Markers + reference

Tragopogon

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 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

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GGA-trnC-GCA LSC 737 0.0014 1.00 59.5 yes View details
psbM-trnD-GUC LSC 656 0.0015 1.00 59.6 yes View details
rpoC2 LSC 4146 0.0005 1.00 54.1 yes View details
trnL-CAA-ndhB IRb 579 0.0035 1.00 60.3 yes View details
ccsA SSC 969 0.0000 1.00 36.3 yes View details
ndhB-trnL-CAA IRa 579 0.0035 1.00 60.3 yes View details
matK-trnK-UUU LSC 730 0.0014 1.00 59.5 yes View details
petA-psbJ LSC 759 0.0013 1.00 59.5 yes View details
ndhF-rpl32 SSC 992 0.0010 1.00 59.3 yes View details
psbE-petL LSC 1283 0.0008 1.00 59.2 yes View details
atpB-rbcL LSC 805 0.0000 1.00 59.0 yes View details
ndhG SSC 531 0.0019 1.00 58.4 yes View details
rbcL-accD LSC 530 0.0000 1.00 57.7 yes View details
clpP LSC 2015 0.0000 1.00 57.7 yes View details
psbA-trnK-UUU LSC 254 0.0000 0.96 56.3 yes View details
trnM-CAU-atpE LSC 214 0.0000 0.97 55.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GAAAGCCGTGTGCAATGAAA 446–456 1.000 78.8
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 361–371 1.000 78.5
psbA-trnK-UUU_p3 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GAAAGCCGTGTGCAATGAAA 447–457 1.000 78.3
psbA-trnK-UUU_p4 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTAGTTCCGGGTTCGAATCC 362–372 1.000 78.0
psbA-trnK-UUU_p5 psbA-trnK-UUU TTTTCGGTGCTGGTTATCCA GAAAGCCGTGTGCAATGAAA 437–447 1.000 76.2
trnK-UUU_p1 trnK-UUU CACTATACATTTTCTATACACTATACA TCGTCCTTTAAATGCTTTGA 2732–2733 1.000 40.1
trnK-UUU_p2 trnK-UUU ACACTATACATTTTCTATACACTATAC TCGTCCTTTAAATGCTTTGA 2733–2734 1.000 40.1
trnK-UUU_p3 trnK-UUU CACTATACATTTTCTATACACTATACA TTCGTCCTTTAAATGCTTTGA 2733–2734 1.000 40.1
trnK-UUU_p4 trnK-UUU ACACTATACATTTTCTATACACTATAC TTCGTCCTTTAAATGCTTTGA 2734–2735 1.000 40.1
trnK-UUU_p5 trnK-UUU CACTATACATTTTCTATACACTATACA TCGTCCTTTAAATGCTTTGATTTCA 2732–2733 1.000 40.1
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 862 1.000 58.8
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 861 1.000 58.8
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 877 1.000 57.0
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 875 1.000 56.5
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 862 1.000 54.8
trnS-GGA-trnC-GCA_p1 trnS-GGA-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 888 1.000 78.2
trnS-GGA-trnC-GCA_p2 trnS-GGA-trnC-GCA ACGAAAACGGAAAGAGAGGG CCGGATTTGAACTGGGGAAA 894 1.000 78.1
trnS-GGA-trnC-GCA_p3 trnS-GGA-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 870 1.000 76.0
trnS-GGA-trnC-GCA_p4 trnS-GGA-trnC-GCA ACGAAAACGGAAAGAGAGGG AAAAGGATTTGCAGTCCCCC 876 1.000 75.9
trnS-GGA-trnC-GCA_p5 trnS-GGA-trnC-GCA CGAAAACGGAAAGAGAGGGA CCGGATTTGAACTGGGGAAA 893 1.000 75.8
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 773 1.000 50.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 767 1.000 50.1
psbM-trnD-GUC_p3 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TCCCCGGGATTGTAGTTCAA 788 1.000 49.9
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCCCCGGGATTGTAGTTCA 789 1.000 49.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TCCCCGGGATTGTAGTTCAA 782 1.000 49.4
rpoC2_p1 rpoC2 AAAAGATCGAAACGGCCTGT CGTTGAATGGTCCTATTCGAGA 330 1.000 63.3
rpoC2_p2 rpoC2 AAAAGATCGAAACGGCCTGT TCGTTGAATGGTCCTATTCGAG 331 1.000 63.3
rpoC2_p3 rpoC2 AAAAGATCGAAACGGCCTGT TCGTTGAATGGTCCTATTCGA 331 1.000 62.4
rpoC2_p4 rpoC2 AAAAGATCGAAACGGCCTGT CGTTGAATGGTCCTATTCGAG 330 1.000 59.8
rpoC2_p5 rpoC2 ACAAAAAGATCGAAACGGCC CGTTGAATGGTCCTATTCGAGA 333 1.000 58.6

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
Tragopogon dubius NC_085463.1 153017 View on NCBI ↗
Tragopogon pratensis NC_083964.1 153002 View on NCBI ↗