Markers + reference

Dipodium

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 141–142 kb
Candidate markers 268
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 541 0.0355 0.89 65.5 yes View details
trnG-GCC LSC 27 0.0370 1.00 65.6 yes View details
petN-psbM LSC 796 0.0307 0.86 73.1 yes View details
trnT-GGU-psbD LSC 905 0.0145 0.99 53.6 yes View details
accD-psaI LSC 735 0.0204 1.00 58.5 yes View details
petA-psbJ LSC 1056 0.0201 0.94 60.5 yes View details
clpP LSC 2223 0.0135 1.00 51.9 yes View details
trnN-GUU-rpl32 SSC 1036 0.0499 0.89 89.9 yes View details
ndhD SSC 1179 0.0738 0.82 80.6 yes View details
rps3-rpl22 LSC 46 0.0444 0.98 80.0 yes View details
psbF-psbE LSC 10 0.1000 1.00 77.0 yes View details
atpB-rbcL LSC 951 0.0132 0.95 70.7 yes View details
psaA-ycf3 LSC 645 0.0097 0.96 68.2 yes View details
psbL-psbF LSC 22 0.0455 1.00 68.1 yes View details
petD-rpoA LSC 143 0.0559 1.00 67.8 yes View details
trnT-UGU-trnL-UAA LSC 658 0.0106 0.86 67.0 yes View details
atpH-atpI LSC 665 0.0105 1.00 64.8 yes View details
rps16-trnQ-UUG LSC 899 0.0100 1.00 64.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATGGTGGATGCCAGAATCC GAGGTTCGAATCCTTCCGTC 1011–1040 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 972–1001 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 983–1012 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATGGTGGATGCCAGAATCC CTCGGAGGTTCGAATCCTTC 1015–1044 1.000 78.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 976–1005 1.000 77.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CATCGTTAGCTTGGAAGGCT 1261–1322 1.000 84.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CATCGTTAGCTTGGAAGGCT 1260–1321 1.000 84.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGTTAGCTTGGAAGGCTAGG 1258–1319 1.000 84.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGTTAGCTTGGAAGGCTAGG 1257–1318 1.000 84.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GGGATTTGAACCCTCGGTAC CATCGTTAGCTTGGAAGGCT 1304–1365 1.000 84.4
trnG-GCC_p1 trnG-GCC TGAAAGTTGAAGTTCAGTATTCT TGTCCTATTGAGGGGTAAAGGA 192 1.000 40.4
trnG-GCC_p2 trnG-GCC TCTAAATGAAAGTTGAAGTTCAGT TGTCCTATTGAGGGGTAAAGGA 198 1.000 40.4
trnG-GCC_p3 trnG-GCC ATGAAAGTTGAAGTTCAGTATTCT TGTCCTATTGAGGGGTAAAGGA 193 1.000 40.4
trnG-GCC_p4 trnG-GCC TGAAAGTTGAAGTTCAGTATTCT TGTCCTATTGAGGGGTAAAGG 192 1.000 40.4
trnG-GCC_p5 trnG-GCC TGAAAGTTGAAGTTCAGTATTC TGTCCTATTGAGGGGTAAAGGA 192 1.000 40.4
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 834–841 1.000 79.2
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 783–790 1.000 79.1
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 762–769 1.000 78.6
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 782–789 1.000 78.5
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 761–768 1.000 78.0
petN-psbM_p1 petN-psbM TAGTAAGTCTGGCTTGGGCT ACGTCAAAACAGTCAGCCAA 809–905 1.000 83.5
petN-psbM_p2 petN-psbM GGGACATCATTCGCATGGAT ACGTCAAAACAGTCAGCCAA 830–926 1.000 83.1
petN-psbM_p3 petN-psbM TAGTAAGTCTGGCTTGGGCT TACGTCAAAACAGTCAGCCA 810–906 1.000 80.7
petN-psbM_p4 petN-psbM GGGACATCATTCGCATGGAT TACGTCAAAACAGTCAGCCA 831–927 1.000 80.3
petN-psbM_p5 petN-psbM TAGTATGGGGAAGGAGTGGG ACGTCAAAACAGTCAGCCAA 752–848 1.000 80.1
trnT-GGU-psbD_p1 trnT-GGU-psbD GGTTCAGGTTACGAATCCCC AAGGAAAGAGCAATAGGCCG 1397–1398 1.000 81.6
trnT-GGU-psbD_p2 trnT-GGU-psbD GGTTCAGGTTACGAATCCCC CTGCTACACCAAAACTGGGT 1807–1809 1.000 81.4
trnT-GGU-psbD_p3 trnT-GGU-psbD GGTTCAGGTTACGAATCCCC TAAGACTCCAGCAACTCCCA 1893–1895 1.000 81.3
trnT-GGU-psbD_p4 trnT-GGU-psbD GGTTCAGGTTACGAATCCCC GGTCGCAATTGAACAGAACG 1697–1699 1.000 81.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CTGCTACACCAAAACTGGGT 1495–1505 1.000 80.8

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
Dipodium ensifolium NC_087851.1 142016 View on NCBI ↗
Dipodium roseum NC_046816.1 141209 View on NCBI ↗