Markers + reference

Pluchea

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 259
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 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
DXZ06_pgt001-psbA LSC 416 0.0144 1.00 63.2 yes View details
matK LSC 1521 0.0000 1.00 35.9 yes View details
matK-trnK-UUU LSC 738 0.0014 1.00 59.5 yes View details
rpoC2 LSC 4146 0.0005 1.00 54.1 yes View details
ycf3-trnS-GCU LSC 912 0.0011 1.00 59.4 yes View details
psbH-petB LSC 891 0.0011 0.99 59.9 yes View details
ycf2 IRb 6849 0.0001 1.00 52.6 yes View details
ccsA SSC 969 0.0010 1.00 59.3 yes View details
rpl2-DXZ06_pgt001 IRa 123 0.0000 1.00 71.2 no View details
trnK-UUU-rps16 LSC 827 0.0000 1.00 58.9 yes View details
psbM-trnD-GUC LSC 659 0.0000 1.00 58.9 yes View details
rps4-trnL-UAA LSC 940 0.0000 1.00 58.9 yes View details
trnC-GCA-psbM LSC 1450 0.0000 1.00 58.8 yes View details
trnR-UCU-DXZ06_pgt010 LSC 1209 0.0000 1.00 58.8 yes View details
psbA-matK LSC 536 0.0000 1.00 57.6 yes View details
rpoC1 LSC 2824 0.0000 1.00 56.0 yes View details
rps8-rpl14 LSC 198 0.0000 0.99 53.0 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
DXZ06_pgt001-psbA_p1 DXZ06_pgt001-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 535 1.000 77.2
DXZ06_pgt001-psbA_p2 DXZ06_pgt001-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 549 1.000 77.1
DXZ06_pgt001-psbA_p3 DXZ06_pgt001-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 548 1.000 77.1
DXZ06_pgt001-psbA_p4 DXZ06_pgt001-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 550 1.000 77.1
DXZ06_pgt001-psbA_p5 DXZ06_pgt001-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 536 1.000 76.7
psbA-matK_p1 psbA-matK TAAAGACGGTTTTCGGTGCT CGCGAAGGTTATCTAGAAGGC 695–696 1.000 65.3
psbA-matK_p2 psbA-matK TAAAGACGGTTTTCGGTGCT GCGAAGGTTATCTAGAAGGCG 694–695 1.000 65.3
psbA-matK_p3 psbA-matK GTAAAGACGGTTTTCGGTGC CGCGAAGGTTATCTAGAAGGC 696–697 1.000 64.8
psbA-matK_p4 psbA-matK GTAAAGACGGTTTTCGGTGC GCGAAGGTTATCTAGAAGGCG 695–696 1.000 64.8
psbA-matK_p5 psbA-matK TTTTCGGTGCTGGTTATCCA GCGAAGGTTATCTAGAAGGCG 685–686 1.000 62.7
matK_p1 matK ATTTACAACGTTTCATAAGGAA CCTTGTTTTGACTGTATCGCA 1621 1.000 40.0
matK_p2 matK ATTTACAACGTTTCATAAGGAA ACCTTGTTTTGACTGTATCGC 1622 1.000 40.0
matK_p3 matK ATTTACAACGTTTCATAAGGAA CCTTGTTTTGACTGTATCGCAC 1621 1.000 40.0
matK_p4 matK ATTTACAACGTTTCATAAGGAA CCGAGGTATCTATTCGGTTTGT 1652 1.000 40.0
matK_p5 matK ATTTACAACGTTTCATAAGGAA ACCTTGTTTTGACTGTATCGCA 1622 1.000 40.0
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 870 1.000 58.8
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 869 1.000 58.8
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 885 1.000 57.0
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 883 1.000 56.5
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 870 1.000 54.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1008–1009 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1007–1008 1.000 76.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 947–948 1.000 76.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 946–947 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1032–1033 1.000 75.7
trnC-GCA-psbM_p1 trnC-GCA-psbM GTTGTGTATCGTTTTGGCGG TGCTACTGCACTGTTCATTT 1624–1625 1.000 60.3
trnC-GCA-psbM_p2 trnC-GCA-psbM TTTCCCCAGTTCAAATCCGG TGCTACTGCACTGTTCATTT 1567–1568 1.000 60.0
trnC-GCA-psbM_p3 trnC-GCA-psbM GTTGTGTATCGTTTTGGCGG TGCTACTGCACTGTTCATTTT 1624–1625 1.000 58.6
trnC-GCA-psbM_p4 trnC-GCA-psbM TTTCCCCAGTTCAAATCCGG TGCTACTGCACTGTTCATTTT 1567–1568 1.000 58.3
trnC-GCA-psbM_p5 trnC-GCA-psbM GGGGGACTGCAAATCCTTTT TGCTACTGCACTGTTCATTT 1585–1586 1.000 57.8

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
Pluchea indica NC_038194.1 152298 View on NCBI ↗
Pluchea pteropoda MW554520.1 152300 View on NCBI ↗