Markers + reference

Eulophia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 145–149 kb
Candidate markers 263
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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 989 0.0190 0.96 62.0 yes View details
rpoC2 LSC 4092 0.0122 0.99 48.4 yes View details
trnE-UUC-trnT-GGU LSC 1268 0.0177 0.94 71.3 yes View details
trnF-GAA-ndhC LSC 1898 0.0149 0.21 44.1 yes View details
psbB-psbT LSC 600 0.0273 0.55 56.5 yes View details
rpl16 LSC 1524 0.0122 0.97 63.1 yes View details
trnN-GUU-rpl32 IRb 519 0.0168 0.92 62.2 yes View details
ccsA-ndhD SSC 270 0.0502 0.96 73.6 yes View details
psaC-ndhE SSC 643 0.0272 0.92 69.5 yes View details
ndhA SSC 1055 0.0182 0.99 56.7 yes View details
ndhA-rps15 SSC 87 0.0506 0.91 72.9 yes View details
ndhD-psaC SSC 129 0.0543 1.00 70.5 yes View details
trnK-UUU-rps16 LSC 611 0.0136 0.96 69.9 yes View details
trnW-CCA-trnP-UGG LSC 169 0.0373 0.95 69.0 yes View details
petD-rpoA LSC 181 0.0276 1.00 68.4 yes View details
rps8-rpl14 LSC 208 0.0216 0.89 67.8 yes View details
psbK-psbI LSC 435 0.0144 0.96 67.5 yes View details
rps3-rpl22 LSC 43 0.0465 1.00 66.0 yes View details
psbM-trnD-GUC LSC 1047 0.0195 0.98 64.6 yes View details
rps19-psbA IRa 247 0.0340 0.95 64.5 no 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 AGGATCAGTCGCGGTCTTAT GTGCTCAACCCACAGGAAC 763–789 1.000 68.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT TGCTCAACCCACAGGAACT 762–788 1.000 67.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT GTGCTCAACCCACAGGAACT 763–789 1.000 64.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCAATTAAAAGCCGAGT GTGCTCAACCCACAGGAAC 688–714 1.000 63.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCAATTAAAAGCCGAGT TGCTCAACCCACAGGAACT 687–713 1.000 63.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GACCAAATCAAAATGGGGCG 1076–1116 1.000 78.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG CAAATCAAAATGGGGCGTGG 1073–1113 1.000 76.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG CCAAATCAAAATGGGGCGTG 1074–1114 1.000 76.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGGTTTTGGTCCCGTTACTC 1036–1076 1.000 74.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG ACCAAATCAAAATGGGGCGT 1075–1115 1.000 72.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 537–555 1.000 82.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 538–556 1.000 82.5
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 539–557 1.000 80.7
psbK-psbI_p4 psbK-psbI TTATGCCGGTTATCCCCGTA ACGCCCCGGATCATTAGATA 578–596 1.000 80.5
psbK-psbI_p5 psbK-psbI TTATGCCGGTTATCCCCGTA TACGCCCCGGATCATTAGAT 579–597 1.000 80.4
rpoC2_p1 rpoC2 CCTTGCGTTATGTCACCAGA TGTCTATTGAAATACGGATCAC 206 1.000 44.7
rpoC2_p2 rpoC2 AGACCTTGCGTTATGTCACC TGTCTATTGAAATACGGATCAC 209 1.000 44.6
rpoC2_p3 rpoC2 ACCTTGCGTTATGTCACCAG TGTCTATTGAAATACGGATCAC 207 1.000 44.6
rpoC2_p4 rpoC2 GACCTTGCGTTATGTCACCA TGTCTATTGAAATACGGATCAC 208 1.000 44.6
rpoC2_p5 rpoC2 ACTTTTGGAAGACCTTGCGT TGTCTATTGAAATACGGATCAC 218 1.000 44.4
psbM-trnD-GUC_p1 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT CCATGCATATGGCTGGGATT 1228–1231 1.000 80.1
psbM-trnD-GUC_p2 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT AGTTCAATCGGTCAGAGCAC 1206–1209 1.000 80.0
psbM-trnD-GUC_p3 psbM-trnD-GUC GCAGTGGCAATAAGAGCAAG CCATGCATATGGCTGGGATT 1167–1170 1.000 77.8
psbM-trnD-GUC_p4 psbM-trnD-GUC GCAGTGGCAATAAGAGCAAG AGTTCAATCGGTCAGAGCAC 1145–1148 1.000 77.7
psbM-trnD-GUC_p5 psbM-trnD-GUC TGGCTGACTGTTTTGACGTA CCATGCATATGGCTGGGATT 1227–1230 1.000 77.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1316–1372 1.000 83.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1295–1351 1.000 83.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1292–1348 1.000 83.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1294–1350 1.000 83.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1313–1369 1.000 82.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Eulophia flava MK855051.1 148903 View on NCBI ↗
Eulophia zollingeri NC_037212.1 145201 View on NCBI ↗