Markers + reference

Phaeostigma

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 260
Primer pairs 70

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 6 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1-rps15 SSC 400 0.5118 0.84 76.5 yes View details
rps15 SSC 279 0.4644 0.96 76.8 yes View details
ndhH SSC 1182 0.4662 0.90 82.3 yes View details
ndhA SSC 2155 0.4816 0.87 80.0 yes View details
ndhI SSC 501 0.5011 0.93 81.1 yes View details
ndhG SSC 531 0.4861 0.74 76.4 yes View details
ndhD SSC 1539 0.4636 0.75 77.9 yes View details
ccsA SSC 975 0.5000 0.79 79.2 yes View details
trnH-GTG-psbA LSC 391 0.0809 0.88 88.9 yes View details
rpl32-ndhF SSC 987 0.4463 0.91 82.6 yes View details
trnL-TAG-rpl32 SSC 887 0.4223 0.85 80.9 yes View details
rps15-ndhH SSC 91 0.5412 0.93 76.9 yes View details
ndhF SSC 2232 0.4466 0.75 76.4 yes View details
rpl32 SSC 165 0.4662 0.90 76.3 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 466–510 1.000 84.9
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 480–524 1.000 84.7
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 479–523 1.000 84.7
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 481–525 1.000 84.7
trnH-GTG-psbA_p5 trnH-GTG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 467–511 1.000 84.4
ycf1-rps15_p1 ycf1-rps15 AATAATGGGAGCCGCTTGAG CCGCAGACCTCTCTGAGATA 616 0.500 59.6
ycf1-rps15_p2 ycf1-rps15 AGAATCAGAATGGTGCGCAT CCGCAGACCTCTCTGAGATA 807 0.500 59.4
ycf1-rps15_p3 ycf1-rps15 AATAATGGGAGCCGCTTGAG AACACCATGCATTGATGGGT 893 0.500 59.3
ycf1-rps15_p4 ycf1-rps15 AATAATGGGAGCCGCTTGAG CCCTAATTGCTCTGGTGCAT 1088 0.500 59.3
ycf1-rps15_p5 ycf1-rps15 AGAATCAGAATGGTGCGCAT AACACCATGCATTGATGGGT 1084 0.500 59.1
rps15_p1 rps15 AATAATGGGAGCCGCTTGAG TGAGGTAAATCAGCAGCGAC 1324 0.500 59.7
rps15_p2 rps15 AGAATCAGAATGGTGCGCAT TGAGGTAAATCAGCAGCGAC 1515 0.500 59.5
rps15_p3 rps15 AATAATGGGAGCCGCTTGAG AACACCATGCATTGATGGGT 893 0.500 59.3
rps15_p4 rps15 AATAATGGGAGCCGCTTGAG CCCTAATTGCTCTGGTGCAT 1088 0.500 59.3
rps15_p5 rps15 AGAATCAGAATGGTGCGCAT AACACCATGCATTGATGGGT 1084 0.500 59.1
rps15-ndhH_p1 rps15-ndhH AATAATGGGAGCCGCTTGAG TGAGGTAAATCAGCAGCGAC 1324 0.500 59.7
rps15-ndhH_p2 rps15-ndhH AATAATGGGAGCCGCTTGAG AACACCATGCATTGATGGGT 893 0.500 59.3
rps15-ndhH_p3 rps15-ndhH AATAATGGGAGCCGCTTGAG CCCTAATTGCTCTGGTGCAT 1088 0.500 59.3
rps15-ndhH_p4 rps15-ndhH AATAATGGGAGCCGCTTGAG AGGAGTCTGTGCCCCAATAT 1208 0.500 59.0
rps15-ndhH_p5 rps15-ndhH AATAATGGGAGCCGCTTGAG TTCCCTAATTGCTCTGGTGC 1090 0.500 58.8
ndhH_p1 ndhH TATGCAAACAACCCGATGCT CCTGACATAAGAAGGCCGAC 2308 0.500 58.2
ndhH_p2 ndhH TATGCAAACAACCCGATGCT GACATAAGAAGGCCGACAGG 2305 0.500 58.2
ndhH_p3 ndhH AGGTCTGCGGAAAATTCTGG CCTGACATAAGAAGGCCGAC 1841 0.500 58.1
ndhH_p4 ndhH AGGTCTGCGGAAAATTCTGG GACATAAGAAGGCCGACAGG 1838 0.500 58.1
ndhH_p5 ndhH GTCTGCGGAAAATTCTGGGA GACATAAGAAGGCCGACAGG 1836 0.500 58.1
ndhA_p1 ndhA AGAGTTGAAGCACCAAAGGG TGACCAATATACCTTGCGGC 2507 0.500 59.6
ndhA_p2 ndhA AGTTGAAGCACCAAAGGGAG TGACCAATATACCTTGCGGC 2505 0.500 59.6
ndhA_p3 ndhA GAGTTGAAGCACCAAAGGGA TGACCAATATACCTTGCGGC 2506 0.500 59.5
ndhA_p4 ndhA GTTGAAGCACCAAAGGGAGA TGACCAATATACCTTGCGGC 2504 0.500 59.5
ndhA_p5 ndhA CAACAGGCGCTAGAAGGAAT TGACCAATATACCTTGCGGC 2666 0.500 59.5

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
Phaeostigma variifolium NC_057440.1 151089 View on NCBI ↗
Phaeostigma variifolium var. ramosum OP723184.1 151002 View on NCBI ↗