Markers + reference

Vanilla

5 species · Orchidaceae · Asparagales

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Species 5
Genome length 147–151 kb
Candidate markers 264
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-trnK-UUU LSC 1180 0.0854 0.81 79.2 yes View details
atpH-atpI LSC 1485 0.0866 0.57 66.7 yes View details
atpB-rbcL LSC 1435 0.0734 0.79 77.9 yes View details
petD LSC 2338 0.0326 0.64 57.7 yes View details
rps8-rpl14 LSC 812 0.0852 0.92 81.7 yes View details
ycf2 IRb 7257 0.0302 0.98 62.3 yes View details
trnL-CAA-rps7 IRb 1042 0.0857 0.91 77.5 yes View details
3'rps12-trnV-GAC IRb 967 0.0771 0.81 78.4 yes View details
trnV-GAC-3'rps12 IRa 967 0.0687 0.81 78.4 yes View details
rps7-trnL-CAA IRa 1042 0.0857 0.91 77.5 yes View details
ycf2 IRa 7257 0.0282 0.98 61.1 no View details
trnK-UUU-rps16 LSC 759 0.0470 0.99 86.0 yes View details
rpoB-trnC-GCA LSC 1032 0.0591 0.98 84.4 yes View details
psaC-rpl32 SSC 588 0.0859 0.98 83.9 yes View details
accD-psaI LSC 624 0.0901 0.88 82.6 yes View details
rpl16 LSC 1872 0.0525 0.89 80.5 yes View details
ccsA-psaC SSC 417 0.1057 0.96 80.3 yes View details
trnN-GUU-ycf1 IRb 536 0.0839 0.97 79.9 yes View details
ycf1-trnN-GUU IRa 536 0.0901 0.98 79.5 yes View details
rbcL-accD LSC 985 0.0394 0.99 79.2 yes View details
petB-petD LSC 170 0.0541 1.00 78.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACGATCATGAGCAAGTGAGT TGGGTGGTTTGTTTTCCAGT 1353–1640 1.000 81.7
matK-trnK-UUU_p2 matK-trnK-UUU TCGTGGAAAAACAATCGCAA TGGGTGGTTTGTTTTCCAGT 1811–2098 1.000 80.9
matK-trnK-UUU_p3 matK-trnK-UUU TTCGTGGAAAAACAATCGCA TGGGTGGTTTGTTTTCCAGT 1812–2099 1.000 80.9
matK-trnK-UUU_p4 matK-trnK-UUU AGAACATCTTTGACCCAGCA TGGGTGGTTTGTTTTCCAGT 1778–2065 0.800 74.2
matK-trnK-UUU_p5 matK-trnK-UUU AGAACATCTTTGACCCAGCA TTGGGTTGCTAACTCAACGG 1603–1890 0.800 73.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGTTCATGATATTTTAAGGAAGGCA 836–995 1.000 50.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGTTCATGATATTTTAAGGAAGGCA 835–994 1.000 50.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTGTTCATGATATTTTAAGGAAGGCA 837–996 1.000 50.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTGTTCATGATATTTTAAGGAAGGCA 836–995 1.000 50.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACTGTTCATGATATTTTAAGGAAGGC 837–996 1.000 50.9
atpH-atpI_p1 atpH-atpI GCCACGACCAGTCCATAAAT CAGTTATCACGGCTGTTCGA 1626–2290 0.800 83.1
atpH-atpI_p2 atpH-atpI GCCACGACCAGTCCATAAAT TCAGTTATCACGGCTGTTCG 1627–2291 0.800 83.1
atpH-atpI_p3 atpH-atpI ACGAGTGGATCTGCGAATTC CAGTTATCACGGCTGTTCGA 1873–2510 0.800 81.9
atpH-atpI_p4 atpH-atpI GGTCTCGTGTCAATCGTGAA CAGTTATCACGGCTGTTCGA 2028–2690 0.800 81.5
atpH-atpI_p5 atpH-atpI GGTCTCGTGTCAATCGTGAA TCAGTTATCACGGCTGTTCG 2029–2691 0.800 81.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTAATGCCGCGGGTACAT TTACCACTTGGCTATGTCGC 1314–1887 1.000 90.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CAAATTAATGCCGCGGGTAC TTACCACTTGGCTATGTCGC 1316–1889 1.000 89.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATGCCGGGACTTTGCAATAT TTACCACTTGGCTATGTCGC 1448–2021 1.000 89.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTAATGCCGCGGGTACAT TGAATGATGCCCCTCCCTAT 1537–2453 1.000 89.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTAATGCCGCGGGTACAT TGGGCCGGAATAAGAGAAGA 1961 0.200 46.8
atpB-rbcL_p1 atpB-rbcL GCCGACTGGAACACTTAGAG GTCCACACAGTTGTCCATGT 1604–1983 1.000 91.1
atpB-rbcL_p2 atpB-rbcL GCCGACTGGAACACTTAGAG ACGAAACGATCTCTCCAACG 2048–2427 1.000 90.1
atpB-rbcL_p3 atpB-rbcL AAAGCGGGTGCAGATCTATG ACGAAACGATCTCTCCAACG 2155–2534 1.000 89.8
atpB-rbcL_p4 atpB-rbcL TGCCCCGTGGAAAAATTACA ACGAAACGATCTCTCCAACG 2233 0.200 47.8
atpB-rbcL_p5 atpB-rbcL TGCCCCGTGGAAAAATTACA GTCCACACAGTTGTCCATGT 1789 0.200 47.7
rbcL-accD_p1 rbcL-accD GACCCGGTAGATAAGCCAGA ACTTACTAAACGTACACACAT 1051–1168 1.000 50.1
rbcL-accD_p2 rbcL-accD TCGATTTCGACCCGGTAGAT ACTTACTAAACGTACACACAT 1059–1176 1.000 50.1
rbcL-accD_p3 rbcL-accD ACCCGGTAGATAAGCCAGAT ACTTACTAAACGTACACACAT 1050–1167 1.000 50.1
rbcL-accD_p4 rbcL-accD AGCAAATGGAGCCCTGAATT ACTTACTAAACGTACACACAT 1114–1231 1.000 49.8
rbcL-accD_p5 rbcL-accD CTAGCAAATGGAGCCCTGAA ACTTACTAAACGTACACACAT 1116–1233 1.000 49.8

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
Vanilla aphylla NC_035320.1 150165 View on NCBI ↗
Vanilla calyculata PX058852.1 150748 View on NCBI ↗
Vanilla phaeantha PX058851.1 147372 View on NCBI ↗
Vanilla planifolia NC_026778.1 148011 View on NCBI ↗
Vanilla pompona NC_036809.1 148009 View on NCBI ↗