Markers + reference

Terniopsis

5 species · Podostemaceae · Malpighiales

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Species 5
Genome length 129–130 kb
Candidate markers 254
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 254 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-atpB LSC 865 0.0500 1.00 79.7 yes View details
trnV-UAC-ndhC LSC 690 0.0594 1.00 82.8 yes View details
trnC-GCA-rpoB LSC 965 0.0473 1.00 77.9 yes View details
trnR-UCU-trnG-UCC LSC 666 0.0697 0.93 85.7 yes View details
trnG-UCC-trnS-GCU LSC 660 0.0647 1.00 86.4 yes View details
psbK-trnQ-UUG LSC 462 0.0631 1.00 85.8 yes View details
trnQ-UUG-trnK-UUU LSC 832 0.0808 0.93 87.7 yes View details
petA-psbJ LSC 896 0.0605 1.00 81.1 yes View details
rpl16 LSC 1450 0.0520 0.99 80.6 yes View details
ndhF SSC 2238 0.0407 1.00 70.2 yes View details
ndhF-rpl32 SSC 307 0.0430 1.00 64.2 yes View details
ndhA SSC 2402 0.0405 1.00 75.1 yes View details
trnT-GGU-trnE-UUC LSC 664 0.0545 1.00 85.8 yes View details
trnP-UGG-psaJ LSC 467 0.0540 1.00 84.6 yes View details
trnL-UAA-trnT-UGU LSC 516 0.0628 0.99 83.0 yes View details
trnS-GCU-psbI LSC 153 0.0693 1.00 82.7 yes View details
psbD-trnT-GGU LSC 1236 0.0429 1.00 82.6 yes View details
petN-trnC-GCA LSC 802 0.0569 1.00 82.6 yes View details
trnM-CAU-trnV-UAC LSC 189 0.0607 0.98 81.8 yes View details
atpI-atpH LSC 538 0.0486 0.99 81.5 yes View details
accD-psaI LSC 427 0.0569 1.00 81.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rbcL-atpB_p1 rbcL-atpB GCCTTGAATCCAACACTTGC TTCAAGTGCGGAAACTCCAA 953–959 1.000 88.1
rbcL-atpB_p2 rbcL-atpB GCCTTGAATCCAACACTTGC AAGTGCGGAAACTCCAAGAC 950–956 1.000 85.3
rbcL-atpB_p3 rbcL-atpB GCCTTGAATCCAACACTTGC CAAGTGCGGAAACTCCAAGA 951–957 1.000 85.2
rbcL-atpB_p4 rbcL-atpB GCCTTGAATCCAACACTTGC TCAAGTGCGGAAACTCCAAG 952–958 1.000 85.2
rbcL-atpB_p5 rbcL-atpB TATACTCTTTAACGCCGGCC TTCAAGTGCGGAAACTCCAA 970–976 1.000 84.4
trnM-CAU-trnV-UAC_p1 trnM-CAU-trnV-UAC TTGAACCAATGACTCTCGCC AACGAGTTGCTCTACCGAAC 277–281 1.000 85.1
trnM-CAU-trnV-UAC_p2 trnM-CAU-trnV-UAC TCTCGCCGTATGAAAGCAAT AACGAGTTGCTCTACCGAAC 264–268 1.000 84.6
trnM-CAU-trnV-UAC_p3 trnM-CAU-trnV-UAC CTCTCGCCGTATGAAAGCAA AACGAGTTGCTCTACCGAAC 265–269 1.000 84.1
trnM-CAU-trnV-UAC_p4 trnM-CAU-trnV-UAC CAATGACTCTCGCCGTATGA AACGAGTTGCTCTACCGAAC 271–275 1.000 82.9
trnM-CAU-trnV-UAC_p5 trnM-CAU-trnV-UAC CCAATGACTCTCGCCGTATG AACGAGTTGCTCTACCGAAC 272–276 1.000 82.7
trnV-UAC-ndhC_p1 trnV-UAC-ndhC CCGAGAAGGTCTACGGTTCA AGGGGTGATAAAATTCCGGA 827–868 1.000 66.8
trnV-UAC-ndhC_p2 trnV-UAC-ndhC CGAGAAGGTCTACGGTTCAA AGGGGTGATAAAATTCCGGA 826–867 1.000 65.4
trnV-UAC-ndhC_p3 trnV-UAC-ndhC CCGAGAAGGTCTACGGTTCA AAGGGGTGATAAAATTCCGGA 828–869 1.000 65.0
trnV-UAC-ndhC_p4 trnV-UAC-ndhC CCGAGAAGGTCTACGGTTCA AGGGGTGATAAAATTCCGGAA 827–868 1.000 65.0
trnV-UAC-ndhC_p5 trnV-UAC-ndhC CGAGAAGGTCTACGGTTCAA AGGGGTGATAAAATTCCGGAA 826–867 1.000 63.6
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GCGATGCTCTAACCTCTGAG 561–594 1.000 87.7
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GAGTCGAACCGATGACCATC 592–625 1.000 87.3
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT CTAACCTCTGAGCTAAGCGG 553–586 1.000 84.8
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT ATGCGATGCTCTAACCTCTG 563–596 1.000 84.6
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT TGCGATGCTCTAACCTCTGA 562–595 1.000 84.5
psbD-trnT-GGU_p1 psbD-trnT-GGU ACGTAACCAGTCATCCATAA GTGGTAGAGTAACGCCATGG 1346–1378 1.000 54.2
psbD-trnT-GGU_p2 psbD-trnT-GGU ACGTAACCAGTCATCCATAA TCAGTGGTAGAGTAACGCCA 1349–1381 1.000 54.0
psbD-trnT-GGU_p3 psbD-trnT-GGU ACGTAACCAGTCATCCATAA GGCGTAAGTCATCGGTTCAA 1323–1355 1.000 52.6
psbD-trnT-GGU_p4 psbD-trnT-GGU ACGTAACCAGTCATCCATAAT GTGGTAGAGTAACGCCATGG 1346–1378 1.000 51.4
psbD-trnT-GGU_p5 psbD-trnT-GGU ACGTAACCAGTCATCCATAAT TCAGTGGTAGAGTAACGCCA 1349–1381 1.000 51.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT CGTGAAAGGGAGATGTCCTG 759–791 1.000 86.9
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT AAGGGAGATGTCCTGAACCA 754–786 1.000 86.7
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC CGTGAAAGGGAGATGTCCTG 738–770 1.000 86.6
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA CGTGAAAGGGAGATGTCCTG 735–767 1.000 86.4
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC AAGGGAGATGTCCTGAACCA 733–765 1.000 86.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Terniopsis daoyinensis NC_082927.1 130314 View on NCBI ↗
Terniopsis filiformis NC_082928.1 130077 View on NCBI ↗
Terniopsis heterostaminata NC_082929.1 129763 View on NCBI ↗
Terniopsis sessilis NC_082922.1 129815 View on NCBI ↗
Terniopsis yongtaiensis NC_066797.1 129074 View on NCBI ↗