Markers + reference

Claderia

2 species · Orchidaceae · Asparagales

Back to catalogue

Species 2
Genome length 161–161 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpA LSC 1515 0.0000 1.00 30.8 yes View details
atpH-atpI LSC 734 0.0000 1.00 25.1 yes View details
atpI LSC 744 0.0013 1.00 59.5 yes View details
atpI-rps2 LSC 292 0.0000 1.00 18.8 yes View details
rps2 LSC 720 0.0014 1.00 59.5 yes View details
rpoC2 LSC 4134 0.0000 1.00 35.1 yes View details
atpE LSC 405 0.0049 1.00 57.5 yes View details
infA LSC 234 0.0043 1.00 48.5 yes View details
rpl14 LSC 369 0.0027 1.00 50.4 yes View details
rps19 IRb 279 0.0072 1.00 56.6 yes View details
rps12 IRb 805 0.0025 1.00 60.2 yes View details
trnN-GUU-ndhF IRb 1331 0.0000 1.00 25.1 yes View details
rps12 IRa 805 0.0000 1.00 40.0 no View details
rps19 IRa 279 0.0036 1.00 54.6 no View details
rpl2-rpl23 IRb 24 0.0417 1.00 76.5 yes View details
rpl23-rpl2 IRa 24 0.0417 1.00 76.5 yes View details
rps4 LSC 606 0.0016 1.00 59.7 yes View details
ndhK LSC 774 0.0013 1.00 59.5 yes View details
psbD LSC 1062 0.0009 1.00 59.3 yes View details
psbC LSC 1422 0.0007 1.00 59.2 yes View details
petD LSC 1348 0.0007 1.00 59.2 yes View details
ndhH SSC 1182 0.0008 1.00 59.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AAACCGTGCTTGCAGTTTTC CCGTATCAATGATCTGGTGGA 248–249 1.000 66.0
trnK-UUU_p2 trnK-UUU AAACCGTGCTTGCAGTTTTC TCCGTATCAATGATCTGGTGG 249–250 1.000 66.0
trnK-UUU_p3 trnK-UUU TGCACACGACTTTCCCTATG CCGTATCAATGATCTGGTGGA 226–227 1.000 65.9
trnK-UUU_p4 trnK-UUU TGCACACGACTTTCCCTATG TCCGTATCAATGATCTGGTGG 227–228 1.000 65.9
trnK-UUU_p5 trnK-UUU GCACACGACTTTCCCTATGT CCGTATCAATGATCTGGTGGA 225–226 1.000 65.9
atpA_p1 atpA ACGATCCATTTACATTTATGTTTG TTCCCTTTCCTTCCGAAAAA 1581 1.000 40.0
atpA_p2 atpA ACGATCCATTTACATTTATGTTTG TTTCCCTTTCCTTCCGAAAA 1582 1.000 40.0
atpA_p3 atpA ACGATCCATTTACATTTATGTTTG TTTTCCCTTTCCTTCCGAAA 1583 1.000 40.0
atpA_p4 atpA ACGATCCATTTACATTTATGTTTG TTTTTCCCTTTCCTTCCGAA 1584 1.000 40.0
atpA_p5 atpA ACGATCCATTTACATTTATGTTTG TTTCCCTTTCCTTCCGAAAAA 1582 1.000 40.0
atpH-atpI_p1 atpH-atpI GCCACGACCAGTCCATAAAT CTGCGCCCACGAATGATATA 1308 1.000 79.1
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT CTGCGCCCACGAATGATATA 1216 1.000 78.9
atpH-atpI_p3 atpH-atpI TAAACTCGAAACTCCCAGCG CTGCGCCCACGAATGATATA 1571 1.000 78.8
atpH-atpI_p4 atpH-atpI GCCACGACCAGTCCATAAAT AACTTTGGCTGCGGCTTATA 995 1.000 78.8
atpH-atpI_p5 atpH-atpI ATTGTGCACCCTTTGTTCCT CTGCGCCCACGAATGATATA 1755 1.000 78.7
atpI_p1 atpI CGCATTGCTTGAATTGGGAT AGTTCAATTTCTGTTAGAGGACA 820 1.000 40.1
atpI_p2 atpI CGCATTGCTTGAATTGGGAT GAAGTTCAATTTCTGTTAGAGGACA 822 1.000 40.1
atpI_p3 atpI CGCATTGCTTGAATTGGGAT TGAAGTTCAATTTCTGTTAGAGGAC 823 1.000 40.1
atpI_p4 atpI CGCATTGCTTGAATTGGGAT AAGTTCAATTTCTGTTAGAGGACA 821 1.000 40.1
atpI_p5 atpI CGCATTGCTTGAATTGGGAT AGTTCAATTTCTGTTAGAGGACAA 820 1.000 40.1
atpI-rps2_p1 atpI-rps2 TATATCATTCGTGGGCGCAG AAGCGGGAGTTCATTTTGGT 1371 1.000 79.4
atpI-rps2_p2 atpI-rps2 TATATCATTCGTGGGCGCAG GCAATTTGTGAGGGCCATTC 745 1.000 79.4
atpI-rps2_p3 atpI-rps2 TATATCATTCGTGGGCGCAG ATCAGCAGCAATAAGGGCTC 1160 1.000 79.3
atpI-rps2_p4 atpI-rps2 TATATCATTCGTGGGCGCAG CAGCAATAAGGGCTCGATGT 1155 1.000 79.1
atpI-rps2_p5 atpI-rps2 TATATCATTCGTGGGCGCAG GATGGAAGCGGGAGTTCATT 1376 1.000 79.1
rps2_p1 rps2 ACTCCAAAAGATGCAAACCA ATCCTGGTAGAAGGTTCCGT 914 1.000 60.0
rps2_p2 rps2 ACTCCAAAAGATGCAAACCA TCCTGGTAGAAGGTTCCGTC 913 1.000 58.4
rps2_p3 rps2 AACTCCAAAAGATGCAAACCA ATCCTGGTAGAAGGTTCCGT 915 1.000 58.3
rps2_p4 rps2 ACTCCAAAAGATGCAAACCAA ATCCTGGTAGAAGGTTCCGT 914 1.000 58.3
rps2_p5 rps2 ACTCCAAAAGATGCAAACCAA TCCTGGTAGAAGGTTCCGTC 913 1.000 56.8

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
Claderia leontocampus OQ621597.1 160763 View on NCBI ↗
Claderia viridiflora NC_084191.1 160764 View on NCBI ↗