Markers + reference

Corallorhiza

13 species · Orchidaceae · Asparagales

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Species 13
Genome length 124–152 kb
Candidate markers 238
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 238 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 956 0.0679 0.99 84.6 yes View details
atpB-rbcL LSC 902 0.0581 0.81 76.7 yes View details
ycf1-rpl32 SSC 446 0.1662 0.96 76.4 yes View details
rpl32-trnL-UAG SSC 636 0.0506 0.97 81.0 yes View details
ndhA SSC 449 0.1917 0.81 70.3 yes View details
clpP-psbB LSC 576 0.0480 1.00 84.7 yes View details
psbM-trnD-GUC LSC 1085 0.0508 0.99 83.0 yes View details
trnS-GCU-trnG-UCC LSC 760 0.0556 0.95 82.3 yes View details
trnG-UCC-trnR-UCU LSC 145 0.0884 1.00 80.8 yes View details
ndhC-trnV-UAC LSC 592 0.0497 0.97 80.0 yes View details
trnT-UGU-trnL-UAA LSC 590 0.0511 0.91 79.6 yes View details
matK-trnK-UUU LSC 1025 0.0418 0.93 79.5 yes View details
accD-psaI LSC 537 0.0486 0.99 78.4 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU AGAATTCTTGTGCCCCCAAG TCGATCCCGAAGAGAAGGAA 1888–2093 0.692 78.0
matK-trnK-UUU_p2 matK-trnK-UUU GAATTCTTGTGCCCCCAAGA TCGATCCCGAAGAGAAGGAA 1887–2092 0.692 78.0
matK-trnK-UUU_p3 matK-trnK-UUU AGAATTCTTGTGCCCCCAAG ACGGTAGAGTACTCGGCTTT 1258–1373 0.692 77.8
matK-trnK-UUU_p4 matK-trnK-UUU AGAATTCTTGTGCCCCCAAG ATCCGGGTTGCTAACTCAAC 1276–1391 0.462 67.1
matK-trnK-UUU_p5 matK-trnK-UUU GAATTCTTGTGCCCCCAAGA ATCCGGGTTGCTAACTCAAC 1275–1390 0.462 67.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CTACGTCGAGACAAGAGCAC GACCAAATCAAAATGGGGCG 1041–1250 1.000 91.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CTACGTCGAGACAAGAGCAC GAGGTTCGAATCCTTCCGTC 980–1189 1.000 90.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CTACGTCGAGACAAGAGCAC CAAGTGGTAAGGCAATGGGT 1017–1226 1.000 90.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCGGTTCCTAGCAGAACAAA GACCAAATCAAAATGGGGCG 1061–1216 0.462 67.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGATCCGGTTCCTAGCAGAA GACCAAATCAAAATGGGGCG 1160–1220 0.385 61.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 815–856 1.000 59.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 814–855 1.000 59.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 816–857 1.000 58.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 815–856 1.000 58.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTTACCACTAAACTATACCCGC 817–858 1.000 57.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 225–237 1.000 73.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 228–240 1.000 73.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 231–243 1.000 72.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 234–246 1.000 72.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCAACGTCGACTATAACCCC AGAAGACCTCTGTCCTATCCA 246–258 1.000 71.8
psbM-trnD-GUC_p1 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT AGTTCAATCGGTCAGAGCAC 980–1231 0.462 64.3
psbM-trnD-GUC_p2 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT AGTTCAATCGGTCAGAGCAC 1032–1283 0.462 64.2
psbM-trnD-GUC_p3 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT AAACAGAAATCCCGGATCCG 1496–1541 0.385 55.8
psbM-trnD-GUC_p4 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT AAACAGAAATCCCGGATCCG 1444–1489 0.385 55.8
psbM-trnD-GUC_p5 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA AAACAGAAATCCCGGATCCG 1443–1488 0.385 54.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG GAGTCTCTGCACCTATCCCT 802–871 1.000 90.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AGAAAAAGAGCCGGCTATCG GCTTCCATTGAGTCTCTGCA 811–880 1.000 90.7
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA TAAAACCTGGCCTGTTGACC GAGTCTCTGCACCTATCCCT 1379–1448 0.923 88.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA TAAAACCTGGCCTGTTGACC GCTTCCATTGAGTCTCTGCA 1388–1457 0.923 88.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TAAAACCTGGCCTGTTGACC CCGTAGCGTCTACCAATTCC 1261–1262 0.308 54.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Corallorhiza bentleyi NC_040979.1 124482 View on NCBI ↗
Corallorhiza bulbosa NC_025659.1 148643 View on NCBI ↗
Corallorhiza cf. striata 'CA' NC_040982.1 137068 View on NCBI ↗
Corallorhiza macrantha NC_025660.1 151031 View on NCBI ↗
Corallorhiza maculata var. mexicana KM390015.1 151506 View on NCBI ↗
Corallorhiza maculata var. occidentalis KM390016.1 146595 View on NCBI ↗
Corallorhiza mertensiana NC_025661.1 147941 View on NCBI ↗
Corallorhiza odontorhiza NC_025664.1 147317 View on NCBI ↗
Corallorhiza striata var. involuta NC_040981.1 124433 View on NCBI ↗
Corallorhiza striata var. striata NC_040978.1 141202 View on NCBI ↗
Corallorhiza striata var. vreelandii JX087681.1 137505 View on NCBI ↗
Corallorhiza trifida NC_025662.1 149384 View on NCBI ↗
Corallorhiza wisteriana NC_025663.1 146437 View on NCBI ↗