Markers + reference

Leibnitzia

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–154 kb
Candidate markers 274
Primer pairs 80

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 8 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2235 0.4672 0.88 80.2 yes View details
ccsA SSC 969 0.4977 0.88 81.7 yes View details
ndhD SSC 1503 0.4849 0.84 80.4 yes View details
psaC SSC 246 0.4972 0.74 71.4 yes View details
ndhI SSC 501 0.4869 0.91 80.5 yes View details
ndhA SSC 2138 0.4705 0.88 80.6 yes View details
ndhH SSC 1182 0.4734 0.91 82.4 yes View details
rps15-ycf1 SSC 401 0.4830 0.88 77.6 yes View details
ndhF-rpl32 SSC 1038 0.4291 0.79 79.2 yes View details
ndhG SSC 531 0.4804 0.82 78.4 yes View details
rpl32-trnL-UAG SSC 528 0.4400 0.80 78.0 yes View details
trnL-UAG-ccsA SSC 97 0.4783 0.95 77.3 yes View details
ndhG-ndhI SSC 351 0.4548 0.88 76.5 yes View details
rps15 SSC 279 0.4542 0.90 76.1 yes View details
psaC-ndhE SSC 234 0.4493 0.97 75.5 yes View details
trnM-CAU-atpE LSC 226 0.0398 1.00 75.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnM-CAU-atpE_p1 trnM-CAU-atpE TATTGCTTTCATACGGCGGG CAAATCTAGCTCTCCGACGG 334–348 1.000 77.8
trnM-CAU-atpE_p2 trnM-CAU-atpE TATTGCTTTCATACGGCGGG GGCAAATCTAGCTCTCCGAC 336–350 1.000 77.7
trnM-CAU-atpE_p3 trnM-CAU-atpE TATTGCTTTCATACGGCGGG GAGGCAAATCTAGCTCTCCG 338–352 1.000 77.6
trnM-CAU-atpE_p4 trnM-CAU-atpE TATTGCTTTCATACGGCGGG AGGCAAATCTAGCTCTCCGA 337–351 1.000 77.1
trnM-CAU-atpE_p5 trnM-CAU-atpE TATTGCTTTCATACGGCGGG CTAGGACACGAGTAGAGGCT 313–327 1.000 76.3
ndhF_p1 ndhF CTAGCACTGGGTAGACCTCA CGAAAGAGGTAAGATCCGTTGA 2594 0.500 42.0
ndhF_p2 ndhF CTAGCACTGGGTAGACCTCA TCGAAAGAGGTAAGATCCGTTG 2595 0.500 42.0
ndhF_p3 ndhF ATCAATTCGGTCGTTGTGGT CGAAAGAGGTAAGATCCGTTGA 2792 0.500 41.7
ndhF_p4 ndhF ATCAATTCGGTCGTTGTGGT TCGAAAGAGGTAAGATCCGTTG 2793 0.500 41.7
ndhF_p5 ndhF TCTCTTCCTTCTCCGAGCTC CGAAAGAGGTAAGATCCGTTGA 2724 0.500 41.2
ndhF-rpl32_p1 ndhF-rpl32 AAGGGGAAATTGTGCGGATT ACGCCGACCAATATCCTTTC 1861 0.500 59.1
ndhF-rpl32_p2 ndhF-rpl32 AGGGGAAATTGTGCGGATTT ACGCCGACCAATATCCTTTC 1860 0.500 59.1
ndhF-rpl32_p3 ndhF-rpl32 GGGAAATTGTGCGGATTTCG ACGCCGACCAATATCCTTTC 1858 0.500 58.9
ndhF-rpl32_p4 ndhF-rpl32 AACAGGTCGTGTGAACCAAA ACGCCGACCAATATCCTTTC 1633 0.500 58.7
ndhF-rpl32_p5 ndhF-rpl32 ACAGGTCGTGTGAACCAAAA ACGCCGACCAATATCCTTTC 1632 0.500 58.7
rpl32-trnL-UAG_p1 rpl32-trnL-UAG GAAAGGATATTGGTCGGCGT TGATCCACAAAGAAGAGCCG 1267 0.500 58.8
rpl32-trnL-UAG_p2 rpl32-trnL-UAG GAAAGGATATTGGTCGGCGT TCCTAAGAGCAGCGTGTCTA 667 0.500 58.6
rpl32-trnL-UAG_p3 rpl32-trnL-UAG GAAAGGATATTGGTCGGCGT AGCAGCGTGTCTACCAATTT 660 0.500 58.1
rpl32-trnL-UAG_p4 rpl32-trnL-UAG GAAAGGATATTGGTCGGCGT CCTAAGAGCAGCGTGTCTAC 666 0.500 58.0
rpl32-trnL-UAG_p5 rpl32-trnL-UAG GAAAGGATATTGGTCGGCGT CTAAGAGCAGCGTGTCTACC 665 0.500 58.0
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GAAAGGATATTGGTCGGCGT TGATCCACAAAGAAGAGCCG 1267 0.500 58.8
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TAGACACGCTGCTCTTAGGA TGATCCACAAAGAAGAGCCG 620 0.500 58.2
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GAAAGGATATTGGTCGGCGT TAGCCCATACTGCTCCTGAA 1541 0.500 58.2
trnL-UAG-ccsA_p4 trnL-UAG-ccsA GAAAGGATATTGGTCGGCGT TTAGCCCATACTGCTCCTGA 1542 0.500 58.2
trnL-UAG-ccsA_p5 trnL-UAG-ccsA AAATTGGTAGACACGCTGCT TGATCCACAAAGAAGAGCCG 627 0.500 57.7
ccsA_p1 ccsA TAGACACGCTGCTCTTAGGA AGAACCGCGTGAATCACTAC 1236 0.500 58.9
ccsA_p2 ccsA AAATTGGTAGACACGCTGCT AGAACCGCGTGAATCACTAC 1243 0.500 58.5
ccsA_p3 ccsA GGTAGACACGCTGCTCTTAG AGAACCGCGTGAATCACTAC 1238 0.500 58.4
ccsA_p4 ccsA GTAGACACGCTGCTCTTAGG AGAACCGCGTGAATCACTAC 1237 0.500 58.4
ccsA_p5 ccsA TAGACACGCTGCTCTTAGGA GCATTACCGGGTATGAGTGG 1725 0.500 58.0

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
Leibnitzia anandria PP566209.1 154168 View on NCBI ↗
Leibnitzia nepalensis NC_073547.1 151518 View on NCBI ↗