Markers + reference

Jenufa

2 species

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Species 2
Genome length 198–207 kb
Candidate markers 259
Primer pairs 75

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 6735 0.4710 0.77 72.3 yes View details
psbF-rpoBa LSC 2074 0.4905 0.69 75.4 yes View details
rrs IRb 1121 0.4935 0.83 80.2 no View details
trnL(caa)-ycf1 SSC 1515 0.4847 0.78 79.0 yes View details
rrs IRa 1121 0.5295 0.60 73.9 yes View details
rrf-rpoC2 IRa 1024 0.4949 0.57 73.5 no View details
trnE(uuc)-trnF(gaa) SSC 469 0.4424 0.91 85.2 yes View details
cemA LSC 1212 0.2397 0.94 84.1 yes View details
trnY(gua)-psbK LSC 796 0.4882 0.95 83.6 yes View details
chlL LSC 891 0.1983 0.94 83.4 yes View details
orf333-orf579 SSC 1350 0.4878 0.94 83.4 yes View details
clpP SSC 1581 0.4364 0.95 83.4 yes View details
orf579-trnG(gcc) SSC 1426 0.4187 0.95 83.3 yes View details
orf333 SSC 1002 0.4584 0.94 83.2 yes View details
rps4-trnS(gga) SSC 597 0.4347 0.94 83.1 yes View details
trnW(cca)-atpA LSC 721 0.4127 0.92 83.0 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoC2_p1 rpoC2 AAGCATTGCACACGTTAACG GCTGGGTACTTGACTCGAAG 1519 0.500 59.7
rpoC2_p2 rpoC2 AAGCATTGCACACGTTAACG AGGGGCTCAAATGCTTCAAA 907 0.500 59.6
rpoC2_p3 rpoC2 AAGCATTGCACACGTTAACG ATTGGAGAACCTGGGACTCA 1129 0.500 59.4
rpoC2_p4 rpoC2 AAGCATTGCACACGTTAACG TGGAGAACCTGGGACTCAAT 1127 0.500 59.4
rpoC2_p5 rpoC2 AAGCATTGCACACGTTAACG TATGGGTGAAGTCTGGCTGA 1201 0.500 59.4
psbF-rpoBa_p1 psbF-rpoBa GGCTGGCATATCGTTAACCA AGCTCCCCCGTTCAGTATAA 2908 0.500 58.3
psbF-rpoBa_p2 psbF-rpoBa TGGCTGGCATATCGTTAACC AGCTCCCCCGTTCAGTATAA 2909 0.500 58.3
psbF-rpoBa_p3 psbF-rpoBa GGAGTTTTTCTTTGGCTGGC AGCTCCCCCGTTCAGTATAA 2921 0.500 57.4
psbF-rpoBa_p4 psbF-rpoBa GGCTGGCATATCGTTAACCA CTAGCTCCCCCGTTCAGTAT 2910 0.500 57.3
psbF-rpoBa_p5 psbF-rpoBa TGGCTGGCATATCGTTAACC CTAGCTCCCCCGTTCAGTAT 2911 0.500 57.3
trnY(gua)-psbK_p1 trnY(gua)-psbK CTCGTGAAGGTGGCGAAATA CACCCCCACCGTTTAGTTTT 2091 0.500 57.5
trnY(gua)-psbK_p2 trnY(gua)-psbK TACGTTGGTTCGAATCCGAC CACCCCCACCGTTTAGTTTT 1397 0.500 57.4
trnY(gua)-psbK_p3 trnY(gua)-psbK AGTCCTGAATTAGCTGCTGC CACCCCCACCGTTTAGTTTT 2050 0.500 57.3
trnY(gua)-psbK_p4 trnY(gua)-psbK TTTGCCTACGTTGGTTCGAA CACCCCCACCGTTTAGTTTT 1403 0.500 57.2
trnY(gua)-psbK_p5 trnY(gua)-psbK TTCAGAACACCCCCTGGTAT CACCCCCACCGTTTAGTTTT 1721 0.500 57.1
chlL_p1 chlL TGGCTTCTGCGAAAAAGCTA GGGCCTATCTGTTACACGTG 1782 0.500 58.6
chlL_p2 chlL TGGCTTCTGCGAAAAAGCTA GCACAGGCCAAAAGGTAAAC 1858 0.500 57.9
chlL_p3 chlL AAAAGGCAAAGGCTAGCGTA GGGCCTATCTGTTACACGTG 1854 0.500 57.9
chlL_p4 chlL AAAGGCAAAGGCTAGCGTAA GGGCCTATCTGTTACACGTG 1853 0.500 57.9
chlL_p5 chlL AAGGCAAAGGCTAGCGTAAA GGGCCTATCTGTTACACGTG 1852 0.500 57.9
trnW(cca)-atpA_p1 trnW(cca)-atpA AGGTGGGTTTTTAACGTCCC GTAGCTCCAGTGTAAGGTGC 1885 0.500 59.8
trnW(cca)-atpA_p2 trnW(cca)-atpA AGGTGGGTTTTTAACGTCCC ATCAACTGGGCGAGCTAAAG 1502 0.500 59.6
trnW(cca)-atpA_p3 trnW(cca)-atpA AGGTGGGTTTTTAACGTCCC ATACAGAACGACGCGAAACA 1581 0.500 59.4
trnW(cca)-atpA_p4 trnW(cca)-atpA TTATCATTCCCGCGACACAG GTAGCTCCAGTGTAAGGTGC 2151 0.500 59.4
trnW(cca)-atpA_p5 trnW(cca)-atpA GTCGTGGGTTCAAGTCCTAC GTAGCTCCAGTGTAAGGTGC 1483 0.500 59.3
cemA_p1 cemA AAGGCCAAAAGGTGAACGAT TTCATGCGCTATCAACTGCT 2482 0.500 59.7
cemA_p2 cemA AGGCCAAAAGGTGAACGATT TTCATGCGCTATCAACTGCT 2481 0.500 59.7
cemA_p3 cemA AATGACCCAGCACGTAATCC TTCATGCGCTATCAACTGCT 2299 0.500 59.5
cemA_p4 cemA AAGGCCAAAAGGTGAACGAT TTTTTCTCCCCAATCAGCCC 2062 0.500 59.5
cemA_p5 cemA AGGCCAAAAGGTGAACGATT TTTTTCTCCCCAATCAGCCC 2061 0.500 59.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Jenufa minuta NC_028582.1 206680 View on NCBI ↗
Jenufa perforata NC_028581.1 198040 View on NCBI ↗