Markers + reference

Cypripedium

9 species · Orchidaceae · Asparagales

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Species 9
Genome length 189–246 kb
Candidate markers 272
Primer pairs 95

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 2421 0.2237 0.96 78.3 yes View details
petN-psbM LSC 2112 0.2033 0.93 78.5 yes View details
ndhC-trnV-UAC LSC 5932 0.2047 0.63 68.1 no View details
atpB-rbcL LSC 4056 0.2074 0.87 75.4 yes View details
trnP-UGG-psaJ LSC 1486 0.2759 0.98 86.4 yes View details
clpP1-psbB LSC 3107 0.1975 0.86 77.2 yes View details
rps8-rpl14 LSC 3016 0.2121 0.72 73.2 yes View details
ndhF-rpl32 SSC 1479 0.2263 0.90 79.5 yes View details
trnL-UAG-ccsA SSC 1233 0.2335 0.96 78.9 yes View details
psaC-ndhE SSC 2983 0.2102 0.66 71.4 yes View details
trnE-UUC-trnT-GGU LSC 1487 0.1061 0.98 89.0 yes View details
trnL-CAA-ndhB IRb 597 0.0472 0.95 86.9 yes View details
psbM-trnD-GUC LSC 759 0.0633 0.99 85.8 yes View details
petA-psbJ LSC 1633 0.1319 0.97 85.0 yes View details
trnK-UUU-rps16 LSC 737 0.0569 0.99 83.8 yes View details
trnT-UGU-trnL-UAA LSC 1404 0.0665 0.91 83.7 yes View details
ndhB-trnL-CAA IRa 597 0.0400 0.95 83.5 yes View details
rbcL-accD LSC 914 0.0456 1.00 83.3 yes View details
pafII-cemA LSC 936 0.0834 0.98 83.1 yes View details
rps16-trnQ-UUG LSC 1487 0.1418 0.92 82.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 894–1000 1.000 89.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 1368–1774 0.556 68.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1367–1773 0.556 68.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCACGATTTCACGACATGCT GCAAAGACAACGAATTCCGG 1500–1514 0.444 58.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCACGATTTCACGACATGCT TCGATCCCGAAGAGAAGGAA 1061–1076 0.444 57.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 1413–2784 0.778 82.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1390–2761 0.778 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1411–2782 0.778 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 1417–2788 0.778 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1401–2772 0.778 80.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TCTACTCGCGGGATCCTAAG 2364–2947 0.556 73.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TCTACTCGCGGGATCCTAAG 2363–2946 0.556 73.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTAGTCCACTCAGCCACC TCTACTCGCGGGATCCTAAG 2354–2937 0.556 72.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATTTCTACTCGCGGGATCCT 2367–2950 0.556 71.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATTTCTACTCGCGGGATCCT 2366–2949 0.556 71.8
petN-psbM_p1 petN-psbM TCCTATTTTGACTCTGCGCC CGTTTATTGCTACTGCGCTG 1698–2982 0.889 86.7
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTTTATTGCTACTGCGCTG 1592–2881 0.889 85.7
petN-psbM_p3 petN-psbM TTGACTCTGCGCCATTGATT CGTTTATTGCTACTGCGCTG 1691–2975 0.889 85.5
petN-psbM_p4 petN-psbM TTTGACTCTGCGCCATTGAT CGTTTATTGCTACTGCGCTG 1692–2976 0.889 85.5
petN-psbM_p5 petN-psbM TCCTATTTTGACTCTGCGCC AACTTTGTTTGTGCATCCGC 2832–2954 0.333 63.1
psbM-trnD-GUC_p1 psbM-trnD-GUC CGCAAGAATATTGACTTCCA AGTTCAATCGGTCAGAGCAC 846–1417 1.000 57.0
psbM-trnD-GUC_p2 psbM-trnD-GUC CGCAAGAATATTGACTTCCAT AGTTCAATCGGTCAGAGCAC 846–1417 1.000 54.1
psbM-trnD-GUC_p3 psbM-trnD-GUC CGCAAGAATATTGACTTCCA GTTCAATCGGTCAGAGCACC 845–1416 1.000 52.0
psbM-trnD-GUC_p4 psbM-trnD-GUC CGCAAGAATATTGACTTCCA GTAGTTCAATCGGTCAGAGCA 848–1419 1.000 52.0
psbM-trnD-GUC_p5 psbM-trnD-GUC CGCAAGAATATTGACTTCCA TAGTTCAATCGGTCAGAGCAC 847–1418 1.000 52.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1410–2067 0.667 77.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 1375–2032 0.667 76.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1388–2045 0.667 76.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1407–2064 0.667 76.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TACCGCTGAGTTAAAAGGGC 1353–2010 0.667 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Cypripedium calcicola OR698926.1 200587 View on NCBI ↗
Cypripedium elegans OR698927.1 207625 View on NCBI ↗
Cypripedium forrestii OR698931.1 246177 View on NCBI ↗
Cypripedium franchetii OR698932.1 196239 View on NCBI ↗
Cypripedium himalaicum OR698935.1 189472 View on NCBI ↗
Cypripedium ludlowii OR698937.1 203989 View on NCBI ↗
Cypripedium micranthum OR698938.1 229932 View on NCBI ↗
Cypripedium shanxiense OR698940.1 191697 View on NCBI ↗
Cypripedium wardii OR698942.1 226879 View on NCBI ↗