Markers + reference

Baccharis

3 species · Asteraceae · Asterales

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Species 3
Genome length 152–153 kb
Candidate markers 268
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnY-GUA-rpoB LSC 1085 0.0123 1.00 55.4 yes View details
trnG-UCC-trnT-GGU LSC 282 0.0402 1.00 71.5 yes View details
trnT-UGU-trnL-UAA LSC 648 0.0221 0.91 67.8 yes View details
ndhC-trnV-UAC LSC 731 0.0235 0.99 71.3 yes View details
accD-psaI LSC 907 0.0379 1.00 77.2 yes View details
psbE-petL LSC 1248 0.0085 1.00 58.3 yes View details
petD LSC 1217 0.0112 1.00 57.1 yes View details
rps19 LSC 279 0.0335 1.00 63.4 yes View details
rpl32-ndhF SSC 1052 0.0163 0.97 71.7 yes View details
rps19 IRa 60 0.0111 1.00 32.1 no View details
psaC-ndhD SSC 111 0.0450 1.00 81.7 yes View details
psbI-trnS-GCU LSC 146 0.0365 1.00 75.8 yes View details
rpl22-rps19 LSC 84 0.0476 1.00 74.7 yes View details
rpl14-rpl16 LSC 120 0.0333 1.00 73.7 yes View details
trnW-CCA-trnP-UGG LSC 167 0.0162 0.99 66.6 yes View details
trnF-GAA-ndhJ LSC 673 0.0061 0.98 65.5 yes View details
rps11-rpl36 LSC 100 0.0200 1.00 65.3 yes View details
trnL-UAG-rpl32 SSC 835 0.0114 0.84 64.5 yes View details
psaA-ycf3 LSC 773 0.0060 1.00 63.9 yes View details
infA-rps8 LSC 115 0.0189 0.92 63.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 262–264 1.000 74.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA CGAGTTATTCGTACCGAGGG 210–212 1.000 72.4
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 262–264 1.000 71.8
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCCAATGATCCAGGACG ATTGGGAGAGATGGCTGAGT 281–283 1.000 70.8
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GATGGCTGAGTGGACGAAAG 253–255 1.000 70.0
trnY-GUA-rpoB_p1 trnY-GUA-rpoB CAACGAATTTACAGTCCGCC TCTGATTAAATCCAGGTATTGTGG 1159–1363 1.000 42.1
trnY-GUA-rpoB_p2 trnY-GUA-rpoB AACGAATTTACAGTCCGCCC TCTGATTAAATCCAGGTATTGTGG 1158–1362 1.000 42.1
trnY-GUA-rpoB_p3 trnY-GUA-rpoB CCATTAACCACTCGGGCATC TCTGATTAAATCCAGGTATTGTGG 1138–1342 1.000 42.1
trnY-GUA-rpoB_p4 trnY-GUA-rpoB AGATTGGCAAATTGTTGGGC TCTGATTAAATCCAGGTATTGTGG 1212–1416 1.000 42.0
trnY-GUA-rpoB_p5 trnY-GUA-rpoB GATTGGCAAATTGTTGGGCC TCTGATTAAATCCAGGTATTGTGG 1211–1415 1.000 42.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU AATGAAACCGAAAGACCCCT TCCCCTATCGGATCTGAACC 425–659 0.667 60.3
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ATGAAACCGAAAGACCCCTT TCCCCTATCGGATCTGAACC 424–658 0.667 60.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU AATGAAACCGAAAGACCCCT GATCTGAACCGAGGGCTTAC 415–649 0.667 58.6
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ATGAAACCGAAAGACCCCTT GATCTGAACCGAGGGCTTAC 414–648 0.667 58.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAATGAAACCGAAAGACCCCT TCCCCTATCGGATCTGAACC 426–660 0.667 58.4
psaA-ycf3_p1 psaA-ycf3 GAGAAATGACCCGGTCTAGC AGCCGCTGAGTATTGGAAAC 961–1006 1.000 77.4
psaA-ycf3_p2 psaA-ycf3 GAGAAATGACCCGGTCTAGC CAAGCCGCTGAGTATTGGAA 963–1008 1.000 77.4
psaA-ycf3_p3 psaA-ycf3 GAGAAATGACCCGGTCTAGC AAGCCGCTGAGTATTGGAAA 962–1007 1.000 75.6
psaA-ycf3_p4 psaA-ycf3 TTTTACTTCTGGTTCCGGCG AGCCGCTGAGTATTGGAAAC 896–941 1.000 75.4
psaA-ycf3_p5 psaA-ycf3 TTTTACTTCTGGTTCCGGCG CAAGCCGCTGAGTATTGGAA 898–943 1.000 75.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 709–724 1.000 83.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 741–756 1.000 82.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 703–718 1.000 81.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CGTCTACCGATTTCGCCATA 735–750 1.000 80.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTAGCGTCTACCGATTTCG 708–723 1.000 80.1
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ AATCCTCGTGTCACCAGTTC TGGATAGGATGGCCTTTACG 749–763 1.000 69.3
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ AATCCTCGTGTCACCAGTTC GGATAGGATGGCCTTTACGT 748–762 1.000 69.3
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ AATCCTCGTGTCACCAGTTC TGAAAGTTGGATAGGATGGCC 756–770 1.000 68.7
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ TGGTAGAGCAGAGGACTGAA TGGATAGGATGGCCTTTACG 769–783 1.000 68.1
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ TTGGTAGAGCAGAGGACTGA TGGATAGGATGGCCTTTACG 770–784 1.000 68.1

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
Baccharis aliena NC_034855.1 152252 View on NCBI ↗
Baccharis genistelloides NC_034852.1 153239 View on NCBI ↗
Baccharis tricuneata NC_034868.1 152360 View on NCBI ↗