Markers + reference

Verbesina

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 271
Primer pairs 95

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-rpoB LSC 918 0.0177 0.98 57.5 yes View details
atpI-atpH LSC 1171 0.0128 1.00 65.4 yes View details
atpH-atpF LSC 366 0.0329 1.00 73.0 yes View details
trnS-UGA-psbZ LSC 338 0.0178 1.00 63.8 yes View details
pafI-trnS-GCU LSC 985 0.0124 0.90 61.5 yes View details
rpoA LSC 1014 0.0059 1.00 48.4 yes View details
ycf1 IRb 585 0.0017 0.98 46.8 no View details
ndhF SSC 2229 0.0067 1.00 46.3 yes View details
ndhF-rpl32 SSC 1004 0.0140 1.00 64.2 yes View details
rpl32-trnL-UAG SSC 679 0.0385 0.96 70.2 yes View details
ycf1 SSC 5046 0.0097 1.00 43.6 yes View details
atpA-trnR-UCU LSC 128 0.0391 1.00 73.8 yes View details
ycf1-ndhF SSC 14 0.1429 1.00 73.2 yes View details
psaA-pafI LSC 711 0.0114 0.99 66.4 yes View details
atpF-atpA LSC 73 0.0145 0.95 65.4 yes View details
psbI-trnS-GCU LSC 138 0.0217 1.00 65.0 yes View details
psbE-petL LSC 1297 0.0093 1.00 64.5 yes View details
petA-psbJ LSC 788 0.0077 0.99 63.9 yes View details
rps18-rpl20 LSC 248 0.0165 0.98 63.9 yes View details
trnW-CCA-trnP-UGG LSC 162 0.0185 1.00 63.1 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 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 CCTATCCAATGATCCAGGACG ATTGGGAGAGATGGCTGAGT 273 1.000 69.4
psbI-trnS-GCU_p2 psbI-trnS-GCU CCTATCCAATGATCCAGGACG AGTTAGTCGTACCGAGGGTT 219 1.000 68.8
psbI-trnS-GCU_p3 psbI-trnS-GCU CCTATCCAATGATCCAGGACG GAGTTAGTCGTACCGAGGGT 220 1.000 68.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCCAATGATCCAGGACG GTTAGTCGTACCGAGGGTTC 218 1.000 66.1
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTATCCAATGATCCAGGACG GATGGCTGAGTGGACGAAAG 264 1.000 65.2
trnE-UUC-rpoB_p1 trnE-UUC-rpoB TAACCACTGGACCATAGGGG TGATTAAATCCAGGTATTGTGG 955–965 1.000 42.7
trnE-UUC-rpoB_p2 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TGATTAAATCCAGGTATTGTGG 996–1006 1.000 42.6
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA TGATTAAATCCAGGTATTGTGG 986–996 1.000 42.6
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG TGATTAAATCCAGGTATTGTGG 991–1001 1.000 42.6
trnE-UUC-rpoB_p5 trnE-UUC-rpoB TCTCCGTGAAAGAGAGAGGT TGATTAAATCCAGGTATTGTGG 977–987 1.000 42.6
atpI-atpH_p1 atpI-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1305–1318 1.000 79.6
atpI-atpH_p2 atpI-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1361–1374 1.000 79.0
atpI-atpH_p3 atpI-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1321–1334 1.000 78.7
atpI-atpH_p4 atpI-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1306–1319 1.000 78.5
atpI-atpH_p5 atpI-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1365–1378 1.000 78.4
atpH-atpF_p1 atpH-atpF GCCTGGTTGTAGCATTAGCA TGGCCCAAAGAAACGAAAGA 451–452 1.000 79.8
atpH-atpF_p2 atpH-atpF GCCTGGTTGTAGCATTAGCA ATTAAACCCGAAACTCCCGG 482–483 1.000 79.2
atpH-atpF_p3 atpH-atpF GCCTGGTTGTAGCATTAGCA GTGGCCCAAAGAAACGAAAG 452–453 1.000 79.2
atpH-atpF_p4 atpH-atpF TGGCCTGGTTGTAGCATTAG TGGCCCAAAGAAACGAAAGA 453–454 1.000 78.5
atpH-atpF_p5 atpH-atpF GCCTGGTTGTAGCATTAGCA AGTGGCCCAAAGAAACGAAA 453–454 1.000 78.5
atpF-atpA_p1 atpF-atpA CATATTGGCGGCGATGAAAC GTCGGCTTGAATGGTTACCA 124–128 1.000 81.4
atpF-atpA_p2 atpF-atpA CATATTGGCGGCGATGAAAC ATTTCGTCGGCTTGAATGGT 129–133 1.000 81.3
atpF-atpA_p3 atpF-atpA CATATTGGCGGCGATGAAAC TCGTCGGCTTGAATGGTTAC 126–130 1.000 80.6
atpF-atpA_p4 atpF-atpA CATATTGGCGGCGATGAAAC TTTCGTCGGCTTGAATGGTT 128–132 1.000 79.6
atpF-atpA_p5 atpF-atpA CATATTGGCGGCGATGAAAC ACTTGAAGTACGGTACCGGT 207–211 1.000 78.6
atpA-trnR-UCU_p1 atpA-trnR-UCU TACTTCAGGAACAAGCAGCC GGTTCAAATCCTATTGGACGC 173–177 1.000 67.3
atpA-trnR-UCU_p2 atpA-trnR-UCU CAGGAACAGAGGGAACGTTT GGTTCAAATCCTATTGGACGC 195–199 1.000 66.4
atpA-trnR-UCU_p3 atpA-trnR-UCU TACTTCAGGAACAAGCAGCC CAATGAAAGCGTCCATTGTCT 231–235 1.000 65.5
atpA-trnR-UCU_p4 atpA-trnR-UCU CTTCAGGAACAAGCAGCCTA GGTTCAAATCCTATTGGACGC 171–175 1.000 64.9
atpA-trnR-UCU_p5 atpA-trnR-UCU CAGGAACAGAGGGAACGTTT CAATGAAAGCGTCCATTGTCT 253–257 1.000 64.8

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
Verbesina alternifolia PP639077.1 152050 View on NCBI ↗
Verbesina encelioides PX334460.1 152213 View on NCBI ↗