Markers + reference

Oncidium

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 146–148 kb
Candidate markers 259
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbM-trnD-GUC LSC 1136 0.0132 1.00 55.1 yes View details
trnE-UUC-trnT-GGU LSC 1023 0.0559 0.98 86.5 yes View details
trnF-GAA-ndhJ LSC 602 0.0183 1.00 61.0 yes View details
accD-psaI LSC 447 0.0771 0.99 73.9 yes View details
psbE-petL LSC 885 0.0910 0.96 96.4 yes View details
rpl20-rps12 LSC 636 0.0206 0.99 60.0 yes View details
rpl14 LSC 369 0.0217 1.00 52.1 yes View details
rps15-trnN-GUU SSC 6049 0.0068 1.00 56.4 yes View details
ndhJ-ndhC LSC 101 0.0891 1.00 80.6 yes View details
trnA-UGC IRb 55 0.0370 0.98 75.5 yes View details
rpl14-rpl16 LSC 120 0.0917 1.00 71.7 yes View details
atpA-atpF LSC 72 0.0278 1.00 68.5 yes View details
trnT-GGU-psbD LSC 938 0.0096 1.00 61.4 yes View details
rpoA LSC 1020 0.0029 1.00 60.4 yes View details
rps12-clpP LSC 126 0.0397 1.00 60.3 yes View details
petB LSC 1358 0.0022 1.00 60.0 yes View details
trnA-UGC IRa 38 0.0263 1.00 52.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpA-atpF_p1 atpA-atpF CACTTGAAGTACGGTACCGG ATTGGTATCCTCAGGTCCGT 216 1.000 79.2
atpA-atpF_p2 atpA-atpF CCACTTGAAGTACGGTACCG ATTGGTATCCTCAGGTCCGT 217 1.000 79.2
atpA-atpF_p3 atpA-atpF CACTTGAAGTACGGTACCGG TATCCTCAGGTCCGTGGAAG 211 1.000 78.9
atpA-atpF_p4 atpA-atpF CCACTTGAAGTACGGTACCG TATCCTCAGGTCCGTGGAAG 212 1.000 78.9
atpA-atpF_p5 atpA-atpF GCCCACTTGAAGTACGGTAC ATTGGTATCCTCAGGTCCGT 219 1.000 77.1
psbM-trnD-GUC_p1 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT CCATGCATATGGCTGGGATT 1268–1295 1.000 78.5
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT AGTTCAATCGGTCAGAGCAC 1246–1273 1.000 78.3
psbM-trnD-GUC_p3 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA CCATGCATATGGCTGGGATT 1267–1294 1.000 77.5
psbM-trnD-GUC_p4 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA AGTTCAATCGGTCAGAGCAC 1245–1272 1.000 77.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGCGCAGTAGCAATAAGAGC CCATGCATATGGCTGGGATT 1262–1289 1.000 77.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1127–1359 1.000 83.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1106–1338 1.000 83.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1103–1335 1.000 83.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1105–1337 1.000 82.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1124–1356 1.000 82.5
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1097–1098 1.000 79.3
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1100–1101 1.000 79.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1087–1088 1.000 78.3
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCTCCGTAACCAATCATCC 1071–1072 1.000 78.2
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1090–1091 1.000 78.1
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CCTATGATGTAGCACCAGGC 709 1.000 79.4
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GCCTATGATGTAGCACCAGG 710 1.000 79.4
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ TATGCTAGGATGATGCACGC CCTATGATGTAGCACCAGGC 774 1.000 79.1
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ TATGCTAGGATGATGCACGC GCCTATGATGTAGCACCAGG 775 1.000 79.1
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CTCCCAGTGTGCCTATGATG 720 1.000 78.8
ndhJ-ndhC_p1 ndhJ-ndhC TATCCCTCGGCAATCAAAGC AAAAGGAGCGTTGGAATGGT 202 1.000 83.3
ndhJ-ndhC_p2 ndhJ-ndhC AAAGTCTCTATCCCTCGGCA AAAAGGAGCGTTGGAATGGT 210 1.000 82.1
ndhJ-ndhC_p3 ndhJ-ndhC AAGTCTCTATCCCTCGGCAA AAAAGGAGCGTTGGAATGGT 209 1.000 82.1
ndhJ-ndhC_p4 ndhJ-ndhC TATCCCTCGGCAATCAAAGC GGTTCAGTTTATGCATGGCG 222 1.000 81.4
ndhJ-ndhC_p5 ndhJ-ndhC TATCCCTCGGCAATCAAAGC CGAAAAGGAGCGTTGGAATG 204 1.000 81.3

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
Oncidium hybrid cultivar NC_014056.1 146484 View on NCBI ↗
Oncidium sphacelatum NC_028148.1 147761 View on NCBI ↗