Markers + reference

Adonis

5 species · Ranunculaceae · Ranunculales

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Species 5
Genome length 157–158 kb
Candidate markers 265
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnT-UGU LSC 692 0.0189 1.00 68.0 yes View details
trnS-GGA-ycf3 LSC 872 0.0161 0.99 70.8 yes View details
trnY-GUA-trnD-GUC LSC 413 0.0295 1.00 68.1 yes View details
ndhC-trnV-UAC LSC 1385 0.0190 0.96 70.3 yes View details
rps12-clpP LSC 296 0.0316 0.90 69.0 yes View details
trnN-GUU-ndhF IRb 1516 0.0157 1.00 60.4 yes View details
ndhF SSC 2226 0.0050 1.00 34.9 yes View details
ndhF-trnL-UAG SSC 1852 0.0137 1.00 60.2 yes View details
ndhG-ndhI SSC 415 0.0306 1.00 66.2 yes View details
ycf1 SSC 5262 0.0112 1.00 48.1 yes View details
psbT-pbf1 LSC 77 0.0584 1.00 65.1 yes View details
psbM-petN LSC 1148 0.0114 0.99 64.2 yes View details
rpl2-trnH-GUG IRa 153 0.0379 1.00 64.1 no View details
trnH-GUG-psbA LSC 267 0.0228 1.00 62.4 yes View details
atpH-atpF LSC 456 0.0202 1.00 62.0 yes View details
trnC-GCA-rpoB LSC 1251 0.0062 0.99 60.9 yes View details
ccsA-ndhD SSC 261 0.0230 1.00 60.7 yes View details
trnT-GGU-trnE-UUC LSC 691 0.0134 1.00 60.6 yes View details
trnD-GUC-psbM LSC 592 0.0068 1.00 60.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 383–393 1.000 82.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 397–407 1.000 82.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 396–406 1.000 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 398–408 1.000 82.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCGCGCTAACCTTGGTATG 386–396 1.000 81.6
trnK-UUU-trnT-UGU_p1 trnK-UUU-trnT-UGU TCTAGCCGCACTTAAAAGCC GCGATGCTCTAACCTCTGAG 689–844 1.000 83.7
trnK-UUU-trnT-UGU_p2 trnK-UUU-trnT-UGU TCTAGCCGCACTTAAAAGCC GGAATCGAACCGATGACCAT 721–876 1.000 82.7
trnK-UUU-trnT-UGU_p3 trnK-UUU-trnT-UGU TACCGTTGAGTTAGCAACCC GCGATGCTCTAACCTCTGAG 661–816 1.000 82.3
trnK-UUU-trnT-UGU_p4 trnK-UUU-trnT-UGU TACCGTTGAGTTAGCAACCC GGAATCGAACCGATGACCAT 693–848 1.000 81.3
trnK-UUU-trnT-UGU_p5 trnK-UUU-trnT-UGU CGAATCCGTTGCTTCATCCA GCGATGCTCTAACCTCTGAG 723–878 1.000 80.7
trnS-GGA-ycf3_p1 trnS-GGA-ycf3 TGTTCGTGACTTAGGCGAAG CATTTATCCGCGATCTAGGCA 988–1023 1.000 75.6
trnS-GGA-ycf3_p2 trnS-GGA-ycf3 CCCTCGGTAAACAAAAGCCT CATTTATCCGCGATCTAGGCA 945–980 1.000 75.5
trnS-GGA-ycf3_p3 trnS-GGA-ycf3 GCGAAGGTACGGAAAGAGAG CATTTATCCGCGATCTAGGCA 974–1009 1.000 75.4
trnS-GGA-ycf3_p4 trnS-GGA-ycf3 CGTGACTTAGGCGAAGGTAC CATTTATCCGCGATCTAGGCA 984–1019 1.000 75.3
trnS-GGA-ycf3_p5 trnS-GGA-ycf3 GTGACTTAGGCGAAGGTACG CATTTATCCGCGATCTAGGCA 983–1018 1.000 75.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TTTCGTAGTACCCTACCCCC 828–846 1.000 81.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC CAGACCGGAGTTTTGTGGAA TTTCGTAGTACCCTACCCCC 867–885 1.000 80.6
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TTCAGACCGGAGTTTTGTGG TTTCGTAGTACCCTACCCCC 869–887 1.000 80.6
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC TACCGCTGAGTTAAAAGGGC TTTCGTAGTACCCTACCCCC 793–811 1.000 80.3
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 790–808 1.000 80.3
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC TGGCAATATGTCTACGCTGG TACTAAGTCGGGACTGACGG 535–558 1.000 80.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGCAATATGTCTACGCTGGT TACTAAGTCGGGACTGACGG 534–557 1.000 80.3
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG TACTAAGTCGGGACTGACGG 556–579 1.000 79.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT TACTAAGTCGGGACTGACGG 555–578 1.000 79.1
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGCAATATGTCTACGCTGG CGGTGCTCTGACCAATTGAA 483–506 1.000 79.0
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 677–686 1.000 50.7
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 678–687 1.000 47.7
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 677–686 1.000 47.7
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 678–687 1.000 46.6
trnD-GUC-psbM_p5 trnD-GUC-psbM GCATGCCTTATTTCTCTGGGA TGCGAGAATATTGACTTCCA 704–713 1.000 45.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Adonis amurensis NC_056353.1 157032 View on NCBI ↗
Adonis coerulea MK253469.1 157033 View on NCBI ↗
Adonis pseudoamurensis NC_065037.1 156917 View on NCBI ↗
Adonis ramosa NC_072342.1 157057 View on NCBI ↗
Adonis sutchuenensis NC_041474.1 157603 View on NCBI ↗