Markers + reference

Oreorchis

3 species · Orchidaceae · Asparagales

Back to catalogue

Species 3
Genome length 158–159 kb
Candidate markers 271
Primer pairs 110

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 987 0.0182 1.00 70.8 yes View details
trnS-GCU-trnG-GCC LSC 885 0.0144 0.99 66.0 yes View details
rpoB-trnC-GCA LSC 1285 0.0119 1.00 52.3 yes View details
atpB-rbcL LSC 838 0.0124 1.00 69.3 yes View details
rbcL LSC 1464 0.0027 1.00 50.5 yes View details
psaJ-rpl33 LSC 604 0.0188 1.00 60.5 yes View details
clpP-psbB LSC 820 0.0175 1.00 57.6 yes View details
ndhD SSC 1509 0.0062 1.00 53.0 yes View details
psaC-ndhE SSC 584 0.0228 1.00 62.3 yes View details
ycf1 SSC 5364 0.0089 1.00 48.3 yes View details
ccsA-ndhD SSC 219 0.0457 1.00 79.4 yes View details
psaA-ycf3 LSC 652 0.0153 1.00 69.1 yes View details
atpH-atpI LSC 756 0.0097 1.00 67.7 yes View details
psbI-trnS-GCU LSC 114 0.0351 1.00 66.9 yes View details
trnR-ACG-trnN-GUU IRb 584 0.0126 1.00 66.4 yes View details
trnN-GUU-trnR-ACG IRa 584 0.0126 1.00 66.4 yes View details
trnH-GUG-rpl2 IRb 43 0.0310 1.00 65.1 yes View details
rpl2-trnH-GUG IRa 43 0.0310 1.00 65.1 yes View details
psbM-trnD-GUC LSC 1126 0.0084 0.99 64.9 yes View details
ndhC-trnV-UAC LSC 691 0.0145 1.00 64.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCTTCCTTTTGTATGGGTTGA TCATATATACACTTCATATTGATCC 2981–2994 1.000 41.5
trnK-UUU_p2 trnK-UUU TTCTTCCTTTTGTATGGGTTGA TCATATATACACTTCATATTGATCC 2982–2995 1.000 41.5
trnK-UUU_p3 trnK-UUU TCTTCCTTTTGTATGGGTTGA GATCATATATACACTTCATATTGATCC 2983–2996 1.000 41.5
trnK-UUU_p4 trnK-UUU TCTTCCTTTTGTATGGGTTGA ATCATATATACACTTCATATTGATCC 2982–2995 1.000 41.5
trnK-UUU_p5 trnK-UUU TTTCTTCCTTTTGTATGGGTTGA TCATATATACACTTCATATTGATCC 2983–2986 0.667 27.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GACCAAATCAAAATGGGGCG 1087–1144 1.000 85.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 1026–1083 1.000 84.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CAAGTGGTAAGGCAATGGGT 1063–1120 1.000 84.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACCAAATCAAAATGGGGCG 1064–1121 1.000 84.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GACCAAATCAAAATGGGGCG 1085–1142 1.000 84.5
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 227 1.000 81.5
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 228 1.000 81.5
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 228 1.000 81.5
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 229 1.000 81.5
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GGGTTCGAATCCCTCTCTCT 177 1.000 80.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 883–954 1.000 75.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 882–953 1.000 75.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 883–954 1.000 75.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 882–953 1.000 75.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACGAATCGCACTTTTACCAC 884–955 1.000 73.3
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 917–925 1.000 81.0
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 866–874 1.000 81.0
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 845–853 1.000 80.6
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 865–873 1.000 80.4
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 844–852 1.000 80.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAAGACGGCGGGTA AGTATCGACAGACCTAGCCC 1718–1719 1.000 81.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAAGACGGCGGGTA GTATCGACAGACCTAGCCCT 1717–1718 1.000 81.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT AGTATCGACAGACCTAGCCC 2160–2161 1.000 80.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT GTATCGACAGACCTAGCCCT 2159–2160 1.000 80.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCAAATTAAGACGGCGGGTA GCCCTACGGGTTCTCAAAAT 1740–1741 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Oreorchis angustata MN990443.1 158654 View on NCBI ↗
Oreorchis foliosa MN990441.1 158496 View on NCBI ↗
Oreorchis patens NC_046804.1 158542 View on NCBI ↗