Markers + reference

Vandopsis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 149–149 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1186 0.0144 1.00 52.9 yes View details
accD-psaI LSC 860 0.0116 1.00 60.4 yes View details
rpl16 LSC 1638 0.0135 0.99 66.9 yes View details
ycf2 IRb 6843 0.0029 1.00 54.2 yes View details
ycf1-rpl32 SSC 463 0.0485 0.89 71.7 yes View details
ndhG SSC 515 0.0121 0.96 53.4 yes View details
ycf2 IRa 6843 0.0029 1.00 54.2 no View details
rpoA-rps11 LSC 84 0.0357 1.00 71.2 yes View details
clpP-psbB LSC 706 0.0136 0.94 70.3 yes View details
matK-trnK-UUU LSC 1170 0.0225 0.99 68.9 yes View details
trnE-UUC-trnT-GGU LSC 839 0.0112 0.96 68.9 yes View details
ndhC-trnV-UAC LSC 703 0.0088 0.97 66.7 yes View details
rps16-trnQ-UUG LSC 867 0.0104 1.00 64.8 yes View details
petA-psbJ LSC 950 0.0105 1.00 64.8 yes View details
psbE-petL LSC 1101 0.0091 1.00 64.2 yes View details
rpoB-trnC-GCA LSC 1662 0.0026 0.93 64.1 yes View details
psbB-psbT LSC 380 0.0084 0.94 63.5 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
trnK-UUU_p1 trnK-UUU TAAGAAGGGAAGCTCGTTGC ATAAGACCGCGACTGATCCT 270–272 1.000 81.2
trnK-UUU_p2 trnK-UUU CTTTTCCCACATCAGGCACT ATAAGACCGCGACTGATCCT 340–342 1.000 80.6
trnK-UUU_p3 trnK-UUU GACCCTTTTCCCACATCAGG ATAAGACCGCGACTGATCCT 344–346 1.000 80.0
trnK-UUU_p4 trnK-UUU TCGCAACCCAATCACTCTTT ATAAGACCGCGACTGATCCT 480–482 1.000 78.2
trnK-UUU_p5 trnK-UUU TTCGCAACCCAATCACTCTT ATAAGACCGCGACTGATCCT 481–483 1.000 78.2
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TCCGGGTTGCTAACTCAATG 1317–1318 1.000 73.3
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA CGGGTTGCTAACTCAATGGT 1315–1316 1.000 72.8
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1319–1320 1.000 71.0
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1321–1322 1.000 71.0
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT TCCGGGTTGCTAACTCAATG 1317–1318 1.000 69.5
rps16_p1 rps16 CATTGAGTTAGCAACCCGGA AAGTGAAATCCTTTCCGGGT 1823–1850 1.000 72.4
rps16_p2 rps16 ACCATTGAGTTAGCAACCCG AAGTGAAATCCTTTCCGGGT 1825–1852 1.000 71.8
rps16_p3 rps16 CATTGAGTTAGCAACCCGGA TGTATCGGTTCAGCCAATGA 1765–1792 1.000 71.6
rps16_p4 rps16 CATTGAGTTAGCAACCCGGA GTATCGGTTCAGCCAATGACT 1764–1791 1.000 71.4
rps16_p5 rps16 ACCATTGAGTTAGCAACCCG TGTATCGGTTCAGCCAATGA 1767–1794 1.000 71.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 962–963 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 939–940 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 960–961 1.000 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 966–967 1.000 78.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 950–951 1.000 78.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CCGGGGATAAAGGATTTGCA 1698–1817 1.000 82.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ACCGGGGATAAAGGATTTGC 1699–1818 1.000 82.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TCGAACCGGGGATAAAGGAT 1703–1822 1.000 81.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTCGAACCGGGGATAAAGGA 1704–1823 1.000 79.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT CCGGGGATAAAGGATTTGCA 1699–1818 1.000 79.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 914–943 1.000 82.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 893–922 1.000 81.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 890–919 1.000 81.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 892–921 1.000 81.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 911–940 1.000 81.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Vandopsis gigantea MN124403.1 149130 View on NCBI ↗
Vandopsis lissochiloides MN124443.1 148866 View on NCBI ↗