> [7]    28 PYVCRECGRGFTQKSNLIQHQRTHTGEK                      KF462403.1_cds_AH...
#> [8]    28 PYVCRECGRGFTANSNLIQHQRTHTGEK                      KF462403.1_cds_AH...
#> [9]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                      KF462403.1_cds_AH...
#> 
#> $AB843917.1_Mmc_MG503
#> AAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843917.1_Mmc_MG...
#>  [2]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                     AB843917.1_Mmc_MG...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843917.1_Mmc_MG...
#>  [4]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843917.1_Mmc_MG...
#>  [5]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843917.1_Mmc_MG...
#>  ...   ... ...
#>  [8]    28 PYVCRECGRGFTEKSNLIKHQRTHTGEK                     AB843917.1_Mmc_MG...
#>  [9]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843917.1_Mmc_MG...
#> [10]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843917.1_Mmc_MG...
#> [11]    28 PYVCRECGRGFTHKSNLIKHQRTHTGEK                     AB843917.1_Mmc_MG...
#> [12]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB843917.1_Mmc_MG...
#> 
#> $`AB844112.1_Mmd_PGN2/Ms`
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQKSDLIQHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [2]    28 PYVCRECGRGFTVKSNLIQHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [3]    28 PYVCRECGRGFTAKSSLIKHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [4]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [5]    28 PYVCRECGRGFTEKSSLIKHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [6]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [7]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [8]    28 PYVCRECGRGFTQKSNLIQHQRTHTGEK                     AB844112.1_Mmd_PG...
#>  [9]    28 PYVCRECGRGFTANSNLIQHQRTHTGEK                     AB844112.1_Mmd_PG...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB844112.1_Mmd_PG...
#> 
#> $`AB843908.1_Mmd_BFM/2Ms`
#> AAStringSet object of length 10:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQKSDLIQHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [2]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [3]    28 PYVCRECGRGFTAKSSLIKHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [4]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [5]    28 PYVCRECGRGFTEKSSLIKHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [6]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [7]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [8]    28 PYVCRECGRGFTQKSNLIQHQRTHTGEK                     AB843908.1_Mmd_BF...
#>  [9]    28 PYVCRECGRGFTANSNLIQHQRTHTGEK                     AB843908.1_Mmd_BF...
#> [10]    28 PYVCRECGWGFTQKSDLIQHQRTHTREK                     AB843908.1_Mmd_BF...
#> 
#> $AB843947.1_Mmc_HI159
#> AAStringSet object of length 12:
#>      width seq                                              names               
#>  [1]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843947.1_Mmc_HI...
#>  [2]    28 PYVCRECGRGFTVKSVLIQHQRTHTGEK                     AB843947.1_Mmc_HI...
#>  [3]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843947.1_Mmc_HI...
#>  [4]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843947.1_Mmc_HI...
#>  [5]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843947.1_Mmc_HI...
#>  ...   ... ...
#>  [8]    28 PYVCRECGRGFTAKSNLIQHQRTHTGEK                     AB843947.1_Mmc_HI...
#>  [9]    28 PYVCRECGRGFTEKSNLIKHQRTHTGEK                     AB843947.1_Mmc_HI...
#> [10]    28 PYVCRECGRGFTQKSDLIKHQRTHTGEK                     AB843947.1_Mmc_HI...
#> [11]    28 PYVCRECGRGFTAKSNLIKHQRTHTGGK                     AB843947.1_Mmc_HI...
#> [12]    28 PYVCRECGWGFTQKSNLIKHQRTHTREK                     AB843947.1_Mmc_HI...
#> 
##get abundance of repeat units
sort(table(as.character(repeatR::collapse_XStringSetList(
    mousePRDM9.random.split$aa))))
#> 
#> PYVCRECGRGFTAKSHLIKHQRTHTGEK PYVCRECGRGFTAKSNLIKHQRTHTGGK 
#>                            1                            1 
#> PYVCRECGRGFTHKSNLIKHQRTHTGEK PYVCRECGRGFTQNSHLTQHQRTHTGEK 
#>                            1                            1 
#> PYVCRECGRGFTVKSDLIKHQRTHTGEK PYVCRECGRGFTVKSNLIQHQRTHTGEK 
#>                            1                            1 
#> PYVCRECGWGFTQKSNLIKHQRTHTREK PYVCRGCGRGFTAKSSLIQHQRTHTGEK 
#>                            1                            1 
#> PYVCRECGRGFIAKSNLIQHQRTHTGEK PYVCRECGRGFTAKSSLVQHQRTHTGEK 
#>                            2                            2 
#> PYVCRECGRGFTEKSNLIKHQRTHTGEK PYVCRECGRGFTQKSDLIQHQRTHTREK 
#>                            2                            2 
#> PYVCRECGRGFTQKSHLIKHQRTHTGEK PYVCRECGWGFTAKSNLIQHQRTHTGEK 
#>                            2                            2 
#> PYVCRECGRGFTAKSDLIKHQRTHTGEK PYVCRECGRGFTAKSSLIKHQRTHTGEK 
#>                            3                            3 
#> PYVCRECGRGFTANSNLIQHQRTHTGEK PYVCRECGRGFTQKSSLIKHQRTHTGEK 
#>                            3                            3 
#> PYVCRECGRGFTQKSVLIQHQRTHTGEK PYVCRECGRGFTTKSDLIKHQRTHTGEK 
#>                            3                            3 
#> PYVCRECGRGFTVKSVLIKHQRTHTGEK PYVCRECGWGFTQKSNLIKHQRTHTGEK 
#>                            3                            4 
#> PYVCRECGRGFTQKSNLIQHQRTHTGEK PYVCRECGRGFTQNSHLIKHQRTHTGEK 
#>                            5                            5 
#> PYVCRECGRGFTAKSNLIKHQRTHTGEK PYVCRECGRGFTQKSDLIQHQRTHTGEK 
#>                            6                            6 
#> PYVCRECGRGFTEKSSLIKHQRTHTGEK PYVCRECGRGFTQKSNLIKHQRTHTGEK 
#>                            7                            9 
#> PYVCRECGRGFTQKSVLIKHQRTHTGEK PYVCRECGRGFTVKSVLIQHQRTHTGEK 
#>                            9                            9 
#> PYVCRECGRGFTAKSVLIQHQRTHTGEK PYVCRECGWGFTQKSDLIQHQRTHTREK 
#>                           15                           16 
#> PYVCRECGRGFTQNSHLIQHQRTHTGEK PYVCRECGRGFTAKSNLIQHQRTHTGEK 
#>                           18                           25 
#> PYVCRECGRGFTQKSDLIKHQRTHTGEK 
#>                           37 
##get -1, +3, +6 position
myStart<-c(37,46,55)
myEnd<-c(39,48,57)
mousePRDM9.random.split.varPos<-MSA2dist::subString(
    repeatR::collapse_XStringSetList(mousePRDM9.random.split$cds),
    myStart, myEnd)
##get nucleotide diversity
pegas::nuc.div(ape::as.DNAbin(mousePRDM9.random.split.varPos), TRUE)
#> [1] 0.28533389 0.02893311