Markers + reference

Kadsura

6 species · Schisandraceae · Austrobaileyales

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Species 6
Genome length 145–153 kb
Candidate markers 256
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG Genome 1670 0.0211 0.99 67.8 yes View details
trnS-GCU-trnG-UCC Genome 524 0.0924 0.97 80.7 yes View details
atpH-atpI Genome 895 0.0265 0.98 65.6 yes View details
petN-psbM Genome 1041 0.0820 0.97 87.2 yes View details
ndhC-trnV-UAC Genome 1189 0.0186 0.99 67.8 yes View details
psbE-petL Genome 1312 0.0337 0.54 60.6 yes View details
ndhF Genome 2235 0.0135 1.00 62.1 yes View details
rpl32-trnL-UAG Genome 882 0.0384 0.98 78.0 yes View details
ccsA-ndhD Genome 301 0.0609 0.96 74.5 yes View details
ndhD Genome 1521 0.0077 1.00 49.4 yes View details
ycf1 Genome 5502 0.0151 1.00 54.4 yes View details
trnL-UAG-ccsA Genome 94 0.0621 1.00 80.0 yes View details
trnH-GUG-psbA Genome 244 0.0527 0.98 78.3 yes View details
ndhB-trnH-GUG Genome 546 0.0195 0.98 74.8 no View details
trnM-CAU-atpE Genome 220 0.0349 0.99 74.5 yes View details
ndhF-rpl32 Genome 838 0.0233 1.00 68.2 yes View details
ycf4-cemA Genome 999 0.0059 0.98 67.7 yes View details
petA-psbJ Genome 609 0.0180 1.00 67.7 yes View details
rps14-psaB Genome 137 0.0650 1.00 67.5 yes View details
rps8-rpl14 Genome 218 0.0208 1.00 66.1 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 95 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 CTCACAACTTCCCGCTAGAC 196–323 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTCACAACTTCCCGCTAGAC 209–336 1.000 90.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTCACAACTTCCCGCTAGAC 210–337 1.000 90.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTCACAACTTCCCGCTAGAC 211–338 1.000 90.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGACCTAGCTGCTGTCGAA 181–308 1.000 89.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 800–1772 1.000 86.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 788–1760 1.000 85.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA AAAATCTAACTGGGGCGTGG 858–1830 1.000 85.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA CTCGGAGGTTCGAATCCTTC 804–1776 1.000 85.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAAATCTAACTGGGGCGTGG 846–1818 1.000 85.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 593–1060 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 592–1059 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 596–1063 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 595–1062 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 594–1061 1.000 62.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAAGGC 713–956 1.000 80.2
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGTGAATCCATGGAAGGC 714–957 1.000 79.0
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT GGTGAATCCATGGAAGGCC 711–954 1.000 79.0
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TAGGTGAATCCATGGAAGGC 723–966 1.000 78.4
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GGTGAATCCATGGAAGGCC 712–955 1.000 77.8
petN-psbM_p1 petN-psbM CTTGGGCGGCTTTAATGGTA TGCTACTGCACTGTTCATTCT 797–1191 1.000 78.8
petN-psbM_p2 petN-psbM TTGGGCGGCTTTAATGGTAG TGCTACTGCACTGTTCATTCT 796–1190 1.000 78.8
petN-psbM_p3 petN-psbM GGCGGCTTTAATGGTAGTCT TGCTACTGCACTGTTCATTCT 793–1187 1.000 78.1
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 748–1142 1.000 77.9
petN-psbM_p5 petN-psbM AGTAAATCTTGCTTGGGCGG TGCTACTGCACTGTTCATTCT 808–1202 1.000 76.5
rps14-psaB_p1 rps14-psaB CGGTGGGGATTGCAATTTTC TTTCCTGGCGTGGATATTGG 498–507 1.000 87.3
rps14-psaB_p2 rps14-psaB ATGAAGACGTATGGGTGCAC TTTCCTGGCGTGGATATTGG 525–534 1.000 87.0
rps14-psaB_p3 rps14-psaB CGGTGGGGATTGCAATTTTC TGATATTTCGGCTTGGGACG 788–797 1.000 86.5
rps14-psaB_p4 rps14-psaB ATGAAGACGTATGGGTGCAC TGATATTTCGGCTTGGGACG 815–824 1.000 86.3
rps14-psaB_p5 rps14-psaB GCTACCAAACTGCTCTACCC TTTCCTGGCGTGGATATTGG 828–837 1.000 86.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Kadsura ananosma NC_057265.1 145903 View on NCBI ↗
Kadsura coccinea NC_040116.1 145413 View on NCBI ↗
Kadsura heteroclita NC_057266.1 153289 View on NCBI ↗
Kadsura interior NC_050348.1 153201 View on NCBI ↗
Kadsura longipedunculata NC_040144.1 149288 View on NCBI ↗
Kadsura oblongifolia PX548869.1 152745 View on NCBI ↗