Markers + reference

Paphiopedilum

67 species · Orchidaceae · Asparagales

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Species 67
Genome length 153–163 kb
Candidate markers 264
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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 976 0.0360 0.99 82.0 yes View details
petN-psbM LSC 1179 0.0660 0.89 89.6 yes View details
trnE-UUC-trnT-GGU LSC 1504 0.1211 0.87 84.8 yes View details
trnP-UGG-psaJ LSC 761 0.1117 0.97 89.2 yes View details
psbB-psbT LSC 427 0.1094 0.81 78.0 yes View details
rpl16 LSC 1653 0.0223 0.98 71.1 yes View details
ndhD-trnL-UAG IRb 1268 0.0531 0.98 78.8 yes View details
trnK-UUU-rps16 LSC 872 0.0363 0.97 86.9 yes View details
rps8-rpl14 LSC 447 0.0469 0.98 85.8 yes View details
trnL-UAG-rpl32 SSC 433 0.0491 0.93 79.3 yes View details
trnT-UGU-trnL-UAA LSC 1084 0.0182 0.98 76.8 yes View details
rps15-psaC IRb 650 0.0201 0.99 76.6 yes View details
psaC-rps15 IRa 650 0.0175 0.99 76.1 yes View details
trnC-GCA-petN LSC 784 0.0256 1.00 75.4 yes View details
trnR-UCU-atpA LSC 239 0.0701 0.99 75.2 yes View details
rpl33-rps18 LSC 356 0.0655 0.95 75.1 yes View details
psaA-ycf3 LSC 640 0.0244 0.99 72.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 863–1273 0.985 76.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 862–1272 0.985 76.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 862–1272 1.000 76.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 861–1271 1.000 76.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GTGCTCAACCCACAGGAAC 849–1259 0.985 74.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATGGAAAGACCGCTTAACT 1083–1597 1.000 67.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATGGAAAGACCGCTTAACT 1082–1596 1.000 67.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC AATGGAAAGACCGCTTAACT 1073–1587 1.000 66.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGGAAAGACCGCTTAACTATTGA 1081–1595 0.985 66.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGGAAAGACCGCTTAACTATTGA 1080–1594 0.985 66.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CACTGAAGAAGCTGAAACCCT 280–542 1.000 69.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCACTGAAGAAGCTGAAACCC 281–543 1.000 69.3
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACTGAAGAAGCTGAAACCCT 279–541 1.000 67.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CACTGAAGAAGCTGAAACCC 280–542 1.000 67.6
trnR-UCU-atpA_p5 trnR-UCU-atpA GGGCGCCCATTGTCTAATG CACTGAAGAAGCTGAAACCCT 332–594 1.000 67.1
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 681–1205 1.000 87.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 706–1230 1.000 86.6
trnC-GCA-petN_p3 trnC-GCA-petN GACATGGCCAAGTGGTAAGG AGCCCAAGCGAGACTTACTA 727–1251 1.000 86.5
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC CCCACTCCTTCCCCATACTA 738–1262 1.000 84.3
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTA CCCACTCCTTCCCCATACTA 763–1287 1.000 83.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTTTATTGCTACTGCGCTG 617–1858 0.985 89.6
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 612–1853 1.000 88.7
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TATTGCTACTGCGCTGTTCA 613–1854 1.000 87.8
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGCTGTTCATTT 610–1851 1.000 87.0
petN-psbM_p5 petN-psbM TAGTATGGGGAAGGAGTGGG CGTTTATTGCTACTGCGCTG 573–1801 0.970 86.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 584–2598 0.970 89.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 549–2563 0.970 88.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 562–2576 0.970 88.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 581–2595 0.970 88.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTTTCCGCCGAAAAACGAAG 646–2660 0.940 87.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (67)

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

Species Accession Length (bp) Link
Paphiopedilum acmodontum NC_069650.1 156480 View on NCBI ↗
Paphiopedilum agusii NC_069954.1 153654 View on NCBI ↗
Paphiopedilum argus NC_069956.1 154493 View on NCBI ↗
Paphiopedilum armeniacum f. markii OL875121.1 162590 View on NCBI ↗
Paphiopedilum barbatum NC_069957.1 158590 View on NCBI ↗
Paphiopedilum barbigerum NC_050870.1 156329 View on NCBI ↗
Paphiopedilum barbigerum x Paphiopedilum dianthum NC_058832.1 160503 View on NCBI ↗
Paphiopedilum bellatulum NC_058833.1 156567 View on NCBI ↗
Paphiopedilum braemii NC_069958.1 157293 View on NCBI ↗
Paphiopedilum bullenianum NC_069959.1 158953 View on NCBI ↗
Paphiopedilum callosum NC_069960.1 155231 View on NCBI ↗
Paphiopedilum canhii NC_069961.1 160522 View on NCBI ↗
Paphiopedilum ciliolare NC_069962.1 157709 View on NCBI ↗
Paphiopedilum coccineum NC_069963.1 156639 View on NCBI ↗
Paphiopedilum dayanum NC_069965.1 160487 View on NCBI ↗
Paphiopedilum dianthum NC_036958.1 154699 View on NCBI ↗
Paphiopedilum druryi NC_069966.1 158780 View on NCBI ↗
Paphiopedilum exul NC_069967.1 160590 View on NCBI ↗
Paphiopedilum fairrieanum NC_069968.1 160932 View on NCBI ↗
Paphiopedilum fowliei NC_069970.1 158113 View on NCBI ↗
Paphiopedilum gigantifolium NC_069971.1 159389 View on NCBI ↗
Paphiopedilum glaucophyllum NC_069973.1 162803 View on NCBI ↗
Paphiopedilum gratrixianum NC_056912.1 157292 View on NCBI ↗
Paphiopedilum haynaldianum NC_069870.1 158279 View on NCBI ↗
Paphiopedilum hennisianum NC_069871.1 156991 View on NCBI ↗
Paphiopedilum henryanum NC_058834.1 155886 View on NCBI ↗
Paphiopedilum hookerae NC_069873.1 156614 View on NCBI ↗
Paphiopedilum insigne NC_069874.1 159798 View on NCBI ↗
Paphiopedilum intaniae NC_069875.1 159457 View on NCBI ↗
Paphiopedilum javanicum NC_069876.1 153641 View on NCBI ↗
Paphiopedilum kolopakingii NC_058210.1 159848 View on NCBI ↗
Paphiopedilum lawrenceanum NC_069877.1 158493 View on NCBI ↗
Paphiopedilum liemianum NC_069879.1 161541 View on NCBI ↗
Paphiopedilum lowii NC_069880.1 158194 View on NCBI ↗
Paphiopedilum mastersianum NC_069883.1 156485 View on NCBI ↗
Paphiopedilum moquetteanum NC_069884.1 160001 View on NCBI ↗
Paphiopedilum nataschae NC_069885.1 159259 View on NCBI ↗
Paphiopedilum niveum NC_026776.1 159108 View on NCBI ↗
Paphiopedilum papuanum NC_069886.1 157446 View on NCBI ↗
Paphiopedilum parishii NC_059788.1 154689 View on NCBI ↗
Paphiopedilum parnatanum NC_069887.1 157331 View on NCBI ↗
Paphiopedilum philippinense NC_058209.1 158653 View on NCBI ↗
Paphiopedilum primulinum NC_069888.1 162612 View on NCBI ↗
Paphiopedilum randsii NC_069889.1 157799 View on NCBI ↗
Paphiopedilum rothschildianum NC_069890.1 160044 View on NCBI ↗
Paphiopedilum sanderianum NC_069892.1 157236 View on NCBI ↗
Paphiopedilum sangii NC_069893.1 157058 View on NCBI ↗
Paphiopedilum schoseri NC_069894.1 157306 View on NCBI ↗
Paphiopedilum stonei NC_069895.1 159933 View on NCBI ↗
Paphiopedilum sugiyamanum NC_069896.1 162380 View on NCBI ↗
Paphiopedilum sukhakulii NC_069897.1 158536 View on NCBI ↗
Paphiopedilum supardii NC_069898.1 160720 View on NCBI ↗
Paphiopedilum superbiens NC_069899.1 156831 View on NCBI ↗
Paphiopedilum tigrinum NC_062049.1 152850 View on NCBI ↗
Paphiopedilum tonsum NC_069900.1 157912 View on NCBI ↗
Paphiopedilum tranlienianum NC_058208.1 156495 View on NCBI ↗
Paphiopedilum urbanianum NC_069901.1 155338 View on NCBI ↗
Paphiopedilum vejvarutianum NC_069902.1 156308 View on NCBI ↗
Paphiopedilum venustum NC_069903.1 156362 View on NCBI ↗
Paphiopedilum victoria-mariae NC_058211.1 161300 View on NCBI ↗
Paphiopedilum villosum NC_069906.1 162715 View on NCBI ↗
Paphiopedilum villosum var. affine OL875115.1 156946 View on NCBI ↗
Paphiopedilum violascens NC_058212.1 157868 View on NCBI ↗
Paphiopedilum wardii NC_069907.1 158707 View on NCBI ↗
Paphiopedilum wilhelminae NC_069909.1 153064 View on NCBI ↗
Paphiopedilum x areeanum NC_069955.1 159468 View on NCBI ↗
Paphiopedilum x herrmannii NC_069872.1 156476 View on NCBI ↗