Markers + reference

Adenostyles

2 species · Asteraceae · Asterales

Back to catalogue

Species 2
Genome length 150–150 kb
Candidate markers 270
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1096 0.0018 1.00 53.1 yes View details
petN-psbM LSC 507 0.0039 1.00 59.1 yes View details
atpF LSC 1258 0.0024 1.00 59.1 yes View details
trnG-UCC-psbD LSC 1483 0.0027 1.00 60.5 yes View details
ycf3 LSC 1950 0.0015 1.00 58.7 yes View details
trnT-UGU-trnL-UAA LSC 544 0.0055 1.00 60.8 yes View details
ndhC-trnV-UAC LSC 757 0.0040 1.00 61.0 yes View details
rpl14 LSC 369 0.0000 1.00 20.9 yes View details
ndhF SSC 2226 0.0018 1.00 58.3 yes View details
ndhF-rpl32 SSC 1086 0.0037 0.99 61.0 yes View details
matK-trnK-UUU LSC 752 0.0080 1.00 62.6 yes View details
rpl14-rpl16 LSC 115 0.0174 1.00 62.5 yes View details
rps16-trnQ-UUG LSC 969 0.0031 0.99 61.0 yes View details
trnC-GCA-petN LSC 833 0.0024 1.00 60.1 yes View details
psbM-trnD-GUC LSC 613 0.0016 1.00 60.0 yes View details
atpI-atpH LSC 1116 0.0018 1.00 60.0 yes View details
ycf1 IRb 627 0.0016 1.00 59.7 yes View details
cemA LSC 690 0.0014 1.00 59.6 yes View details
atpB-rbcL LSC 735 0.0014 1.00 59.5 yes View details
petA-psbJ LSC 754 0.0013 1.00 59.5 yes View details
ycf1 SSC 5064 0.0010 1.00 46.6 no 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ACTATGACAATGCGTTGAACA TTCGTAGATTAATGCTTTGATTT 2731–2745 1.000 40.6
trnK-UUU_p2 trnK-UUU ACTATGACAATGCGTTGAACA TTTCGTAGATTAATGCTTTGATT 2732–2746 1.000 40.6
trnK-UUU_p3 trnK-UUU ACTATGACAATGCGTTGAACA TTTCGTAGATTAATGCTTTGATTT 2732–2746 1.000 40.6
trnK-UUU_p4 trnK-UUU ACTATGACAATGCGTTGAACA ATTTCGTAGATTAATGCTTTGAT 2733–2747 1.000 40.6
trnK-UUU_p5 trnK-UUU AACTATGACAATGCGTTGAACA TTCGTAGATTAATGCTTTGATTT 2732–2746 1.000 40.6
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 883–884 1.000 59.3
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 882–883 1.000 59.3
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 898–899 1.000 57.5
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 896–897 1.000 57.0
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 883–884 1.000 55.3
rps16_p1 rps16 TGAATAGAGCAAGAAAAGAAGGA CTGTGTCTATGTACCGAGCG 1288–1289 1.000 40.2
rps16_p2 rps16 AGAGCAAGAAAAGAAGGAAA CTGTGTCTATGTACCGAGCG 1283–1284 1.000 40.2
rps16_p3 rps16 TGAATAGAGCAAGAAAAGAAGGA GTCTATGTACCGAGCGAACC 1284–1285 1.000 40.2
rps16_p4 rps16 AGAGCAAGAAAAGAAGGAAA GTCTATGTACCGAGCGAACC 1279–1280 1.000 40.2
rps16_p5 rps16 TGAATAGAGCAAGAAAAGAAGGA CCGAGCGAACCAATGACTAT 1275–1276 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1037–1042 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTAAGGCATCGGGTTTTGA 1069–1074 1.000 78.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGAATAAGAATCCACGCCGG GAGGTTCGAATCCTTCCGTC 1069–1074 1.000 78.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGAATAAGAATCCACGCCGG GGTAAGGCATCGGGTTTTGA 1101–1106 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1051–1056 1.000 77.0
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 956 1.000 78.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 899 1.000 78.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 917 1.000 76.1
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 957 1.000 73.6
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 955 1.000 72.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 669 1.000 59.6
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 669 1.000 58.0
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 670 1.000 53.7
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 661 1.000 53.6
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 655 1.000 52.9

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
Adenostyles alliariae OR896870.1 150423 View on NCBI ↗
Adenostyles glabra OR896871.1 150405 View on NCBI ↗