Markers + reference

Erythrodes

2 species · Orchidaceae · Asparagales

Back to catalogue

Species 2
Genome length 155–155 kb
Candidate markers 275
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 457 0.0153 1.00 53.8 yes View details
atpF LSC 1357 0.0089 1.00 49.2 yes View details
atpF-atpH LSC 523 0.0189 0.81 61.2 yes View details
trnE-UUC-trnT-GGU LSC 416 0.0145 1.00 58.9 yes View details
trnT-UGU-trnL-UAA LSC 993 0.0262 1.00 69.9 yes View details
accD-psaI LSC 798 0.0113 0.99 65.9 yes View details
ycf4-cemA LSC 723 0.0153 1.00 54.8 yes View details
rpl20 LSC 384 0.0078 1.00 51.5 yes View details
ycf1 IRb 1070 0.0019 1.00 59.8 no View details
ndhF-rpl32 SSC 796 0.0176 1.00 62.3 yes View details
rpl32-trnL-UAG SSC 878 0.0139 0.99 55.9 yes View details
psaC-ndhE SSC 324 0.0216 1.00 52.2 yes View details
ycf1 SSC 5463 0.0099 1.00 50.1 yes View details
ndhJ-ndhK LSC 125 0.0320 1.00 70.9 yes View details
clpP-psbB LSC 652 0.0156 0.98 69.5 yes View details
atpH-atpI LSC 534 0.0079 0.94 66.6 yes View details
ndhC-trnV-UAC LSC 585 0.0157 0.98 66.0 yes View details
psaA-ycf3 LSC 638 0.0096 0.98 65.7 yes View details
ndhH-rps15 SSC 149 0.0365 0.92 65.0 yes View details
trnK-UUU-rps16 LSC 686 0.0073 0.99 63.5 yes View details
petN-psbM LSC 594 0.0051 0.98 63.4 yes View details
trnF-GAA-ndhJ LSC 556 0.0055 0.98 62.9 yes View details
rpoB-trnC-GCA LSC 1178 0.0051 1.00 61.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAGGGCGCTCAAC 796–798 1.000 67.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAGGGCGCTCAAC 795–797 1.000 67.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT CTTGAAAAGGGCGCTCAAC 881–883 1.000 66.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC CTTGAAAAGGGCGCTCAAC 782–784 1.000 65.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CTTGAAAAGGGCGCTCAAC 807–809 1.000 64.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACTACTGTGTAGACGAAGAGT 522–541 1.000 52.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACTACTGTGTAGACGAAGAGTT 522–541 1.000 50.9
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACTACTGTGTAGACGAAGAGT 519–538 1.000 50.8
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACTACTGTGTAGACGAAGAGT 520–539 1.000 50.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACTACTGTGTAGACGAAGAGT 521–540 1.000 50.8
atpF_p1 atpF CACTTGAAGTACGGTACCGG ATTTATGGACTGGTCGTGGC 2016–2111 1.000 84.4
atpF_p2 atpF CCACTTGAAGTACGGTACCG ATTTATGGACTGGTCGTGGC 2017–2112 1.000 84.4
atpF_p3 atpF CACTTGAAGTACGGTACCGG TGACACGAGACCTCAGAACT 1752–1757 1.000 80.6
atpF_p4 atpF CCACTTGAAGTACGGTACCG TGACACGAGACCTCAGAACT 1753–1758 1.000 80.6
atpF_p5 atpF CCCCTCCTTCCTGGAAAGTA TGACACGAGACCTCAGAACT 2299–2304 1.000 80.3
atpF-atpH_p1 atpF-atpH AAAACTCCCAACGGATGACC ATTTATGGACTGGTCGTGGC 537–637 1.000 84.0
atpF-atpH_p2 atpF-atpH AAAACTCCCAACGGATGACC GGTCGTGGCATTAGCTCTTT 526–626 1.000 82.3
atpF-atpH_p3 atpF-atpH AACTCAAAACTCCCAACGGA ATTTATGGACTGGTCGTGGC 542–642 1.000 79.0
atpF-atpH_p4 atpF-atpH CAACTCAAAACTCCCAACGG ATTTATGGACTGGTCGTGGC 543–643 1.000 78.6
atpF-atpH_p5 atpF-atpH TCAAAACTCCCAACGGATGA ATTTATGGACTGGTCGTGGC 539–639 1.000 77.3
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 603–631 1.000 82.2
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 602–630 1.000 81.7
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG AACTTTGGCTGCGGCTTATA 597–625 1.000 81.4
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA GGCTGCGGCTTATATAGGTG 597–625 1.000 81.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC GGCTGCGGCTTATATAGGTG 596–624 1.000 80.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA TAAAGGATTTGCAGTCCCCC 1318 1.000 75.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA CGACACCCAGATTCGAACTG 1342 1.000 74.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA TTTGTTGATCAGGCGACACC 1355 1.000 73.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCC TAAAGGATTTGCAGTCCCCC 1327 1.000 72.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA ATAAAGGATTTGCAGTCCCCC 1319 1.000 71.7

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
Erythrodes blumei MW589509.1 154866 View on NCBI ↗
Erythrodes hirsuta MW589510.1 155066 View on NCBI ↗