Markers + reference

Corybas

5 species · Orchidaceae · Asparagales

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Species 5
Genome length 131–135 kb
Candidate markers 253
Primer pairs 100

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 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
MFP44_pgt003-MFP44_pgt004 LSC 436 0.0612 0.58 64.4 yes View details
atpH LSC 246 0.0138 1.00 40.1 yes View details
rpoB-MFP44_pgt006 LSC 823 0.0645 0.96 84.7 yes View details
MFP44_pgt010-psbD LSC 773 0.0429 0.92 74.3 yes View details
MFP44_pgt015-MFP44_pgt016 LSC 689 0.0479 0.97 87.3 yes View details
accD-psaI LSC 510 0.0423 0.97 77.4 yes View details
petA-psbJ LSC 731 0.0540 0.95 83.0 yes View details
rps15-psaC IRb 967 0.0395 0.98 88.5 yes View details
rpl32-psaC IRa 436 0.1606 0.93 68.7 yes View details
psaC-rps15 IRa 967 0.0395 0.98 88.5 yes View details
MFP44_pgt020-MFP44_pgt021 LSC 122 0.0557 1.00 83.7 yes View details
rps16-MFP44_pgt002 LSC 331 0.0585 1.00 83.5 yes View details
matK-MFP44_pgt001 LSC 912 0.0447 1.00 83.1 yes View details
clpP-psbB LSC 503 0.0447 1.00 83.0 yes View details
MFP44_pgt021-psaJ LSC 290 0.0481 0.99 82.9 yes View details
MFP44_pgt017-MFP44_pgt018 LSC 694 0.0430 0.98 82.7 yes View details
atpH-atpI LSC 393 0.0656 0.99 80.9 yes View details
ycf4-cemA LSC 357 0.0503 1.00 79.8 yes View details
MFP44_pgt001-rps16 LSC 427 0.0511 0.98 79.3 yes View details
ycf3-MFP44_pgt014 LSC 252 0.0484 0.94 78.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-MFP44_pgt001_p1 matK-MFP44_pgt001 TCGCGACGAGAATGGAATTT ATCCGGGTTGCTAACTCAAC 1216–1282 1.000 89.7
matK-MFP44_pgt001_p2 matK-MFP44_pgt001 TCGCGACGAGAATGGAATTT AACGGTAGAGTACTCGGCTT 1199–1265 1.000 89.3
matK-MFP44_pgt001_p3 matK-MFP44_pgt001 TCGCGACGAGAATGGAATTT ACGGTAGAGTACTCGGCTTT 1198–1264 1.000 89.3
matK-MFP44_pgt001_p4 matK-MFP44_pgt001 TCGCGACGAGAATGGAATTT ATTGACAATGGCGTCTCGAA 1462–1525 0.800 80.5
matK-MFP44_pgt001_p5 matK-MFP44_pgt001 TCGCGACGAGAATGGAATTT TACGTTTCTAGGGGGCATCT 1926–1954 0.800 76.5
MFP44_pgt001-rps16_p1 MFP44_pgt001-rps16 CTTTTCCCACATCAGGCACT GCAAAGACAACGAATTCCGG 1273–1351 1.000 89.8
MFP44_pgt001-rps16_p2 MFP44_pgt001-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 908–987 1.000 89.0
MFP44_pgt001-rps16_p3 MFP44_pgt001-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 907–986 1.000 89.0
MFP44_pgt001-rps16_p4 MFP44_pgt001-rps16 CTTTTCCCACATCAGGCACT CGCAAAGCAAAGACAACGAA 1279–1357 1.000 88.6
MFP44_pgt001-rps16_p5 MFP44_pgt001-rps16 CTTTTCCCACATCAGGCACT TACGTTTCTAGGGGGCATCT 1070–1076 0.800 77.0
rps16-MFP44_pgt002_p1 rps16-MFP44_pgt002 ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 427–763 1.000 88.0
rps16-MFP44_pgt002_p2 rps16-MFP44_pgt002 AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 404–740 1.000 87.6
rps16-MFP44_pgt002_p3 rps16-MFP44_pgt002 CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 425–761 1.000 87.3
rps16-MFP44_pgt002_p4 rps16-MFP44_pgt002 TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 415–751 1.000 87.0
rps16-MFP44_pgt002_p5 rps16-MFP44_pgt002 ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 431–767 1.000 86.9
MFP44_pgt003-MFP44_pgt004_p1 MFP44_pgt003-MFP44_pgt004 CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 310–565 1.000 59.9
MFP44_pgt003-MFP44_pgt004_p2 MFP44_pgt003-MFP44_pgt004 AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 309–564 1.000 59.9
MFP44_pgt003-MFP44_pgt004_p3 MFP44_pgt003-MFP44_pgt004 CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 311–566 1.000 58.8
MFP44_pgt003-MFP44_pgt004_p4 MFP44_pgt003-MFP44_pgt004 AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 310–565 1.000 58.8
MFP44_pgt003-MFP44_pgt004_p5 MFP44_pgt003-MFP44_pgt004 CGGAGAGAGAGGGATTCGAA TACCACTAAACTATACCCGC 363–618 1.000 56.8
atpH_p1 atpH TACACAACTCGCACACACTC AACTTTGGCTGCGGCTTATA 1053–1218 1.000 89.6
atpH_p2 atpH TCTAAAGAAAGTGCAGCCGG AACTTTGGCTGCGGCTTATA 1096–1261 1.000 89.0
atpH_p3 atpH TCGAGATTGTGCACCCTTTT AACTTTGGCTGCGGCTTATA 1149–1315 1.000 88.3
atpH_p4 atpH TTGTGCACCCTTTTCCCTAG AACTTTGGCTGCGGCTTATA 1143–1309 1.000 88.2
atpH_p5 atpH AGTCCTTCCCGGAGTATTGT AACTTTGGCTGCGGCTTATA 827–831 0.800 71.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT AACTTTGGCTGCGGCTTATA 472–477 1.000 90.7
atpH-atpI_p2 atpH-atpI CCTCTGCTTCTGGTTGTCTC AACTTTGGCTGCGGCTTATA 579–584 1.000 89.7
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT GTCAGGCGCTCTTTTACCTT 838–843 1.000 87.5
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT GGGCCTTGGGTTCCATTTAT 894–899 1.000 87.3
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT ATCCACAAACCATTCCGACC 989–994 1.000 86.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Corybas diemenicus NC_060526.1 133425 View on NCBI ↗
Corybas dienemus NC_060525.1 134859 View on NCBI ↗
Corybas macranthus NC_060530.1 134625 View on NCBI ↗
Corybas taliensis NC_046022.1 131393 View on NCBI ↗
Corybas vitreus NC_060498.1 134734 View on NCBI ↗