Markers + reference

Dactylorhiza

5 species · Orchidaceae · Asparagales

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Species 5
Genome length 154–155 kb
Candidate markers 274
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 624 0.0159 0.98 66.4 yes View details
trnF-GAA-ndhJ LSC 539 0.0438 0.99 77.1 yes View details
rbcL-accD LSC 760 0.0107 0.99 56.2 yes View details
trnP-UGG-psaJ LSC 363 0.0130 1.00 46.4 yes View details
psaJ-rpl33 LSC 562 0.0338 0.99 72.1 yes View details
psbB-psbT LSC 390 0.0179 1.00 57.6 yes View details
infA LSC 234 0.0000 1.00 19.4 yes View details
ycf1 IRb 1017 0.0018 1.00 44.9 no View details
ndhF-rpl32 SSC 744 0.0188 0.97 54.1 yes View details
rps15 SSC 273 0.0015 1.00 25.6 yes View details
ycf1 SSC 5448 0.0073 1.00 38.9 yes View details
rpl36-infA LSC 116 0.0629 1.00 80.0 yes View details
rpl16-rps3 LSC 179 0.0283 1.00 64.0 yes View details
atpF-atpH LSC 112 0.0143 0.96 63.2 yes View details
ndhH-rps15 SSC 143 0.0266 1.00 62.5 yes View details
trnE-UUC-trnT-GGU LSC 901 0.0092 0.97 62.4 yes View details
ccsA SSC 978 0.0054 1.00 62.3 yes View details
trnC-GCA-petN LSC 881 0.0082 0.99 60.8 yes View details
rpoC1 LSC 2792 0.0036 1.00 59.9 yes View details
rps4-trnT-UGU LSC 303 0.0075 0.97 58.0 yes View details
petD-rpoA LSC 218 0.0174 1.00 57.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TTCACTTTGGTATGGATTGA AGTTGTGCAGTGCAATTTCA 2996–3000 0.600 25.3
trnK-UUU_p2 trnK-UUU TTCACTTTGGTATGGATTGA CAGTTGTGCAGTGCAATTTCA 2997 0.400 16.0
trnK-UUU_p3 trnK-UUU TTTCACTTTGGTATGGATTGA CAGTTGTGCAGTGCAATTTCA 2998 0.400 16.0
trnK-UUU_p4 trnK-UUU TTTCACTTTGGTATGGATTGA AGTTGTGCAGTGCAATTTCA 2997 0.400 16.0
trnK-UUU_p5 trnK-UUU TTTTCACTTTGGTATGGATTGA CAGTTGTGCAGTGCAATTTCA 2999 0.400 16.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 654–679 1.000 66.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 653–678 1.000 66.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATCGGAGAGAGAGGGATTCG ACCACTAAACTATACCCGCT 709–734 1.000 65.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GGAATCGGAGAGAGAGGGAT ACCACTAAACTATACCCGCT 712–737 1.000 63.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA ACCACTAAACTATACCCGCT 707–732 1.000 63.5
atpF-atpH_p1 atpF-atpH AACTCGAAACTTCCAACGGA ATTTATGGACTGGTCGTGGC 223–231 1.000 78.7
atpF-atpH_p2 atpF-atpH AACTCGAAACTTCCAACGGA GGTCGTGGCATTAGCTCTTT 212–220 1.000 77.1
atpF-atpH_p3 atpF-atpH ACTCGAAACTTCCAACGGAT ATTTATGGACTGGTCGTGGC 222–230 1.000 76.9
atpF-atpH_p4 atpF-atpH CCACGGAAACAAAAGAATCGG ATTTATGGACTGGTCGTGGC 192–200 1.000 75.6
atpF-atpH_p5 atpF-atpH ACTCGAAACTTCCAACGGAT GGTCGTGGCATTAGCTCTTT 211–219 1.000 75.3
rpoC1_p1 rpoC1 ACACGAGTATGGGCATCACT TTGCTCGTTCGAGAACTACG 2942–2974 1.000 74.6
rpoC1_p2 rpoC1 TACACGAGTATGGGCATCAC TTGCTCGTTCGAGAACTACG 2943–2975 1.000 74.0
rpoC1_p3 rpoC1 TTACACGAGTATGGGCATCAC TTGCTCGTTCGAGAACTACG 2944–2976 1.000 71.7
rpoC1_p4 rpoC1 CACGAGTATGGGCATCACTA TTGCTCGTTCGAGAACTACG 2941–2973 1.000 71.7
rpoC1_p5 rpoC1 ACCAGTTAAATCGGGGAGAC TTGCTCGTTCGAGAACTACG 2970–3000 0.600 56.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTGGATGAAATTTGGCGGC CCCACTCCTTCCCCATACTA 672–1060 1.000 80.4
trnC-GCA-petN_p2 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC CCCACTCCTTCCCCATACTA 611–999 1.000 79.0
trnC-GCA-petN_p3 trnC-GCA-petN TTTGGATGAAATTTGGCGGC TCTAAAGCCCACTCCTTCCC 679–1067 1.000 78.6
trnC-GCA-petN_p4 trnC-GCA-petN GATGAAATTTGGCGGCATGG CCCACTCCTTCCCCATACTA 668–1056 1.000 77.7
trnC-GCA-petN_p5 trnC-GCA-petN GGATGAAATTTGGCGGCATG CCCACTCCTTCCCCATACTA 669–1057 1.000 77.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 948–986 1.000 82.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 945–983 1.000 82.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 926–964 1.000 82.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TGGCGTTACTCTACCACTGA 923–961 1.000 82.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA AACTTACGCCTTACCATGGC 961–999 1.000 81.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Dactylorhiza fuchsii PP335050.1 154115 View on NCBI ↗
Dactylorhiza majalis NC_044644.1 154108 View on NCBI ↗
Dactylorhiza sambucina PP335052.1 153500 View on NCBI ↗
Dactylorhiza viridis NC_056192.1 155328 View on NCBI ↗
Dactylorhiza viridis var. coreana MN200382.1 153549 View on NCBI ↗