Markers + reference

Adenostemma

2 species · Asteraceae · Asterales

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Species 2
Genome length 150–150 kb
Candidate markers 272
Primer pairs 80

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 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5043 0.3806 0.79 73.0 yes View details
ndhH SSC 1182 0.4742 0.87 81.4 yes View details
ndhA SSC 2146 0.4827 0.82 78.7 yes View details
ndhI-ndhG SSC 360 0.4784 0.90 77.2 yes View details
ndhG SSC 531 0.4768 0.89 80.5 yes View details
ndhD SSC 1503 0.4881 0.89 82.0 yes View details
ccsA SSC 969 0.4752 0.83 80.5 yes View details
ndhF SSC 2226 0.4516 0.89 80.4 yes View details
ycf1 IRa 565 0.0000 1.00 24.3 no View details
trnL-UAG-rpl32 SSC 741 0.4432 0.94 83.3 yes View details
rpl32-ndhF SSC 868 0.4258 0.96 82.3 yes View details
ndhI SSC 501 0.4458 0.83 78.1 yes View details
ycf1-rps15 SSC 394 0.4464 0.88 77.4 yes View details
rps15-ndhH SSC 88 0.4474 0.86 75.2 yes View details
ndhE-psaC SSC 240 0.4306 0.87 75.2 yes View details
ndhG-ndhE SSC 216 0.4545 0.87 75.0 yes View details
ccsA-trnL-UAG SSC 124 0.4380 0.98 74.8 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
ycf1_p1 ycf1 ATGGTCTCCTGGTTAGCCTC AACATACTAAAGCGGCTCCC 607 0.500 53.4
ycf1_p2 ycf1 GGTCTCCTGGTTAGCCTCAT AACATACTAAAGCGGCTCCC 605 0.500 53.4
ycf1_p3 ycf1 ATGGTCTCCTGGTTAGCCTC GGCTCCCATTATTGGTGTCA 594 0.500 52.5
ycf1_p4 ycf1 GGTCTCCTGGTTAGCCTCAT GGCTCCCATTATTGGTGTCA 592 0.500 52.5
ycf1_p5 ycf1 GGTCTCCTGGTTAGCCTCAT CATACTAAAGCGGCTCCCAT 603 0.500 51.6
ycf1-rps15_p1 ycf1-rps15 AATTATGGAACCTGCCCGTC CCGCAGACCTCTCTGAGATA 1064 0.500 59.4
ycf1-rps15_p2 ycf1-rps15 AATTATGGAACCTGCCCGTC AACACCATGCATTGATGGGT 1338 0.500 59.1
ycf1-rps15_p3 ycf1-rps15 AATTATGGAACCTGCCCGTC TAAGCCAGTAACCGTTGACG 1099 0.500 59.0
ycf1-rps15_p4 ycf1-rps15 TATGGAACCTGCCCGTCTAT CCGCAGACCTCTCTGAGATA 1061 0.500 59.0
ycf1-rps15_p5 ycf1-rps15 TATGGAACCTGCCCGTCTAT AACACCATGCATTGATGGGT 1335 0.500 58.8
rps15-ndhH_p1 rps15-ndhH CGTCAACGGTTACTGGCTTA GTAAATCAGCAGCGACTCCA 686 0.500 59.4
rps15-ndhH_p2 rps15-ndhH CGTCAACGGTTACTGGCTTA TAAATCAGCAGCGACTCCAC 685 0.500 59.4
rps15-ndhH_p3 rps15-ndhH CGTCAACGGTTACTGGCTTA AACACCATGCATTGATGGGT 259 0.500 59.0
rps15-ndhH_p4 rps15-ndhH CGTCAACGGTTACTGGCTTA AGGAGTCTGTGCCCCAATAT 574 0.500 58.6
rps15-ndhH_p5 rps15-ndhH AGGTCTGCGGAAAATTCTGG TAAATCAGCAGCGACTCCAC 710 0.500 58.5
ndhH_p1 ndhH CGTCAACGGTTACTGGCTTA CGTTGTTGTATACCCGCAGA 1549 0.500 59.4
ndhH_p2 ndhH CGTCAACGGTTACTGGCTTA AAGAATTCCCAAAGGCCCTG 1586 0.500 59.0
ndhH_p3 ndhH CGTCAACGGTTACTGGCTTA CCTGACATAAGAAGGCCGAC 1813 0.500 59.0
ndhH_p4 ndhH CGTCAACGGTTACTGGCTTA GACATAAGAAGGCCGACAGG 1810 0.500 59.0
ndhH_p5 ndhH CGTCAACGGTTACTGGCTTA TGAAGAATTCCCAAAGGCCC 1588 0.500 58.9
ndhA_p1 ndhA GTGGAGTCGCTGCTGATTTA TGCAGCTCGTACTGTTTGTT 2983 0.500 59.5
ndhA_p2 ndhA GTGGAGTCGCTGCTGATTTA TTGCAGCTCGTACTGTTTGT 2984 0.500 59.5
ndhA_p3 ndhA TGGAGTCGCTGCTGATTTAC TGCAGCTCGTACTGTTTGTT 2982 0.500 59.5
ndhA_p4 ndhA TGGAGTCGCTGCTGATTTAC TTGCAGCTCGTACTGTTTGT 2983 0.500 59.5
ndhA_p5 ndhA TCAACAGGCCCTAGAAGGAA TGCAGCTCGTACTGTTTGTT 2640 0.500 59.3
ndhI_p1 ndhI AGCCGAGTGTGAACGATTAC AAAAACAATTCTCGCCCCCT 1105 0.500 59.9
ndhI_p2 ndhI TACATATCCGTTCCCGAGCT AAAAACAATTCTCGCCCCCT 921 0.500 59.9
ndhI_p3 ndhI TTTGTGACCTTTGAGGAGCC AAAAACAATTCTCGCCCCCT 1311 0.500 59.8
ndhI_p4 ndhI GACCTTTGAGGAGCCGTATG AAAAACAATTCTCGCCCCCT 1306 0.500 59.5
ndhI_p5 ndhI GTACATATCCGTTCCCGAGC AAAAACAATTCTCGCCCCCT 922 0.500 59.4

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
Adenostemma lavenia MW583043.1 150063 View on NCBI ↗
Adenostemma madurense NC_072116.1 150054 View on NCBI ↗