Markers + reference

Geodorum

3 species · Orchidaceae · Asparagales

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Species 3
Genome length 149–150 kb
Candidate markers 247
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 10 remaining regions by MarkerSeek score (out of 247 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 995 0.0080 1.00 58.1 yes View details
trnS-GCU-trnG-GCC LSC 566 0.0130 1.00 60.5 yes View details
trnE-UUC-trnT-GGU LSC 1215 0.0055 1.00 58.5 yes View details
trnF-GAA-trnV-UAC LSC 2882 0.0032 1.00 34.4 yes View details
rbcL-accD LSC 838 0.0080 1.00 51.3 yes View details
psaJ-rpl33 LSC 594 0.0056 1.00 48.7 yes View details
clpP-psbB LSC 685 0.0088 1.00 57.8 yes View details
rpoA LSC 1020 0.0026 1.00 41.8 yes View details
trnN-GUU-rpl32 IRb 479 0.0097 1.00 57.8 yes View details
ccsA-psaC SSC 1897 0.0067 1.00 49.1 yes View details
ycf1 SSC 4473 0.0033 1.00 55.6 yes View details
trnL-UAG-ccsA SSC 140 0.0238 1.00 67.7 yes View details
psbB-psbT LSC 570 0.0058 1.00 65.1 yes View details
ycf4-cemA LSC 756 0.0044 1.00 63.2 yes View details
atpB-rbcL LSC 985 0.0020 1.00 62.8 yes View details
psbM-trnD-GUC LSC 1112 0.0054 1.00 62.2 yes View details
accD LSC 1449 0.0018 1.00 60.1 yes View details
trnR-UCU-atpA LSC 142 0.0094 1.00 59.3 yes View details
psaC-rps15 SSC 3082 0.0035 1.00 58.9 yes View details
rps19-psbA IRa 290 0.0207 1.00 57.5 no View details
trnT-UGU-trnL-UAA LSC 617 0.0032 1.00 57.3 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GACCAAATCAAAATGGGGCG 1130–1143 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GACCAAATCAAAATGGGGCG 1141–1154 1.000 79.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CAAATCAAAATGGGGCGTGG 1127–1140 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CCAAATCAAAATGGGGCGTG 1128–1141 1.000 77.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CAAATCAAAATGGGGCGTGG 1138–1151 1.000 77.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 635 1.000 53.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 634 1.000 53.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GGGATTTGAACCCTCGGTAC ACGAATCACACTTTTACCACT 678 1.000 52.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 637 1.000 52.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TCTCAAGTGATCAGAGGGGG ACGAATCACACTTTTACCACT 709 1.000 51.9
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAAGAGCGTCCATTGTCT CCGAAGAAGCTGAAACCCTT 298 1.000 71.4
trnR-UCU-atpA_p2 trnR-UCU-atpA ATGAAGAGCGTCCATTGTCT TCACCGAAGAAGCTGAAACC 301 1.000 71.3
trnR-UCU-atpA_p3 trnR-UCU-atpA AGGAATGAAGAGCGTCCATT CCGAAGAAGCTGAAACCCTT 302 1.000 71.3
trnR-UCU-atpA_p4 trnR-UCU-atpA AGGAATGAAGAGCGTCCATT TCACCGAAGAAGCTGAAACC 305 1.000 71.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAGAGCGTCCATTG CCGAAGAAGCTGAAACCCTT 301 1.000 71.0
psbM-trnD-GUC_p1 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT CCATGCATATGGCTGGGATT 1296 1.000 78.0
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT CCATGCATATGGCTGGGATT 1244 1.000 78.0
psbM-trnD-GUC_p3 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT AGTTCAATCGGTCAGAGCAC 1274 1.000 77.8
psbM-trnD-GUC_p4 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT AGTTCAATCGGTCAGAGCAC 1222 1.000 77.8
psbM-trnD-GUC_p5 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA CCATGCATATGGCTGGGATT 1243 1.000 77.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1305–1345 1.000 80.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 1284–1324 1.000 79.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 1281–1321 1.000 79.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1283–1323 1.000 79.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 1302–1342 1.000 79.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG ACCAATTTCGCCATATCCCC 718 1.000 79.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG TAGCGTCTACCAATTTCGCC 726 1.000 79.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 667 1.000 79.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 675 1.000 78.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 699 1.000 78.5

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
Geodorum attenuatum NC_072631.1 149350 View on NCBI ↗
Geodorum densiflorum NC_072632.1 149534 View on NCBI ↗
Geodorum recurvum NC_072527.1 149434 View on NCBI ↗