Markers + reference

Klasea

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1113 0.0000 1.00 45.2 yes View details
psbM-trnD-GUC LSC 646 0.0031 1.00 60.5 yes View details
rpoC2 LSC 4134 0.0000 1.00 24.1 yes View details
psbC LSC 1422 0.0000 1.00 30.7 yes View details
psbC-trnS-UGA LSC 240 0.0127 0.98 61.4 yes View details
atpB-rbcL LSC 765 0.0026 1.00 60.3 yes View details
accD-psaI LSC 673 0.0015 0.98 61.3 yes View details
psbE-petL LSC 1283 0.0008 1.00 59.3 yes View details
ndhF SSC 2232 0.0018 1.00 58.3 yes View details
trnS-GCU-trnC-GCA LSC 764 0.0000 0.98 60.8 yes View details
rbcL LSC 1434 0.0000 0.98 60.4 yes View details
matK-trnK-UUU LSC 734 0.0027 1.00 60.3 yes View details
matK LSC 1521 0.0020 1.00 59.8 yes View details
ndhC-trnV-UAC LSC 1170 0.0017 1.00 59.7 yes View details
trnF-GAA-ndhJ LSC 669 0.0015 1.00 59.6 yes View details
ndhK LSC 678 0.0015 1.00 59.6 yes View details
trnK-UUU-rps16 LSC 789 0.0013 1.00 59.5 yes View details
rps16-trnQ-UUG LSC 940 0.0011 1.00 59.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ATATGCCCGTGTCAACCAAT CGATTCCGATTTAGTCATTTTTCTG 2840–2841 1.000 40.2
trnK-UUU_p2 trnK-UUU ATGCCCGTGTCAACCAATAC CGATTCCGATTTAGTCATTTTTCTG 2838–2839 1.000 40.2
trnK-UUU_p3 trnK-UUU ATATGCCCGTGTCAACCAAT CGATTCCGATTTAGTCATTTTTCT 2840–2841 1.000 40.2
trnK-UUU_p4 trnK-UUU ATATGCCCGTGTCAACCAAT TCCGATTTAGTCATTTTTCTGTTTCA 2836–2837 1.000 40.2
trnK-UUU_p5 trnK-UUU ATATGCCCGTGTCAACCAAT TCCGATTTAGTCATTTTTCTGT 2836–2837 1.000 40.2
matK_p1 matK ACATACTACATCAACATTTCAGA CCCCCAAATCCTCTACCTTTC 1676–1677 1.000 40.2
matK_p2 matK ACATACTACATCAACATTTCAGAA CCCCCAAATCCTCTACCTTTC 1676–1677 1.000 40.2
matK_p3 matK ACATACTACATCAACATTTCAGA CCCCCAAATCCTCTACCTTT 1676–1677 1.000 40.2
matK_p4 matK ACTACATACTACATCAACATTTCAGA CCCCCAAATCCTCTACCTTTC 1679–1680 1.000 40.2
matK_p5 matK ACATACTACATCAACATTTCAGAA CCCCCAAATCCTCTACCTTT 1676–1677 1.000 40.2
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 866 1.000 58.9
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 865 1.000 58.9
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 881 1.000 57.0
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 879 1.000 56.6
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 866 1.000 54.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 986–990 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 985–989 1.000 76.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 925–929 1.000 76.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 924–928 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1010–1014 1.000 75.7
rps16_p1 rps16 ACTTGTGTTGGATTGGCACT ATTGAGTCACGTGAAGAGGC 1789–1792 1.000 79.0
rps16_p2 rps16 ACTTGTGTTGGATTGGCACT CGTGAAGAGGCAGAGTCAAA 1780–1783 1.000 78.4
rps16_p3 rps16 GAGTTCGAATGAAAACCGCC ATTGAGTCACGTGAAGAGGC 1631–1634 1.000 77.6
rps16_p4 rps16 ACTTGTGTTGGATTGGCACT TCTCTGTACCGACTGAACCA 1559–1562 1.000 77.4
rps16_p5 rps16 ACTTGTGTTGGATTGGCACT GGGAAGTTGGAAATGGGTCA 1818–1821 1.000 77.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1013 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1028 1.000 76.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1027 1.000 76.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1084 1.000 75.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1017 1.000 73.6

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
Klasea lycopifolia BK071850.1 152975 View on NCBI ↗
Klasea nudicaulis BK071851.1 152883 View on NCBI ↗