Markers + reference

Cephalanthera

6 species · Orchidaceae · Asparagales

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Species 6
Genome length 161–162 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 715 0.0166 1.00 61.1 yes View details
rps16-trnQ-UUG LSC 1138 0.0263 0.97 73.6 yes View details
trnC-GCA-petN LSC 1008 0.0147 0.99 61.6 yes View details
trnE-UUC-trnT-GGU LSC 1736 0.0126 0.99 64.5 yes View details
accD-psaI LSC 862 0.0136 1.00 58.4 yes View details
clpP-psbB LSC 759 0.0157 1.00 72.4 yes View details
psbB-psbT LSC 336 0.0177 1.00 64.6 yes View details
rps8 LSC 396 0.0030 1.00 29.8 yes View details
rps8-rpl14 LSC 279 0.0346 0.97 77.9 yes View details
ndhE-psaC SSC 835 0.0161 1.00 63.9 yes View details
rpl32-ndhF SSC 1326 0.0182 0.99 72.6 yes View details
trnW-CCA-trnP-UGG LSC 167 0.0253 0.99 65.0 yes View details
psbM-trnD-GUC LSC 1097 0.0062 1.00 64.2 yes View details
rpl20-rps12 LSC 789 0.0056 0.99 64.2 yes View details
psbE-petL LSC 1287 0.0095 1.00 64.1 yes View details
psbT-psbN LSC 70 0.0610 1.00 64.0 yes View details
rps15-ndhH SSC 143 0.0177 1.00 62.1 yes View details
trnS-GCU-trnG-GCC LSC 757 0.0096 0.99 61.6 yes View details
rps12-trnV-GAC IRb 1747 0.0020 1.00 61.2 yes View details
trnV-GAC-rps12 IRa 1747 0.0018 1.00 61.0 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CACATCCGTCTCCAATCCAG GCAAAGACAACGAATTCCGG 1856–1866 1.000 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAAGAAGGGAAGCTCGTTGC GCAAAGACAACGAATTCCGG 1699–1709 1.000 82.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CACATCCGTCTCCAATCCAG TCGATCCCGAAGAGAAGGAA 1446–1454 1.000 82.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACATCCGTCTCCAATCCAGA GCAAAGACAACGAATTCCGG 1855–1865 1.000 81.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CTTTTCCCACATCAGGCACT GCAAAGACAACGAATTCCGG 1772–1782 0.833 75.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 1015–1242 1.000 87.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 992–1219 1.000 87.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1013–1240 1.000 87.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 1019–1246 1.000 86.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1003–1230 1.000 86.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC ACGAATCACACTTTTACCACT 798–822 1.000 55.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC TTTAGTCCCCTCAGCCATCT ACGAATCACACTTTTACCACT 799–823 1.000 55.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA ACGAATCACACTTTTACCACT 863–887 1.000 54.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC AGAACGAATCACACTTTTACCAC 801–825 1.000 54.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC GAACGAATCACACTTTTACCACT 800–824 1.000 54.8
trnC-GCA-petN_p1 trnC-GCA-petN ATTTAATTTGGCGGCATGGC GCTCTAAAGCCCACTCCTTC 1144–1195 1.000 86.2
trnC-GCA-petN_p2 trnC-GCA-petN TCTTTCGGAAGTACATGCCG GCTCTAAAGCCCACTCCTTC 1783–1872 1.000 85.2
trnC-GCA-petN_p3 trnC-GCA-petN AAGTTTTTAAGCGACGCGTG GCTCTAAAGCCCACTCCTTC 1382–1450 0.833 78.4
trnC-GCA-petN_p4 trnC-GCA-petN TCTTTCGGAAGTACATGCCG AGCCCAAGCGAGACTTACTA 1717–1806 0.833 77.6
trnC-GCA-petN_p5 trnC-GCA-petN GCGCAACATAGGTTAGGTCA GCTCTAAAGCCCACTCCTTC 1722–1800 0.833 76.7
psbM-trnD-GUC_p1 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG CCATGCATATGGCTGGGATT 1077–1235 1.000 84.0
psbM-trnD-GUC_p2 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG AGTTCAATCGGTCAGAGCAC 1055–1213 1.000 83.9
psbM-trnD-GUC_p3 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT CCATGCATATGGCTGGGATT 1134–1292 1.000 82.6
psbM-trnD-GUC_p4 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT CCATGCATATGGCTGGGATT 1082–1240 1.000 82.6
psbM-trnD-GUC_p5 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT AGTTCAATCGGTCAGAGCAC 1112–1270 1.000 82.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1764–1848 1.000 85.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1743–1827 1.000 84.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1740–1824 1.000 84.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1742–1826 1.000 84.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1761–1845 1.000 83.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Cephalanthera damasonium NC_041179.1 161699 View on NCBI ↗
Cephalanthera erecta PV752076.1 162011 View on NCBI ↗
Cephalanthera falcata NC_082061.1 161391 View on NCBI ↗
Cephalanthera longibracteata NC_041180.1 161986 View on NCBI ↗
Cephalanthera longifolia NC_030704.1 161877 View on NCBI ↗
Cephalanthera rubra NC_041181.1 162277 View on NCBI ↗