Markers + reference

Robinsonia

6 species · Asteraceae · Asterales

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Species 6
Genome length 151–151 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1099 0.0047 1.00 48.1 yes View details
trnC-GCA-petN LSC 817 0.0049 1.00 54.1 yes View details
atpH-atpF LSC 385 0.0078 1.00 50.9 yes View details
atpF LSC 1259 0.0000 1.00 28.1 yes View details
trnR-UCU-trnS-CGA LSC 203 0.0102 1.00 47.2 yes View details
ycf3-trnS-GGA LSC 892 0.0031 1.00 50.0 yes View details
ycf4-cemA LSC 380 0.0064 1.00 47.3 yes View details
psbE-petL LSC 1230 0.0030 1.00 50.7 yes View details
rps18-rpl20 LSC 294 0.0152 0.93 60.7 yes View details
rpl20 LSC 363 0.0015 1.00 26.1 yes View details
ycf1 SSC 5079 0.0031 1.00 54.8 yes View details
ycf1 IRa 564 0.0015 1.00 43.5 no View details
atpF-atpA LSC 83 0.0508 0.96 83.5 yes View details
atpA-trnR-UCU LSC 124 0.0290 1.00 66.4 yes View details
trnT-UGU-trnL-UAA LSC 587 0.0023 0.99 58.7 yes View details
ndhK-ndhC LSC 53 0.0302 1.00 56.6 yes View details
matK-trnK-UUU LSC 754 0.0018 1.00 55.4 yes View details
trnL-UAG-rpl32 SSC 837 0.0023 0.99 55.2 yes View details
ccsA SSC 969 0.0029 1.00 54.6 yes View details
trnF-GAA-ndhJ LSC 692 0.0014 1.00 54.5 yes View details
petA-psbJ LSC 775 0.0021 1.00 54.1 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
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 881–891 1.000 59.9
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 880–890 1.000 59.9
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 896–906 1.000 58.0
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 894–904 1.000 57.5
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 881–891 1.000 55.9
rps16_p1 rps16 AGAAATCACTATCCTACCCTTAGT GTCTATGTACCGAGCGAACC 1227–1230 1.000 40.9
rps16_p2 rps16 AGAAATCACTATCCTACCCT GTCTATGTACCGAGCGAACC 1227–1230 1.000 40.9
rps16_p3 rps16 AGAAATCACTATCCTACCCTT GTCTATGTACCGAGCGAACC 1227–1230 1.000 40.9
rps16_p4 rps16 AGAAATCACTATCCTACCCTTAGT CCGAGCGAACCAATGACTAT 1218–1221 1.000 40.9
rps16_p5 rps16 AGAAATCACTATCCTACCCTTAGT TCTATGTACCGAGCGAACCA 1226–1229 1.000 40.9
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 917–933 1.000 80.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 860–876 1.000 80.2
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 878–894 1.000 78.0
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 918–934 1.000 75.4
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 916–932 1.000 74.5
atpH-atpF_p1 atpH-atpF CGAGGCGGAGGGAAAAATAA TGGCCCAAAGAAACGAAAGA 540–541 1.000 80.4
atpH-atpF_p2 atpH-atpF CGAGGCGGAGGGAAAAATAA ATTAAACCCGAAACTCCCGG 571–572 1.000 79.9
atpH-atpF_p3 atpH-atpF CGAGGCGGAGGGAAAAATAA GTGGCCCAAAGAAACGAAAG 541–542 1.000 79.8
atpH-atpF_p4 atpH-atpF CGAGGCGGAGGGAAAAATAA AGTGGCCCAAAGAAACGAAA 542–543 1.000 79.1
atpH-atpF_p5 atpH-atpF GCCTGGTTGTAGCATTAGCA TGGCCCAAAGAAACGAAAGA 469–470 1.000 78.9
atpF_p1 atpF GGGCAAAGTAAAAAGAACTCTGT TGCCTAAAGTACTAAAGTAGAAGGA 1341 1.000 40.0
atpF_p2 atpF AGGGCAAAGTAAAAAGAACTCTG TGCCTAAAGTACTAAAGTAGAAGGA 1342 1.000 40.0
atpF_p3 atpF GGGCAAAGTAAAAAGAACTCTGT TGCCTAAAGTACTAAAGTAGAAGG 1341 1.000 40.0
atpF_p4 atpF GGGCAAAGTAAAAAGAACTCTGT GCCTAAAGTACTAAAGTAGAAGGA 1340 1.000 40.0
atpF_p5 atpF GGGCAAAGTAAAAAGAACTCTGT ATGCCTAAAGTACTAAAGTAGAAGGA 1342 1.000 40.0
atpF-atpA_p1 atpF-atpA ATATTGGCATATTGGGGGCG GTCGGCTTGAATGGTTACCA 140–145 1.000 85.3
atpF-atpA_p2 atpF-atpA ATATTGGCATATTGGGGGCG ATTTCGTCGGCTTGAATGGT 145–150 1.000 85.2
atpF-atpA_p3 atpF-atpA ATATTGGCATATTGGGGGCG CAATGCCGTCACCTACTTGA 237–242 1.000 84.4
atpF-atpA_p4 atpF-atpA ATATTGGCATATTGGGGGCG TCGTCGGCTTGAATGGTTAC 142–147 1.000 84.4
atpF-atpA_p5 atpF-atpA ATATTGGCATATTGGGGGCG GCTCAATACGTTCGCGGATA 174–179 1.000 84.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Robinsonia berteroi NC_085195.1 151239 View on NCBI ↗
Robinsonia evenia NC_085196.1 151246 View on NCBI ↗
Robinsonia gayana NC_085197.1 151330 View on NCBI ↗
Robinsonia gracilis NC_085198.1 151278 View on NCBI ↗
Robinsonia masafuerae NC_085199.1 151328 View on NCBI ↗
Robinsonia thurifera NC_085201.1 151330 View on NCBI ↗