Markers + reference

Wikstroemia

10 species · Thymelaeaceae · Malvales

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Species 10
Genome length 173–176 kb
Candidate markers 289
Primer pairs 90

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 289 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 330 0.0427 1.00 74.6 yes View details
trnK-UUU-rps16 LSC 690 0.0272 0.98 70.7 yes View details
trnS-GCU-trnG-UCC LSC 771 0.0366 0.95 77.5 yes View details
petN-psbM LSC 1127 0.0242 1.00 71.0 yes View details
psbZ-trnG-GCC LSC 660 0.0361 0.91 76.8 yes View details
rps4-trnT-UGU LSC 541 0.0180 1.00 65.7 yes View details
petA-psbJ LSC 789 0.0299 1.00 80.3 yes View details
ndhF-rpl32 SSC 444 0.0642 0.99 83.8 yes View details
psaA-ycf3 LSC 836 0.0151 0.99 78.4 yes View details
trnT-UGU-trnL-UAA LSC 768 0.0237 1.00 77.6 yes View details
rpl32 SSC 159 0.0478 1.00 76.0 yes View details
ndhK-ndhC LSC 71 0.0448 0.94 73.3 yes View details
psbM-trnD-GUC LSC 775 0.0179 0.96 72.4 yes View details
petG-trnW-CCA LSC 158 0.0352 0.96 71.8 yes View details
psbK-psbI LSC 435 0.0265 1.00 71.6 yes View details
trnT-GGU-psbD LSC 1267 0.0186 0.99 71.6 yes View details
rps18-rpl20 LSC 361 0.0232 0.98 71.5 yes View details
atpH-atpI LSC 1198 0.0195 0.98 71.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGAAGCTCCATCTACAAATGG 374–399 1.000 64.2
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGAAGCTCCATCTACAAATGG 375–400 1.000 64.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TGAAGCTCCATCTACAAATGG 367–392 1.000 62.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTGAAGCTCCATCTACAAATGG 375–400 1.000 62.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTGAAGCTCCATCTACAAATGG 376–401 1.000 62.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGATCCCGAAGAGAAGGAA 886–908 1.000 88.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 885–907 1.000 88.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGTTGCAGTTGATGTTCGA 901–923 0.900 83.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTCCCATGGATTTGCTGGAT 1084–1106 0.800 78.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTCCCATGGATTTGCTGGAT 1083–1105 0.800 78.4
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG ACAAAGAGTTTGAGAGTAAGCA 438–485 1.000 55.4
psbK-psbI_p2 psbK-psbI AGCCGCTGTAAGTTTTCGAT ACAAAGAGTTTGAGAGTAAGCA 436–483 1.000 55.0
psbK-psbI_p3 psbK-psbI AAGCCGCTGTAAGTTTTCGA ACAAAGAGTTTGAGAGTAAGCA 437–484 1.000 54.8
psbK-psbI_p4 psbK-psbI GCCGCTGTAAGTTTTCGATG ACAAAGAGTTTGAGAGTAAGCA 435–482 1.000 54.5
psbK-psbI_p5 psbK-psbI GCAAGCCGCTGTAAGTTTTC ACAAAGAGTTTGAGAGTAAGCA 439–486 1.000 53.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGGGGTTAATAGAACGAATCA 631–838 1.000 61.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC CGGGGTTAATAGAACGAATCAC 630–837 1.000 58.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTCC ACGGGGTTAATAGAACGAATCA 632–839 1.000 57.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTCC CGGGGTTAATAGAACGAATCAC 631–838 1.000 55.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC CGGGGTTAATAGAACGAATCA 630–837 1.000 55.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1174–1304 1.000 88.5
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1166–1296 1.000 88.3
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1144–1274 1.000 88.3
atpH-atpI_p4 atpH-atpI AGCGGCAGAAATCAATGGAT CGAATCCATGGAGGGTCATC 1136–1266 1.000 88.1
atpH-atpI_p5 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCTGCGG 1167–1297 1.000 87.5
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ACTCGTACCCATGGATGACA 1826–1960 1.000 88.7
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA GGTTGTACAAGGAAAGGGGG 1599–1682 0.900 84.5
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA GGAAAGGGGGCAATTGGTTA 1589–1672 0.800 80.1
petN-psbM_p4 petN-psbM AGGGGGCATCTTTCTTTGTG GGAAAGGGGGCAATTGGTTA 2049–2133 0.800 79.0
petN-psbM_p5 petN-psbM CAGGGGGCATCTTTCTTTGT GGAAAGGGGGCAATTGGTTA 2050–2134 0.800 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Wikstroemia alternifolia NC_058000.1 173697 View on NCBI ↗
Wikstroemia canescens NC_057998.1 173667 View on NCBI ↗
Wikstroemia capitata NC_057996.1 172849 View on NCBI ↗
Wikstroemia chamaedaphne NC_045890.1 173042 View on NCBI ↗
Wikstroemia delavayi OR386931.1 173672 View on NCBI ↗
Wikstroemia dolichantha NC_057999.1 172804 View on NCBI ↗
Wikstroemia micrantha NC_063316.1 172610 View on NCBI ↗
Wikstroemia pilosa OR386935.1 175898 View on NCBI ↗
Wikstroemia scytophylla NC_057997.1 173254 View on NCBI ↗
Wikstroemia trichotoma OR386937.1 173595 View on NCBI ↗