Markers + reference

Panax

15 species · Araliaceae · Apiales

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Species 15
Genome length 156–156 kb
Candidate markers 271
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-tRNA-Gln (UUG) LSC 1796 0.0112 0.97 75.0 yes View details
tRNA-Ser (GCU)-tRNA-Gly (UCC) LSC 727 0.0124 0.99 56.5 yes View details
tRNA-Glu (UUC)-tRNA-Thr (GGU) LSC 807 0.0162 1.00 65.5 yes View details
clpP LSC 1994 0.0077 1.00 47.0 yes View details
petB LSC 1431 0.0075 1.00 44.5 yes View details
ycf1 IRb 1649 0.0039 0.93 38.6 no View details
ndhF SSC 2226 0.0065 1.00 47.0 yes View details
ycf1 SSC 5760 0.0114 0.98 55.3 yes View details
tRNA-His (GUG)-psbA LSC 404 0.0178 1.00 69.4 yes View details
tRNA-Lys (UUU)-rps16 LSC 894 0.0098 0.99 64.5 yes View details
rpl14-rpl16 LSC 138 0.0153 1.00 61.9 yes View details
ndhF-rpl32 SSC 1218 0.0119 0.96 57.8 yes View details
rpl32-tRNA-Leu (UAG) SSC 814 0.0101 0.99 57.5 yes View details
psaA-ycf3 LSC 711 0.0050 1.00 57.2 yes View details
psbK-psbI LSC 408 0.0127 1.00 56.5 yes View details
petN-psbM LSC 862 0.0083 1.00 56.4 yes View details
psbC LSC 1422 0.0032 1.00 55.5 yes View details
tRNA-Thr (UGU)-tRNA-Leu (UAA) LSC 796 0.0100 0.99 55.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-His (GUG)-psbA_p1 tRNA-His (GUG)-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 471–480 1.000 86.2
tRNA-His (GUG)-psbA_p2 tRNA-His (GUG)-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 474–483 1.000 86.1
tRNA-His (GUG)-psbA_p3 tRNA-His (GUG)-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 485–494 1.000 85.9
tRNA-His (GUG)-psbA_p4 tRNA-His (GUG)-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 484–493 1.000 85.9
tRNA-His (GUG)-psbA_p5 tRNA-His (GUG)-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 486–495 1.000 85.9
tRNA-Lys (UUU)-rps16_p1 tRNA-Lys (UUU)-rps16 CGAATCCTTCGCTTCATCCA TTCCTTGAAAAAGGCGCTCA 1006–1086 1.000 83.9
tRNA-Lys (UUU)-rps16_p2 tRNA-Lys (UUU)-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1019–1099 1.000 83.6
tRNA-Lys (UUU)-rps16_p3 tRNA-Lys (UUU)-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 958–1038 1.000 83.3
tRNA-Lys (UUU)-rps16_p4 tRNA-Lys (UUU)-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 957–1037 1.000 83.3
tRNA-Lys (UUU)-rps16_p5 tRNA-Lys (UUU)-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1043–1123 0.933 79.4
rps16-tRNA-Gln (UUG)_p1 rps16-tRNA-Gln (UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1809–1869 1.000 86.6
rps16-tRNA-Gln (UUG)_p2 rps16-tRNA-Gln (UUG) CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1824–1884 1.000 84.8
rps16-tRNA-Gln (UUG)_p3 rps16-tRNA-Gln (UUG) GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1823–1883 1.000 84.8
rps16-tRNA-Gln (UUG)_p4 rps16-tRNA-Gln (UUG) AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1813–1873 1.000 81.9
rps16-tRNA-Gln (UUG)_p5 rps16-tRNA-Gln (UUG) AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1839–1899 1.000 81.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 526–536 1.000 83.1
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 527–537 1.000 83.1
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 528–538 1.000 81.3
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 523–533 1.000 81.1
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 524–534 1.000 81.1
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p1 tRNA-Ser (GCU)-tRNA-Gly (UCC) ATTAGCAATCCGCCGCTTTA CAACGAATCACACTTTTACCACT 788–808 1.000 58.8
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p2 tRNA-Ser (GCU)-tRNA-Gly (UCC) ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 786–806 1.000 57.8
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p3 tRNA-Ser (GCU)-tRNA-Gly (UCC) ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 787–807 1.000 55.9
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p4 tRNA-Ser (GCU)-tRNA-Gly (UCC) GCTTTAGTCCACTCAGCCAT CAACGAATCACACTTTTACCACT 774–794 1.000 55.9
tRNA-Ser (GCU)-tRNA-Gly (UCC)_p5 tRNA-Ser (GCU)-tRNA-Gly (UCC) ATTAGCAATCCGCCGCTTTA CAACGAATCACACTTTTACCAC 788–808 1.000 55.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1020–1036 1.000 73.0
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1026–1042 1.000 71.5
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 966–982 1.000 70.4
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTC 1020–1036 1.000 68.8
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA AGTTCCTACTGCTTTTCTGCT 999–1015 0.933 67.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Panax ginseng NC_006290.1 156318 View on NCBI ↗
Panax japonicus NC_028703.1 156188 View on NCBI ↗
Panax japonicus var. bipinnatifidus NC_043952.1 156166 View on NCBI ↗
Panax major NC_053713.1 156402 View on NCBI ↗
Panax notoginseng NC_026447.1 156387 View on NCBI ↗
Panax pseudoginseng MW145449.1 156074 View on NCBI ↗
Panax pseudoginseng var. elegantior NC_062082.1 156071 View on NCBI ↗
Panax quinquefolius NC_027456.1 156088 View on NCBI ↗
Panax stipuleanatus NC_030598.1 156064 View on NCBI ↗
Panax trifolius NC_037994.1 156157 View on NCBI ↗
Panax vietnamensis NC_028704.1 155993 View on NCBI ↗
Panax vietnamensis var. fuscidiscus MT798585.1 156284 View on NCBI ↗
Panax vietnamensis var. langbianensis MT798583.1 155984 View on NCBI ↗
Panax wangianus NC_043953.1 156176 View on NCBI ↗
Panax zingiberensis NC_043954.1 156310 View on NCBI ↗