Markers + reference

Collabium

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 158–158 kb
Candidate markers 279
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2226 0.4655 0.91 81.1 yes View details
rpl32-trnL-UAG SSC 693 0.4724 0.92 82.7 yes View details
ndhD SSC 1509 0.4623 0.84 80.4 yes View details
nad6 SSC 531 0.4706 0.83 78.8 yes View details
ndhI SSC 504 0.4768 0.94 81.3 yes View details
ndhA SSC 2232 0.4656 0.83 78.7 yes View details
ndhH SSC 1182 0.4655 0.83 80.6 yes View details
ycf1 SSC 5349 0.3433 0.80 73.2 yes View details
psbC-trnS-UGA LSC 145 0.0483 1.00 80.3 yes View details
ndhF-rpl32 SSC 1027 0.4205 0.81 79.8 yes View details
ccsA SSC 969 0.4573 0.80 79.3 yes View details
psaC-ndhE SSC 560 0.3931 0.83 79.3 yes View details
trnL-UAG SSC 80 0.5921 0.95 77.3 yes View details
nad6-ndhI SSC 226 0.4813 0.95 77.3 yes View details
ccsA-ndhD SSC 266 0.4677 0.93 76.8 yes View details
ndhI-ndhA SSC 120 0.3932 0.97 75.0 yes View details
rpl32 SSC 174 0.4059 0.98 74.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 267 1.000 80.6
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC ATAGCCCCGGTCTTGAAAAC 247 1.000 80.0
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCGGGGTTTGAAAAAGGAA GAGAGATGGCTGAGTGGTTG 304 1.000 79.9
psbC-trnS-UGA_p4 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GAGAGATGGCTGAGTGGTTG 259 1.000 79.8
psbC-trnS-UGA_p5 psbC-trnS-UGA TTGTGGGACATTTGTGGCAT GAGAGATGGCTGAGTGGTTG 347 1.000 79.2
ndhF_p1 ndhF ACAGGAACAAGAGGGATCCA TGACCAACCTATTGCAACTCT 2621 0.500 45.3
ndhF_p2 ndhF AAGAGGGATCCACCGAAGAA TGACCAACCTATTGCAACTCT 2613 0.500 45.3
ndhF_p3 ndhF AGAGGGATCCACCGAAGAAA TGACCAACCTATTGCAACTCT 2612 0.500 45.3
ndhF_p4 ndhF CAAGTTCCACGTTAGCCAGA TGACCAACCTATTGCAACTCT 2976 0.500 44.4
ndhF_p5 ndhF CACTTGAAAGAGGCACGCTA TGACCAACCTATTGCAACTCT 2459 0.500 44.1
ndhF-rpl32_p1 ndhF-rpl32 ACAGATTGGCCGAAAACCAT ACCCATTTGAGACCCAACAC 1785 0.500 59.3
ndhF-rpl32_p2 ndhF-rpl32 AGCAACTGCACCGACAAATA ACCCATTTGAGACCCAACAC 2327 0.500 59.1
ndhF-rpl32_p3 ndhF-rpl32 ATTTAGCAACTGCACCGACA ACCCATTTGAGACCCAACAC 2331 0.500 59.1
ndhF-rpl32_p4 ndhF-rpl32 TAGCAACTGCACCGACAAAT ACCCATTTGAGACCCAACAC 2328 0.500 59.1
ndhF-rpl32_p5 ndhF-rpl32 ACAGATTGGCCGAAAACCAT CTTTTTGACTGTCCGGTGGA 1336 0.500 59.1
rpl32_p1 rpl32 ACAACGATAAAAAGGAGTCACC ACCCATTTGAGACCCAACAC 615 0.500 33.1
rpl32_p2 rpl32 ACAACGATAAAAAGGAGTCACC CATGGCGGCTTACCCTAAAT 908 0.500 33.0
rpl32_p3 rpl32 ACAACGATAAAAAGGAGTCACC TCCTAAGAGCAGCGTGTCTA 938 0.500 32.2
rpl32_p4 rpl32 ACAACGATAAAAAGGAGTCACC AATTTCACCATGGCGGCTTA 916 0.500 31.9
rpl32_p5 rpl32 ACAACGATAAAAAGGAGTCACC TTCGTTCTCAGTCGGGGTAT 666 0.500 31.9
rpl32-trnL-UAG_p1 rpl32-trnL-UAG TCCACCGGACAGTCAAAAAG ATCCGCATAAAAGAGCTGCA 1424 0.500 59.4
rpl32-trnL-UAG_p2 rpl32-trnL-UAG TCCACCGGACAGTCAAAAAG TCCGCATAAAAGAGCTGCAT 1423 0.500 59.4
rpl32-trnL-UAG_p3 rpl32-trnL-UAG TCCACCGGACAGTCAAAAAG TGGCGAAACCTTGGGTAAAA 1304 0.500 59.1
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TCCACCGGACAGTCAAAAAG TCCTAAGAGCAGCGTGTCTA 792 0.500 58.7
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TCCACCGGACAGTCAAAAAG AGCAGCGTGTCTACCAATTT 785 0.500 58.2
trnL-UAG_p1 trnL-UAG GTGTTGGGTCTCAAATGGGT ATCCGCATAAAAGAGCTGCA 975 0.500 59.6
trnL-UAG_p2 trnL-UAG GTGTTGGGTCTCAAATGGGT TCCGCATAAAAGAGCTGCAT 974 0.500 59.6
trnL-UAG_p3 trnL-UAG GTGTTGGGTCTCAAATGGGT TGGCGAAACCTTGGGTAAAA 855 0.500 59.4
trnL-UAG_p4 trnL-UAG ATACCCCGACTGAGAACGAA ATCCGCATAAAAGAGCTGCA 924 0.500 58.4
trnL-UAG_p5 trnL-UAG ATACCCCGACTGAGAACGAA TCCGCATAAAAGAGCTGCAT 923 0.500 58.4

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
Collabium chinense NC_084155.1 157758 View on NCBI ↗
Collabium formosanum NC_065862.1 157687 View on NCBI ↗