Markers + reference

Eleutherococcus

13 species · Araliaceae · Apiales

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Species 13
Genome length 157–157 kb
Candidate markers 273
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH (GUG)-psbA LSC 390 0.0154 1.00 47.3 yes View details
trnK (UUU)-rps16 LSC 870 0.0097 1.00 50.8 yes View details
atpH-atpI LSC 1128 0.0076 1.00 59.0 yes View details
trnT (UGU)-trnL (UAA) LSC 825 0.0084 0.97 58.6 yes View details
ndhC-trnV (UAC) LSC 1013 0.0067 1.00 54.3 yes View details
trnP (UGG)-psaJ LSC 382 0.0072 1.00 30.8 yes View details
clpP LSC 2004 0.0042 1.00 35.8 yes View details
petB LSC 1439 0.0071 1.00 41.1 yes View details
ycf1 IRb 1478 0.0012 1.00 32.2 no View details
ndhF SSC 2226 0.0041 1.00 39.3 yes View details
ndhF-rpl32 SSC 1197 0.0085 0.98 49.3 yes View details
rpl32-trnL (UAG) SSC 827 0.0084 1.00 52.5 yes View details
ndhG-ndhI SSC 380 0.0121 1.00 44.0 yes View details
ycf1 SSC 5628 0.0057 1.00 36.2 yes View details
ycf1-ndhF SSC 35 0.1143 1.00 64.3 yes View details
accD-psaI LSC 689 0.0078 0.99 58.7 yes View details
trnC (GCA)-petN LSC 721 0.0049 0.96 56.9 yes View details
psbE-petL LSC 1131 0.0063 1.00 55.7 yes View details
trnE (UUC)-trnT (GGU) LSC 831 0.0044 0.98 52.7 yes View details
atpB-rbcL LSC 804 0.0028 0.99 52.0 yes View details
trnG (UCC)-trnR (UCU) LSC 174 0.0138 0.98 51.9 yes View details
rpl20-rps12 LSC 774 0.0035 1.00 51.2 yes View details
psaJ-rpl33 LSC 448 0.0087 0.99 50.5 yes View details
rps16-trnQ (UUG) LSC 1772 0.0055 0.99 49.6 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH (GUG)-psbA_p1 trnH (GUG)-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 455–466 1.000 83.5
trnH (GUG)-psbA_p2 trnH (GUG)-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 458–469 1.000 83.4
trnH (GUG)-psbA_p3 trnH (GUG)-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 469–480 1.000 83.3
trnH (GUG)-psbA_p4 trnH (GUG)-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 468–479 1.000 83.3
trnH (GUG)-psbA_p5 trnH (GUG)-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 470–481 1.000 83.3
trnK (UUU)-rps16_p1 trnK (UUU)-rps16 CGAATCCTTCGCTTCATCCA TTCCTTGAAAAAGGCGCTCA 1024–1080 1.000 79.7
trnK (UUU)-rps16_p2 trnK (UUU)-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1037–1093 1.000 79.5
trnK (UUU)-rps16_p3 trnK (UUU)-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 976–1032 1.000 79.0
trnK (UUU)-rps16_p4 trnK (UUU)-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 975–1031 1.000 79.0
trnK (UUU)-rps16_p5 trnK (UUU)-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1061–1117 1.000 78.3
rps16-trnQ (UUG)_p1 rps16-trnQ (UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1834–1857 1.000 80.8
rps16-trnQ (UUG)_p2 rps16-trnQ (UUG) CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1849–1872 1.000 78.9
rps16-trnQ (UUG)_p3 rps16-trnQ (UUG) GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1848–1871 1.000 78.9
rps16-trnQ (UUG)_p4 rps16-trnQ (UUG) AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1838–1861 1.000 76.0
rps16-trnQ (UUG)_p5 rps16-trnQ (UUG) AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1864–1887 1.000 75.9
trnG (UCC)-trnR (UCU)_p1 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG TCTTTCAAAAGGGCTTCCGA 330–361 1.000 78.8
trnG (UCC)-trnR (UCU)_p2 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG TCTTTCAAAAGGGCTTCCGA 333–364 1.000 78.5
trnG (UCC)-trnR (UCU)_p3 trnG (UCC)-trnR (UCU) CCCTAGCCTTCCAAGCTAAC TCTTTCAAAAGGGCTTCCGA 334–365 1.000 76.3
trnG (UCC)-trnR (UCU)_p4 trnG (UCC)-trnR (UCU) CTAACGATGCGGGTTCGATT TCTTTCAAAAGGGCTTCCGA 319–350 1.000 75.7
trnG (UCC)-trnR (UCU)_p5 trnG (UCC)-trnR (UCU) TAACGATGCGGGTTCGATTC TCTTTCAAAAGGGCTTCCGA 318–349 1.000 75.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1211–1232 1.000 78.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1267–1288 1.000 77.3
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1227–1248 1.000 77.1
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1212–1233 1.000 76.8
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1271–1292 1.000 76.7
trnC (GCA)-petN_p1 trnC (GCA)-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 748–784 1.000 84.7
trnC (GCA)-petN_p2 trnC (GCA)-petN CGATATGGCCGAGTGGTAAG TTAAAGCAGCCCAAGCAAGA 788–824 1.000 84.5
trnC (GCA)-petN_p3 trnC (GCA)-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 742–778 1.000 83.2
trnC (GCA)-petN_p4 trnC (GCA)-petN CGATATGGCCGAGTGGTAAG CAGCCCAAGCAAGACTTACT 782–818 1.000 83.1
trnC (GCA)-petN_p5 trnC (GCA)-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 766–802 1.000 82.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Eleutherococcus brachypus NC_050832.1 156981 View on NCBI ↗
Eleutherococcus divaricatus var. chiisanensis PQ153235.1 156765 View on NCBI ↗
Eleutherococcus eleutheristylus NC_062720.1 157328 View on NCBI ↗
Eleutherococcus giraldii NC_062723.1 156784 View on NCBI ↗
Eleutherococcus gracilistylus NC_062721.1 156855 View on NCBI ↗
Eleutherococcus henryi NC_062719.1 156767 View on NCBI ↗
Eleutherococcus leucorrhizus NC_062722.1 156855 View on NCBI ↗
Eleutherococcus nodiflorus MZ362512.1 156770 View on NCBI ↗
Eleutherococcus scandens PP056230.1 156799 View on NCBI ↗
Eleutherococcus senticosus NC_016430.1 156768 View on NCBI ↗
Eleutherococcus sessiliflorus NC_064364.1 156762 View on NCBI ↗
Eleutherococcus sieboldianus MT991755.1 156691 View on NCBI ↗
Eleutherococcus trifoliatus NC_052849.1 156751 View on NCBI ↗