Markers + reference

Eupatorium

3 species · Asteraceae · Asterales

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Species 3
Genome length 151–151 kb
Candidate markers 275
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 809 0.0087 1.00 64.8 yes View details
psbK-psbI LSC 420 0.0048 1.00 38.9 yes View details
trnC-GCA-petN LSC 598 0.0134 1.00 59.7 yes View details
trnY-GUA-trnE-UUC LSC 181 0.0074 1.00 37.7 yes View details
ycf3-trnS-GGA LSC 892 0.0098 0.99 53.5 yes View details
ndhC-trnV LSC 944 0.0064 0.99 57.0 yes View details
atpB-rbcL LSC 748 0.0071 1.00 63.6 yes View details
clpP1 LSC 2037 0.0043 1.00 40.9 yes View details
ycf1 IRb 573 0.0012 1.00 36.5 no View details
rpl32-trnL-UAG SSC 730 0.0100 1.00 65.2 yes View details
ycf1 SSC 5082 0.0038 1.00 40.8 yes View details
trnT-UGU-trnL-UAA LSC 558 0.0048 1.00 62.1 yes View details
ndhF-rpl32 SSC 973 0.0041 1.00 61.4 yes View details
atpI-atpH LSC 1150 0.0035 1.00 61.0 yes View details
ccsA SSC 969 0.0034 1.00 60.9 yes View details
ycf3 LSC 1961 0.0020 1.00 59.5 yes View details
rrn5-trnR-ACG IRb 264 0.0051 0.98 57.5 yes View details
trnR-ACG-rrn5 IRa 264 0.0051 0.98 57.5 yes View details
rpoB LSC 3183 0.0013 1.00 56.1 yes View details
petA-psbJ LSC 685 0.0019 1.00 55.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 GGTATGGATGAATCCCTCGC TTCCTTGAAAAAGGCGCTCA 999–1003 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 943–947 1.000 77.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 942–946 1.000 77.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1028–1032 1.000 76.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1027–1031 1.000 76.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 557 1.000 72.5
psbK-psbI_p2 psbK-psbI TATGCCAGTCATACCCCTGT TCTTCACGTCCAGGATTACG 597 1.000 71.4
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 554 1.000 70.5
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 555 1.000 70.5
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 556 1.000 70.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 655–656 1.000 79.6
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 673–674 1.000 77.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 654–655 1.000 73.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 663–664 1.000 73.6
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 712–713 1.000 72.8
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC AAAACGAGGGTTCAAGTCCC 255 1.000 77.6
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC AAAACGAGGGTTCAAGTCCC 256 1.000 77.4
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CCCCTATGGTCCAGTGGTTA 296 1.000 76.8
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CGGAGAAAACGAGGGTTCAA 260 1.000 76.8
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC ATTGACAAATTGTTGGGCCG AAAACGAGGGTTCAAGTCCC 309 1.000 76.7
rpoB_p1 rpoB TGATGCGAATCGGGCTTTAA ACCTGGGGTTTTTGATGCAT 267 1.000 80.1
rpoB_p2 rpoB TGCGAATCGGGCTTTAATGA ACCTGGGGTTTTTGATGCAT 264 1.000 80.1
rpoB_p3 rpoB TGCGAATCGGGCTTTAATGA AACCTGGGGTTTTTGATGCA 265 1.000 78.8
rpoB_p4 rpoB TGATGCGAATCGGGCTTTAA AACCTGGGGTTTTTGATGCA 268 1.000 78.7
rpoB_p5 rpoB ATGATGCGAATCGGGCTTTA ACCTGGGGTTTTTGATGCAT 268 1.000 78.3
atpI-atpH_p1 atpI-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1284–1287 1.000 79.0
atpI-atpH_p2 atpI-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1340–1343 1.000 78.4
atpI-atpH_p3 atpI-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1300–1303 1.000 78.2
atpI-atpH_p4 atpI-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1285–1288 1.000 77.9
atpI-atpH_p5 atpI-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1344–1347 1.000 77.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Eupatorium cannabinum OR909652.1 151349 View on NCBI ↗
Eupatorium chinense NC_072212.1 151393 View on NCBI ↗
Eupatorium lindleyanum PQ157700.1 151377 View on NCBI ↗