Markers + reference

Cyclopogon

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 154–155 kb
Candidate markers 276
Primer pairs 130

Genome-wide nucleotide diversity

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

Candidate markers

17 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 549 0.0358 0.97 67.6 yes View details
rpoB-trnC-GCA LSC 1114 0.0257 0.98 60.9 yes View details
trnE-UUC-trnT-GGU LSC 309 0.0404 0.96 71.5 yes View details
trnT-GGU-psbD LSC 997 0.0271 1.00 61.0 yes View details
trnT-UGU-trnL-UAA LSC 863 0.0362 0.93 79.4 yes View details
trnF-GAA-ndhJ LSC 637 0.0349 0.99 67.1 yes View details
rbcL-accD LSC 792 0.0307 0.99 67.9 yes View details
accD-psaI LSC 660 0.0413 0.95 79.1 yes View details
trnP-UGG-psaJ LSC 368 0.0485 0.90 78.7 yes View details
rpl20-rps12 LSC 798 0.0251 1.00 59.0 yes View details
clpP-psbB LSC 729 0.0533 0.85 85.3 yes View details
infA LSC 234 0.0000 1.00 19.2 yes View details
rpl16 LSC 1381 0.0234 0.99 61.6 yes View details
ycf1 IRb 1074 0.0093 1.00 53.3 no View details
ndhF-rpl32 SSC 685 0.0353 0.91 69.5 yes View details
rpl32-trnL-UAG SSC 774 0.0330 0.98 73.4 yes View details
ycf1 SSC 5613 0.0223 0.99 52.9 yes View details
rrn4.5S-rrn5S IRb 209 0.0478 1.00 77.8 yes View details
rrn5S-rrn4.5S IRa 209 0.0478 1.00 77.8 yes View details
trnK-UUU-rps16 LSC 611 0.0287 0.97 76.2 yes View details
petD-rpoA LSC 406 0.0335 0.96 73.7 yes View details
rps11-rpl36 LSC 167 0.0838 1.00 73.7 yes View details
petG-trnW-CCA LSC 121 0.0579 1.00 73.0 yes View details
psbK-psbI LSC 526 0.0296 0.90 72.8 yes View details
psaA-ycf3 LSC 651 0.0262 1.00 72.1 yes View details
infA-rps8 LSC 114 0.0526 1.00 71.9 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 130 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGAACTTTTTACTTTGGTATAGATTGA CAGTTTTTCAGTGCAATTACCT 2973–2992 1.000 42.3
trnK-UUU_p2 trnK-UUU TGAACTTTTTACTTTGGTATAGATTG CAGTTTTTCAGTGCAATTACCT 2973–2992 1.000 42.3
trnK-UUU_p3 trnK-UUU TTGAACTTTTTACTTTGGTATAGA CAGTTTTTCAGTGCAATTACCT 2974–2993 1.000 42.3
trnK-UUU_p4 trnK-UUU TGAACTTTTTACTTTGGTATAGATTGA CAGTTTTTCAGTGCAATTACCTT 2973–2992 1.000 42.3
trnK-UUU_p5 trnK-UUU ACTTTTTACTTTGGTATAGATTGA CAGTTTTTCAGTGCAATTACCT 2970–2989 1.000 42.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGGCGCTCAACCTAC 752–804 1.000 73.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGGCGCTCAACCTAC 751–803 1.000 73.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAAAAGGGCGCTCAACCTAC 753–805 1.000 72.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAAAAGGGCGCTCAACCTAC 752–804 1.000 72.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT AAAAGGGCGCTCAACCTAC 837–889 1.000 72.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCGGGATCATTAGATA 594–646 1.000 84.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCGGGATCATTAGAT 595–647 1.000 84.8
psbK-psbI_p3 psbK-psbI GCCAAATTACCCGAGGCTTA ACGCCCGGGATCATTAGATA 681–733 1.000 84.7
psbK-psbI_p4 psbK-psbI GCCAAATTACCCGAGGCTTA TACGCCCGGGATCATTAGAT 682–734 1.000 84.7
psbK-psbI_p5 psbK-psbI GCCAAATTACCCGAGGCTTA TTACGCCCGGGATCATTAGA 683–735 1.000 82.9
atpH-atpI_p1 atpH-atpI TCCAGCAGCAATAACGGAAG ATGGAGGGTCATCATTGA 604–609 1.000 44.9
atpH-atpI_p2 atpH-atpI AATCCAGCAGCAATAACGGA ATGGAGGGTCATCATTGA 606–611 1.000 44.9
atpH-atpI_p3 atpH-atpI ATCCAGCAGCAATAACGGAA ATGGAGGGTCATCATTGA 605–610 1.000 44.9
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA ATGGAGGGTCATCATTGA 610–615 1.000 44.8
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC ATGGAGGGTCATCATTGA 609–614 1.000 44.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA ACAGACCTAGTTCCTTGCCT 1556–1567 1.000 82.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA TACTCAGAGCCTCTCGTGAG 2000–2043 1.000 82.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA TGAGTACTCAGAGCCTCTCG 2004–2047 1.000 82.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA GAGTACTCAGAGCCTCTCGT 2003–2046 1.000 82.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT TACTCAGAGCCTCTCGTGAG 2439–2482 1.000 81.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 413–502 1.000 82.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 378–467 1.000 82.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 391–480 1.000 82.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CCTTTCGTGATCCACTACCC GAACCGATGACTTACGCCTT 452–541 1.000 81.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CTTTCGTGATCCACTACCCC GAACCGATGACTTACGCCTT 451–540 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
Cyclopogon comosus MW589506.1 154678 View on NCBI ↗
Cyclopogon longibracteatus NC_047205.1 154495 View on NCBI ↗