Markers + reference

Dendropanax

3 species · Araliaceae · Apiales

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Species 3
Genome length 156–157 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 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
rps16 LSC 1119 0.0006 1.00 32.0 yes View details
petN-psbM LSC 871 0.0054 1.00 62.2 yes View details
psbM-trnD(GUC) LSC 1159 0.0035 1.00 61.2 yes View details
rpl33 LSC 201 0.0066 1.00 42.1 yes View details
rpl16 LSC 1360 0.0020 1.00 47.6 yes View details
trnR(ACG)-trnN(GUU) IRb 588 0.0057 1.00 49.6 yes View details
ycf1 IRb 1479 0.0009 1.00 59.3 no View details
ndhF-rpl32 SSC 1179 0.0028 1.00 36.3 yes View details
ycf1 SSC 5652 0.0080 1.00 57.1 yes View details
trnN(GUU)-trnR(ACG) IRa 588 0.0057 1.00 49.6 yes View details
rps16-trnQ(UUG) LSC 1796 0.0019 0.96 64.0 yes View details
trnK(UUU)-rps16 LSC 925 0.0038 0.94 62.8 yes View details
rpl32-trnL(UAG) SSC 809 0.0041 1.00 61.4 yes View details
trnC(GCA)-petN LSC 680 0.0020 1.00 61.1 yes View details
petA-psbJ LSC 1029 0.0026 1.00 61.1 yes View details
rps2 LSC 711 0.0028 1.00 60.5 yes View details
trnT(UGU)-trnL(UAA) LSC 824 0.0018 0.92 60.0 yes View details
ndhC-trnV(UAC) LSC 1011 0.0020 1.00 60.0 yes View details
atpH-atpI LSC 1117 0.0012 1.00 59.9 yes View details
atpB-rbcL LSC 796 0.0017 1.00 59.8 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK(UUU)_p1 trnK(UUU) TGTCCGTGTCAACCAATATCT TCAATGGTTTGATTGCCTTGTC 2782–2783 1.000 46.4
trnK(UUU)_p2 trnK(UUU) TGTCCGTGTCAACCAATATCT CAATGGTTTGATTGCCTTGTCT 2781–2782 1.000 46.4
trnK(UUU)_p3 trnK(UUU) TGTCCGTGTCAACCAATATCT TCAATGGTTTGATTGCCTTGT 2782–2783 1.000 45.2
trnK(UUU)_p4 trnK(UUU) TGTCCGTGTCAACCAATATCT ATGGTTTGATTGCCTTGTCT 2779–2780 1.000 44.5
trnK(UUU)_p5 trnK(UUU) TGTCCGTGTCAACCAATATCT TTCAATGGTTTGATTGCCTTGT 2783–2784 1.000 43.0
trnK(UUU)-rps16_p1 trnK(UUU)-rps16 CGAATCCTTCGCTTCATCCA TTCCTTGAAAAAGGCGCTCA 1024–1079 1.000 81.4
trnK(UUU)-rps16_p2 trnK(UUU)-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1037–1092 1.000 81.2
trnK(UUU)-rps16_p3 trnK(UUU)-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 976–1031 1.000 80.5
trnK(UUU)-rps16_p4 trnK(UUU)-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 975–1030 1.000 80.5
trnK(UUU)-rps16_p5 trnK(UUU)-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1061–1116 1.000 80.0
rps16_p1 rps16 TAGGATCAACCAACTGGGGT AGGTGGGGTCTTGCTAAGAT 1483–1538 1.000 82.7
rps16_p2 rps16 TAGGATCAACCAACTGGGGT AAGTCGCAGATGGGTCAATC 1638–1694 1.000 82.4
rps16_p3 rps16 CAAAGCGAATCCAACGAACC AGGTGGGGTCTTGCTAAGAT 1888–1941 1.000 82.1
rps16_p4 rps16 CAAAGCGAATCCAACGAACC AAGTCGCAGATGGGTCAATC 2043–2097 1.000 82.0
rps16_p5 rps16 CAAAGCGAATCCAACGAACC GAAGTCGCAGATGGGTCAAT 2044–2098 1.000 82.0
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1804–1869 1.000 82.3
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1819–1884 1.000 80.4
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1818–1883 1.000 80.4
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1875–1940 1.000 79.2
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1808–1873 1.000 77.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1205–1206 1.000 75.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1261–1262 1.000 75.3
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1221–1222 1.000 75.1
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1206–1207 1.000 74.8
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1265–1266 1.000 74.7
rps2_p1 rps2 ACCAATCACATAATATCCCCAGT GCTTGGGTCGTGTATCTACG 948–949 1.000 47.6
rps2_p2 rps2 ACCAATCACATAATATCCCCAGT GCGGTAGAAGAGAAGGTTCC 920–921 1.000 46.5
rps2_p3 rps2 ACCAATCACATAATATCCCCAGT ACGGCTAATTTGCGGTAGAA 931–932 1.000 45.8
rps2_p4 rps2 ACCAATCACATAATATCCCCAGT GGGTCGTGTATCTACGGCTA 944–945 1.000 45.7
rps2_p5 rps2 ACCAATCACATAATATCCCCAGT CTTGGGTCGTGTATCTACGG 947–948 1.000 45.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Dendropanax dentigerus NC_026546.1 156687 View on NCBI ↗
Dendropanax morbifer NC_027607.1 156366 View on NCBI ↗
Dendropanax oligodontus NC_053618.1 156403 View on NCBI ↗