Markers + reference

Ranunculus

22 species · Ranunculaceae · Ranunculales

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Species 22
Genome length 155–158 kb
Candidate markers 266
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnN-GUU-ycf1 IRb 1480 0.1546 0.70 69.3 yes View details
ndhF-rpl32 SSC 886 0.0997 0.98 78.9 yes View details
rpl32-trnL-UAG SSC 685 0.0947 0.96 75.8 yes View details
ycf1-trnN-GUU IRa 1480 0.2004 0.77 72.5 yes View details
psbE-petL LSC 1151 0.0460 0.99 83.0 yes View details
trnT-GGU-psbD LSC 1480 0.0452 0.98 81.9 yes View details
trnE-UUC-trnT-GGU LSC 721 0.0438 0.98 81.6 yes View details
rps16-trnQ-UUG LSC 1090 0.0668 0.98 81.0 yes View details
ndhC-trnV-UAC LSC 1321 0.0542 0.97 79.3 yes View details
rpl2-trnH-GUG IRa 66 0.1169 0.99 79.3 no View details
petN-psbM LSC 897 0.0579 0.99 77.7 yes View details
psaA-ycf3 LSC 766 0.0502 0.93 77.0 yes View details
trnK-UUU-rps16 LSC 484 0.0629 0.97 75.7 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG ACGGGAATCAAGCATTCACA 1682–1775 0.909 86.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG CTTGAAAAAGGCGCTCAACC 1040–1124 0.909 86.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG ATTCTTTCTCGAGCCGTACG 1241–1325 0.864 85.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG ACACGGGAATCAAGCATTCA 1684–1777 0.636 75.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG TCACACGGGAATCAAGCATT 1686–1779 0.636 75.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACCGATCACGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1034–1257 1.000 90.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAACCGATCACGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1035–1258 1.000 89.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACCGATCACGTCCTTCAAG CTCGGAGGTTCGAATCCTTC 1038–1261 1.000 89.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATCCACAACCGATCACGTC GAGGTTCGAATCCTTCCGTC 1041–1264 1.000 89.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACCGATCACGTCCTTCAA CTCGGAGGTTCGAATCCTTC 1039–1262 1.000 88.6
petN-psbM_p1 petN-psbM AGTATGGGGAAGAAGTGGACT ACGTAAAAACGGTCAGTCAA 886–1314 1.000 62.9
petN-psbM_p2 petN-psbM AGTATGGGGAAGAAGTGGACT ACGTAAAAACGGTCAGTCAAA 886–1314 1.000 61.1
petN-psbM_p3 petN-psbM AGTATGGGGAAGAAGTGGACT ACGTAAAAACGGTCAGTCAAAA 886–1314 1.000 58.8
petN-psbM_p4 petN-psbM AGTATGGGGAAGAAGTGGAC ACGTAAAAACGGTCAGTCAA 886–1314 1.000 58.4
petN-psbM_p5 petN-psbM GTATGGGGAAGAAGTGGACT ACGTAAAAACGGTCAGTCAA 885–1313 1.000 58.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 834–909 1.000 90.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 799–874 1.000 89.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 796–871 1.000 89.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 775–850 1.000 89.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 831–906 1.000 89.5
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TCTCCGTAACCAGTCATCCA 1519–1648 1.000 89.4
trnT-GGU-psbD_p2 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCTCCGTAACCAGTCATCCA 1482–1611 1.000 87.9
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGTCTCTCCGTAACCAGTCA 1523–1652 1.000 87.5
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGGGAAGAGCAATAGACCAG 1564–1693 1.000 86.1
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGTCTCTCCGTAACCAGTCA 1486–1615 1.000 86.1
psaA-ycf3_p1 psaA-ycf3 TAATGGAACCAACCGGCAAA TATACCGATAGCAGGGGGTG 1648–1735 1.000 91.4
psaA-ycf3_p2 psaA-ycf3 TAATGGAACCAACCGGCAAA TGGTTGAAGATTACGAGGCG 1271–1329 0.773 82.6
psaA-ycf3_p3 psaA-ycf3 TAATGGAACCAACCGGCAAA GTTGAAGATTACGAGGCGGT 1269–1327 0.773 82.6
psaA-ycf3_p4 psaA-ycf3 ACTTTGGAGCAGCTTTGTGA TGGTTGAAGATTACGAGGCG 1291–1349 0.773 82.0
psaA-ycf3_p5 psaA-ycf3 ACTTTGGAGCAGCTTTGTGA GTTGAAGATTACGAGGCGGT 1289–1347 0.773 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (22)

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

Species Accession Length (bp) Link
Ranunculus acris PP541876.1 156596 View on NCBI ↗
Ranunculus arvensis PV621859.1 156925 View on NCBI ↗
Ranunculus aureopetalus PV621860.1 156410 View on NCBI ↗
Ranunculus bulbosus PP840339.1 155505 View on NCBI ↗
Ranunculus bungei OR625572.1 156082 View on NCBI ↗
Ranunculus carinthiacus PP541877.1 156385 View on NCBI ↗
Ranunculus cassubicifolius NC_077490.1 156233 View on NCBI ↗
Ranunculus glareosus PX753853.1 156086 View on NCBI ↗
Ranunculus japonicus MZ169045.1 156981 View on NCBI ↗
Ranunculus kadzusensis PQ246022.1 158301 View on NCBI ↗
Ranunculus mongolicus OR625576.1 158309 View on NCBI ↗
Ranunculus monophyllus OR625578.1 155973 View on NCBI ↗
Ranunculus montanus PP541878.1 156391 View on NCBI ↗
Ranunculus muricatus PV744414.1 155129 View on NCBI ↗
Ranunculus pekinensis NC_060613.1 156139 View on NCBI ↗
Ranunculus polyrhizos OR625579.1 156000 View on NCBI ↗
Ranunculus sieboldii PV621861.1 157020 View on NCBI ↗
Ranunculus tanguticus OR625580.1 156186 View on NCBI ↗
Ranunculus ternatus NC_081908.1 156003 View on NCBI ↗
Ranunculus trichophyllus OR625577.1 158314 View on NCBI ↗
Ranunculus tuberosus PP541880.1 155676 View on NCBI ↗
Ranunculus uncostigma PV621862.1 155515 View on NCBI ↗