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)
DNAStringSet
repeat pattern
repeat length in nucleotides
number of parallel threads [default: 1]
##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