Markers + reference

Dendrobium

72 species · Orchidaceae · Asparagales

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Species 72
Genome length 146–160 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 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-trnQ-UUG LSC 1004 0.0383 0.99 82.3 yes View details
trnS-GCU-trnG-UCC LSC 1042 0.0326 0.99 81.0 yes View details
trnT-UGU-trnL-UAA LSC 603 0.0525 0.98 86.8 yes View details
trnL-UAA-trnL-UAA LSC 802 0.0382 0.98 77.1 yes View details
clpP-psbB LSC 709 0.0456 0.98 82.5 yes View details
psbB-psbT LSC 408 0.0669 0.98 77.9 yes View details
rpl16 LSC 1594 0.0240 0.98 72.1 yes View details
trnN-GUU-rpl32 SSC 2142 0.0403 0.97 76.8 yes View details
rpl32-trnL-UAG SSC 730 0.0413 0.99 87.3 yes View details
psaC-rps15 SSC 3141 0.0324 0.98 73.4 yes View details
trnV-GAC-3'rps12 IRa 1957 0.0234 1.00 83.7 yes View details
trnF-GAA-trnV-UAC LSC 1401 0.0352 1.00 82.9 yes View details
petN-psbM LSC 773 0.0359 0.93 82.8 yes View details
atpH-atpI LSC 731 0.0196 0.99 81.8 yes View details
psbK-psbI LSC 518 0.0346 0.93 79.3 yes View details
psbC-trnS-UGA LSC 133 0.0452 1.00 79.0 yes View details
atpB-rbcL LSC 1019 0.0253 0.99 78.8 yes View details
trnE-UUC-trnT-GGU LSC 542 0.0370 0.98 78.5 yes View details
rpl20-5'rps12 LSC 778 0.0130 0.99 78.2 yes View details
3'rps12-trnV-GAC IRb 1957 0.0093 1.00 77.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TACTCGGAGGTTCGAATCCT 934–1195 1.000 86.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 923–1184 0.986 86.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC ACTCGGAGGTTCGAATCCTT 933–1194 1.000 86.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 922–1183 0.986 86.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGTTACTC 938–1199 0.972 86.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 520–638 1.000 91.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 521–639 1.000 91.0
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 522–640 1.000 89.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 517–635 1.000 89.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 518–636 1.000 89.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGGAAAGACCCCTTAACT 1018–1296 1.000 78.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACGGAAAGACCCCTTAACT 1017–1295 1.000 78.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACGGAAAGACCCCTTAACT 1019–1297 1.000 77.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAACGGAAAGACCCCTTAACT 1018–1296 1.000 77.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACGGAAAGACCCCTTAACT 1071–1349 1.000 76.4
atpH-atpI_p1 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 609–888 1.000 90.4
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 660–939 0.986 89.9
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 588–867 1.000 89.8
atpH-atpI_p4 atpH-atpI TCCGATAGAAGCAAGCCCTA CGAATCCATGGAGGGTCATC 585–864 0.986 89.4
atpH-atpI_p5 atpH-atpI CGCAATACCTTCTACGGCTT CGAATCCATGGAGGGTCATC 636–915 0.972 89.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CTTGCGCTTATTGCTACTGC 883–1088 0.972 88.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTCAAAACAGTCAGCCAA 822–1027 1.000 88.8
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 874–1079 1.000 88.7
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TATTGCTACTGCGCTGTTCA 875–1080 1.000 87.8
petN-psbM_p5 petN-psbM TAGTATGGGGAAGGAGTGGG CTTGCGCTTATTGCTACTGC 826–1031 0.972 86.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TCGTAGTTCACTACCCCCAG GAACCGATGACTTACGCCTT 559–1327 1.000 90.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 524–1292 1.000 90.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCGTAGTTCACTACCCCCAG CCATGGCGTTACTCTACCAC 538–1306 0.931 87.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 503–1271 0.931 87.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCGTAGTTCACTACCCCCAG TGGCGTTACTCTACCACTGA 535–1303 0.931 87.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (72)

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

Species Accession Length (bp) Link
Dendrobium acinaciforme NC_071778.1 150841 View on NCBI ↗
Dendrobium aduncum NC_038077.1 152112 View on NCBI ↗
Dendrobium aphyllum NC_035322.1 151524 View on NCBI ↗
Dendrobium bellatulum NC_037700.1 152107 View on NCBI ↗
Dendrobium bensoniae NC_072269.1 151551 View on NCBI ↗
Dendrobium bicameratum PP479692.1 159762 View on NCBI ↗
Dendrobium brymerianum NC_035323.1 151830 View on NCBI ↗
Dendrobium candidum NC_035745.1 152094 View on NCBI ↗
Dendrobium capillipes NC_072707.1 159400 View on NCBI ↗
Dendrobium cariniferum NC_080348.1 159552 View on NCBI ↗
Dendrobium catenatum NC_037361.1 152185 View on NCBI ↗
Dendrobium christyanum PP479702.1 159984 View on NCBI ↗
Dendrobium chrysanthum NC_035336.1 151790 View on NCBI ↗
Dendrobium chrysocrepis NC_045945.1 154155 View on NCBI ↗
Dendrobium comatum NC_063511.1 158008 View on NCBI ↗
Dendrobium crepidatum NC_035331.1 151717 View on NCBI ↗
Dendrobium crystallinum PP479712.1 151921 View on NCBI ↗
Dendrobium denneanum NC_035324.1 151565 View on NCBI ↗
Dendrobium devonianum NC_035325.1 151945 View on NCBI ↗
Dendrobium ellipsophyllum NC_035340.1 152026 View on NCBI ↗
Dendrobium exile NC_035343.1 151294 View on NCBI ↗
Dendrobium falconeri NC_035326.1 151890 View on NCBI ↗
Dendrobium fanjingshanense NC_035344.1 152108 View on NCBI ↗
Dendrobium fimbriatum NC_035342.1 151673 View on NCBI ↗
Dendrobium findlayanum NC_058618.1 153713 View on NCBI ↗
Dendrobium flexicaule NC_038076.1 152242 View on NCBI ↗
Dendrobium gratiosissimum NC_035327.1 151829 View on NCBI ↗
Dendrobium hainanense NC_067939.1 151367 View on NCBI ↗
Dendrobium hancockii LC500592.1 151688 View on NCBI ↗
Dendrobium henanense LC727398.1 151219 View on NCBI ↗
Dendrobium henryi NC_035335.1 151850 View on NCBI ↗
Dendrobium hercoglossum NC_035328.1 151939 View on NCBI ↗
Dendrobium heterocarpum NC_068067.1 159786 View on NCBI ↗
Dendrobium huoshanense NC_028430.1 153188 View on NCBI ↗
Dendrobium jenkinsii NC_035337.1 151717 View on NCBI ↗
Dendrobium lindleyi NC_071777.1 151947 View on NCBI ↗
Dendrobium lituiflorum PQ576489.1 154560 View on NCBI ↗
Dendrobium loddigesii NC_036355.1 152493 View on NCBI ↗
Dendrobium lohohense NC_035338.1 151812 View on NCBI ↗
Dendrobium longicornu NC_071776.1 151789 View on NCBI ↗
Dendrobium moniliforme NC_035154.1 148778 View on NCBI ↗
Dendrobium moschatum NC_061572.1 159701 View on NCBI ↗
Dendrobium naungmungense NC_061009.1 151883 View on NCBI ↗
Dendrobium nobile NC_029456.1 153660 View on NCBI ↗
Dendrobium odiosum NC_067711.1 157312 View on NCBI ↗
Dendrobium officinale NC_024019.1 152221 View on NCBI ↗
Dendrobium parciflorum NC_035334.1 150073 View on NCBI ↗
Dendrobium parishii NC_035339.1 151689 View on NCBI ↗
Dendrobium pendulum NC_029705.1 153038 View on NCBI ↗
Dendrobium polyanthum PP479698.1 146397 View on NCBI ↗
Dendrobium porphyrochilum PP479730.1 154604 View on NCBI ↗
Dendrobium primulinum NC_035321.1 150767 View on NCBI ↗
Dendrobium pulchellum PP479714.1 159835 View on NCBI ↗
Dendrobium salaccense NC_035332.1 151104 View on NCBI ↗
Dendrobium sanderae PP479746.1 159032 View on NCBI ↗
Dendrobium scoriarum NC_038079.1 151990 View on NCBI ↗
Dendrobium shixingense NC_038078.1 152178 View on NCBI ↗
Dendrobium sinense NC_067940.1 159644 View on NCBI ↗
Dendrobium sinominutiflorum NC_061573.1 150595 View on NCBI ↗
Dendrobium spatella NC_035333.1 151829 View on NCBI ↗
Dendrobium strongylanthum NC_027691.1 153059 View on NCBI ↗
Dendrobium stuposum PP479719.1 160001 View on NCBI ↗
Dendrobium terminale NC_071775.1 151490 View on NCBI ↗
Dendrobium tetrapterum PP375114.1 160120 View on NCBI ↗
Dendrobium tortile PQ576495.1 149496 View on NCBI ↗
Dendrobium transparens PP479697.1 151891 View on NCBI ↗
Dendrobium wangliangii NC_052727.1 160052 View on NCBI ↗
Dendrobium wardianum NC_035329.1 151788 View on NCBI ↗
Dendrobium wattii NC_045856.1 159366 View on NCBI ↗
Dendrobium wilsonii NC_035330.1 152080 View on NCBI ↗
Dendrobium xichouense NC_035341.1 152052 View on NCBI ↗
Dendrobium zhenghuoense MN164627.1 148431 View on NCBI ↗