Markers + reference

Vincetoxicum

12 species · Apocynaceae · Gentianales

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Species 12
Genome length 159–161 kb
Candidate markers 270
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 888 0.0085 0.99 52.8 no View details
ndhF SSC 2220 0.1256 1.00 82.8 yes View details
rpl32-trnL-UAG SSC 896 0.1430 1.00 81.1 yes View details
ccsA-ndhD SSC 246 0.1208 1.00 70.0 yes View details
ndhG-ndhI SSC 536 0.1390 0.93 77.4 yes View details
ndhI SSC 495 0.1389 1.00 74.6 yes View details
ndhA SSC 2154 0.1268 1.00 82.8 yes View details
ndhH SSC 1197 0.1355 1.00 78.4 yes View details
ycf1 SSC 6057 0.1060 0.99 77.1 yes View details
ndhF-rpl32 SSC 791 0.1193 1.00 83.2 yes View details
ndhD SSC 1503 0.1220 1.00 80.8 yes View details
trnQ-UUG-psbK LSC 559 0.0164 1.00 76.2 yes View details
ndhC-trnV-UAC LSC 1423 0.0139 0.98 75.5 yes View details
ccsA SSC 969 0.1208 1.00 71.6 yes View details
rps15-ycf1 SSC 379 0.1168 1.00 69.9 yes View details
trnE-UUC-trnT-GGU LSC 878 0.0061 1.00 69.3 yes View details
ndhG SSC 531 0.0728 1.00 69.3 yes View details
rps4-trnT-UGU LSC 450 0.0153 0.96 69.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TGAATATGCTCTGGGACGGA AAAAAGCGTAGGCCTCGG 731–889 1.000 67.9
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AAAAAGCGTAGGCCTCGG 687–845 1.000 64.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATGAATATGCTCTGGGACGG AAAAAGCGTAGGCCTCGG 732–890 1.000 62.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAATATGCTCTGGGACGGAA AAAAAGCGTAGGCCTCGG 730–888 1.000 62.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AATATGCTCTGGGACGGAAG AAAAAGCGTAGGCCTCGG 729–887 1.000 62.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 949–1053 1.000 84.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU ACTTCCTTTCCTAGTCCCCC GAACCGATGACTTACGCCTT 1011–1115 0.917 81.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CTTCCTTTCCTAGTCCCCCA GAACCGATGACTTACGCCTT 1010–1114 0.917 81.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU ACTTCCTTTCCTAGTCCCCC TACCGCTGAGTTAAAAGGGC 976–1080 0.917 80.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CTTCCTTTCCTAGTCCCCCA TACCGCTGAGTTAAAAGGGC 975–1079 0.917 80.7
rps4-trnT-UGU_p1 rps4-trnT-UGU TCCCGAACGAGATTGGTTTC CTCAGAGGTTAGAGCATCGC 515–643 1.000 85.0
rps4-trnT-UGU_p2 rps4-trnT-UGU CCCGAACGAGATTGGTTTCT CTCAGAGGTTAGAGCATCGC 514–642 1.000 84.9
rps4-trnT-UGU_p3 rps4-trnT-UGU TCCCGAACGAGATTGGTTTC ATGGTCATCGGTTCGATTCC 483–611 1.000 84.3
rps4-trnT-UGU_p4 rps4-trnT-UGU GATCATTTCCGGCTCTAGGC CTCAGAGGTTAGAGCATCGC 492–620 1.000 84.2
rps4-trnT-UGU_p5 rps4-trnT-UGU CCCGAACGAGATTGGTTTCT ATGGTCATCGGTTCGATTCC 482–610 1.000 84.2
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GTCCTTTGTTAATCGGGGCT AGAAGGTCTACGGTTCGAGT 1503–1717 1.000 84.5
ndhC-trnV-UAC_p2 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT AGAAGGTCTACGGTTCGAGT 1489–1703 1.000 84.4
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GTCCTTTGTTAATCGGGGCT GAAGGTCTACGGTTCGAGTC 1502–1716 1.000 81.8
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GAAGGTCTACGGTTCGAGTC 1488–1702 1.000 81.7
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TGGTCCTTTGTTAATCGGGG AGAAGGTCTACGGTTCGAGT 1505–1719 1.000 81.5
ndhF_p1 ndhF TGGCTTGGAGCACTAGTACT TGGGGTCGGTTTAATTTGCA 2907–2991 0.833 76.5
ndhF_p2 ndhF AGCCCTTTTTCGGTGTTCTT TGGGGTCGGTTTAATTTGCA 2843–2927 0.833 76.5
ndhF_p3 ndhF AGGCCGAATCTGCACAAAAT TGGGGTCGGTTTAATTTGCA 2701–2747 0.833 71.9
ndhF_p4 ndhF TGGCTTGGAGCACTAGTACT TAACCGGTTAAATGGGGTCG 2919–2980 0.750 69.2
ndhF_p5 ndhF AGGAAAGAAGGCCGAATCTG TGGGGTCGGTTTAATTTGCA 2709–2733 0.750 68.5
ndhF-rpl32_p1 ndhF-rpl32 CTTGAGGTCGTGTGAACCAA GTTCGAAACCTCTCCCCATC 1644–1881 0.750 75.4
ndhF-rpl32_p2 ndhF-rpl32 CTTGAGGTCGTGTGAACCAA TCGAAACCTCTCCCCATCTT 1642–1879 0.750 75.2
ndhF-rpl32_p3 ndhF-rpl32 CTTGAGGTCGTGTGAACCAA TTCGAAACCTCTCCCCATCT 1643–1880 0.750 75.2
ndhF-rpl32_p4 ndhF-rpl32 GGCACCACCAAATACCAGAA GTTCGAAACCTCTCCCCATC 1844–2081 0.667 71.5
ndhF-rpl32_p5 ndhF-rpl32 GGCACCACCAAATACCAGAA TCGAAACCTCTCCCCATCTT 1842–2079 0.667 71.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Vincetoxicum bungei PV747498.1 159426 View on NCBI ↗
Vincetoxicum forrestii MN383187.1 159917 View on NCBI ↗
Vincetoxicum hainanense NC_051946.1 161280 View on NCBI ↗
Vincetoxicum inamoenum PX975500.1 160787 View on NCBI ↗
Vincetoxicum insigne NC_042760.1 160381 View on NCBI ↗
Vincetoxicum junzifengense NC_062962.1 159666 View on NCBI ↗
Vincetoxicum lindleyi NC_069945.1 160257 View on NCBI ↗
Vincetoxicum microcentrum NC_082943.1 160264 View on NCBI ↗
Vincetoxicum mongolicum NC_065505.1 160157 View on NCBI ↗
Vincetoxicum pingtaoanum NC_067062.1 160591 View on NCBI ↗
Vincetoxicum shaanxiense NC_046785.1 160308 View on NCBI ↗
Vincetoxicum versicolor NC_052877.1 159907 View on NCBI ↗