Markers + reference

Tetraena

3 species · Zygophyllaceae · Zygophyllales

Back to catalogue

Species 3
Genome length 106–107 kb
Candidate markers 217
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 217 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpB-rbcL LSC 805 0.0564 0.99 78.5 yes View details
rbcL-accD LSC 602 0.1873 0.91 82.1 yes View details
accD LSC 1362 0.1043 0.96 82.1 yes View details
psbE-petL LSC 1291 0.0634 0.97 86.5 yes View details
rps18-rpl20 LSC 344 0.1135 0.95 77.9 yes View details
clpP LSC 1437 0.0385 1.00 69.0 yes View details
trnF-GAA-trnV-UAC LSC 388 0.0560 0.95 81.5 yes View details
rpl33-rps18 LSC 633 0.0548 0.98 80.7 yes View details
rpoA LSC 1011 0.0642 0.98 80.2 yes View details
petN-psbM LSC 688 0.0381 0.99 79.5 yes View details
ycf3-trnS-GGA LSC 577 0.0558 0.98 79.4 yes View details
trnR-UCU-atpA LSC 362 0.0534 1.00 77.0 yes View details
trnT-UGU-trnL-UAA LSC 786 0.0337 0.98 76.8 yes View details
trnP-UGG-psaJ LSC 413 0.0475 0.99 75.5 yes View details
rps18 LSC 306 0.0603 0.92 75.2 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGCTTTCTACTTCAGGAACA 411–425 1.000 55.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GTTCAAATCCTATTGGACGCG CGCTTTCTACTTCAGGAACA 410–424 0.667 42.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCG CGCTTTCTACTTCAGGAACAAG 410–424 0.667 42.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GTTCAAATCCTATTGGACGCG CGCTTTCTACTTCAGGAACAA 410–424 0.667 41.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TTCAAATCCTATTGGACGCG CGCTTTCTACTTCAGGAACA 409–423 0.667 39.2
petN-psbM_p1 petN-psbM AAGTCTTTCTTGGGCTGCTT TGGAAGTAAACATTCTCGCA 860–871 1.000 58.3
petN-psbM_p2 petN-psbM AGTCTTTCTTGGGCTGCTTT TGGAAGTAAACATTCTCGCA 859–870 1.000 58.3
petN-psbM_p3 petN-psbM AAGTCTTTCTTGGGCTGCTT TGTTCTAGTTCCAACTGCTTTCT 820–831 1.000 58.2
petN-psbM_p4 petN-psbM AGTCTTTCTTGGGCTGCTTT TGTTCTAGTTCCAACTGCTTTCT 819–830 1.000 58.2
petN-psbM_p5 petN-psbM TCTTGGGCTGCTTTAATGGT TGGAAGTAAACATTCTCGCA 853–864 1.000 56.4
ycf3-trnS-GGA_p1 ycf3-trnS-GGA GAGGCTGCATTAATCGGGAA CTTGATTCATCCCCGCATGA 1435–1460 1.000 84.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA GAGGCTGCATTAATCGGGAA TCTTGATTCATCCCCGCATG 1436–1461 1.000 84.7
ycf3-trnS-GGA_p3 ycf3-trnS-GGA GAGGCTGCATTAATCGGGAA TGATTCATCCCCGCATGAAG 1433–1458 1.000 84.7
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTGTTTCCAACGCCTCTTCA TGATTCATCCCCGCATGAAG 1742–1769 1.000 84.1
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTGTTTCCAACGCCTCTTCA CTTGATTCATCCCCGCATGA 1744–1771 1.000 84.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GAGTCGAACCGATGACCATC CCGTAGCGTCTACCGATTTC 832–878 1.000 84.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GAGTCGAACCGATGACCATC CGTCTACCGATTTCGCCATA 826–872 1.000 83.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AAAAGCCAGCTATCGGAGTC CCGTAGCGTCTACCGATTTC 847–893 1.000 83.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GAAAAGCCAGCTATCGGAGT CCGTAGCGTCTACCGATTTC 848–894 1.000 83.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA AAAAGCCAGCTATCGGAGTC CGTCTACCGATTTCGCCATA 841–887 1.000 81.8
trnF-GAA-trnV-UAC_p1 trnF-GAA-trnV-UAC CCTCGTGTCACCAGTTCAAA AGAAGGTCTACGGTTCGAGT 432–455 1.000 87.4
trnF-GAA-trnV-UAC_p2 trnF-GAA-trnV-UAC AGTTCAAATCTGGTTCCCGG AGAAGGTCTACGGTTCGAGT 420–443 1.000 86.4
trnF-GAA-trnV-UAC_p3 trnF-GAA-trnV-UAC AATGGTCGGGATAGCTCAGT AGAAGGTCTACGGTTCGAGT 475–498 1.000 85.7
trnF-GAA-trnV-UAC_p4 trnF-GAA-trnV-UAC ATGGTCGGGATAGCTCAGTT AGAAGGTCTACGGTTCGAGT 474–497 1.000 85.7
trnF-GAA-trnV-UAC_p5 trnF-GAA-trnV-UAC CCTCGTGTCACCAGTTCAAA GAAGGTCTACGGTTCGAGTC 431–454 1.000 84.7
atpB-rbcL_p1 atpB-rbcL GGGCGATATGTCCCATGTTT CGGTCTCTCCAACGCATAAA 1523–1528 1.000 86.3
atpB-rbcL_p2 atpB-rbcL GGGCGATATGTCCCATGTTT TCTCTCCAACGCATAAACGG 1520–1525 1.000 86.3
atpB-rbcL_p3 atpB-rbcL TTGTCAACGGGTTCTCCAAG TCTCTCCAACGCATAAACGG 1806–1811 1.000 85.5
atpB-rbcL_p4 atpB-rbcL TTGTCAACGGGTTCTCCAAG CGGTCTCTCCAACGCATAAA 1809–1814 1.000 85.4
atpB-rbcL_p5 atpB-rbcL AAAGCGGGTGCAGATCTATG TCTCTCCAACGCATAAACGG 1863–1868 1.000 85.4

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
Tetraena hamiensis var. qatarensis OM809718.1 106720 View on NCBI ↗
Tetraena mongolica NC_039985.1 106259 View on NCBI ↗
Tetraena simplex NC_067950.1 106446 View on NCBI ↗