Markers + reference

Dolomiaea

6 species · Asteraceae · Asterales

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Species 6
Genome length 152–153 kb
Candidate markers 271
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 572 0.0030 1.00 46.0 no View details
ndhF SSC 2235 0.2439 0.88 80.1 yes View details
ndhF-rpl32 SSC 1041 0.2267 0.85 80.7 yes View details
ndhD SSC 1530 0.2545 0.86 81.1 yes View details
psaC SSC 246 0.2477 0.85 58.9 yes View details
ndhI SSC 501 0.2652 0.90 67.5 yes View details
ndhA SSC 2153 0.2447 0.86 80.1 yes View details
ndhH SSC 1182 0.2387 0.82 80.0 yes View details
rps15 SSC 279 0.2741 0.89 69.4 yes View details
rps15-ycf1 SSC 414 0.2581 0.88 77.9 yes View details
ycf1 SSC 5214 0.2066 0.86 75.0 yes View details
ycf1 IRa 573 0.0038 0.99 47.0 no View details
rpl32-trnL-UAG SSC 852 0.1964 0.73 77.3 yes View details
ccsA SSC 969 0.1966 0.69 76.1 yes View details
ndhG SSC 531 0.1972 0.72 75.9 yes View details
ndhE-ndhG SSC 220 0.2052 0.78 72.6 yes View details
trnL-UAG-ccsA SSC 141 0.2047 0.83 67.7 yes View details
rpl32 SSC 165 0.2630 0.92 67.2 yes View details
ndhE SSC 303 0.2189 0.78 66.3 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
ndhF_p1 ndhF TCGTTGTGGTCGGACTCTAT GAGGTAAGATCCGGTGAATCG 2799–2832 0.500 50.8
ndhF_p2 ndhF ATCAATTCGGTCGTTGTGGT GAGGTAAGATCCGGTGAATCG 2809–2842 0.500 50.7
ndhF_p3 ndhF TCTCTTCCTTCTCCGAGCTC GAGGTAAGATCCGGTGAATCG 2741–2774 0.500 50.2
ndhF_p4 ndhF TCGTTGTGGTCGGACTCTAT ACGATTTTGAAAGGCCTCAGA 2889–2922 0.500 49.8
ndhF_p5 ndhF ATCAATTCGGTCGTTGTGGT ACGATTTTGAAAGGCCTCAGA 2899–2932 0.500 49.7
ndhF-rpl32_p1 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG CACCACCACAATGTGAGTGA 1540–1547 0.500 60.4
ndhF-rpl32_p2 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA CACCACCACAATGTGAGTGA 1538–1545 0.500 60.3
ndhF-rpl32_p3 ndhF-rpl32 TTGCCGTCGGAAAAAGAAGA CACCACCACAATGTGAGTGA 1539–1546 0.500 60.3
ndhF-rpl32_p4 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG AATAAGACTCCCCACCACCA 1552–1559 0.500 60.3
ndhF-rpl32_p5 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA AATAAGACTCCCCACCACCA 1550–1557 0.500 60.2
rpl32_p1 rpl32 AGGTGTATTCTTTCCTCGAGT CACCACCACAATGTGAGTGA 852–858 0.500 37.9
rpl32_p2 rpl32 AGGTGTATTCTTTCCTCGAGT AATAAGACTCCCCACCACCA 864–870 0.500 37.8
rpl32_p3 rpl32 AGGTGTATTCTTTCCTCGAGT TCTGCCCTTCTCGAGAAAGA 920–926 0.500 37.7
rpl32_p4 rpl32 AGGTGTATTCTTTCCTCGAGT AGTTTCTTAGGGTGTCCGGT 1341–1359 0.500 37.0
rpl32_p5 rpl32 AGGTGTATTCTTTCCTCGAGTT CACCACCACAATGTGAGTGA 852–858 0.500 35.8
rpl32-trnL-UAG_p1 rpl32-trnL-UAG AAGGAAAGGATATTGGGCGG AGCGTGTCTACCGATTTCAC 984–1016 0.500 59.7
rpl32-trnL-UAG_p2 rpl32-trnL-UAG AAGGAAAGGATATTGGGCGG CAGCGTGTCTACCGATTTCA 985–1017 0.500 59.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CGGCGTTAAAAGCTTTGTCA AGCGTGTCTACCGATTTCAC 967–999 0.500 59.5
rpl32-trnL-UAG_p4 rpl32-trnL-UAG CGGCGTTAAAAGCTTTGTCA CAGCGTGTCTACCGATTTCA 968–1000 0.500 59.5
rpl32-trnL-UAG_p5 rpl32-trnL-UAG AAGGAAAGGATATTGGGCGG TGATCCACAAAGAAGAGCCG 1638–1671 0.500 58.1
trnL-UAG-ccsA_p1 trnL-UAG-ccsA TCACTCACATTGTGGTGGTG TGATCCACAAAGAAGAGCCG 1313–1345 0.500 60.8
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TCTTTCTCGAGAAGGGCAGA TGATCCACAAAGAAGAGCCG 1245–1277 0.500 60.4
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT TGATCCACAAAGAAGAGCCG 674–680 0.500 59.5
trnL-UAG-ccsA_p4 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG TGATCCACAAAGAAGAGCCG 673–679 0.500 59.5
trnL-UAG-ccsA_p5 trnL-UAG-ccsA TGGTGGTGGGGAGTCTTATT TGATCCACAAAGAAGAGCCG 1301–1320 0.333 53.6
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT AGAACCGCGTGAATCACTAC 1296–1302 0.500 60.2
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG AGAACCGCGTGAATCACTAC 1295–1301 0.500 60.2
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT GTTTTTGATTCTGGACCGCG 1571–1578 0.500 60.1
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG GTTTTTGATTCTGGACCGCG 1570–1577 0.500 60.0
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT TAGCTTTTCGATGGCTTCCC 1794–1801 0.500 60.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Dolomiaea calophylla MT128668.1 152641 View on NCBI ↗
Dolomiaea costus NC_067730.1 152704 View on NCBI ↗
Dolomiaea denticulata MT128669.1 152581 View on NCBI ↗
Dolomiaea edulis MT128670.1 152645 View on NCBI ↗
Dolomiaea souliei MT128671.1 152466 View on NCBI ↗
Dolomiaea wardii PP525142.1 152638 View on NCBI ↗