Markers + reference

Anemonastrum

4 species · Ranunculaceae · Ranunculales

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Species 4
Genome length 157–159 kb
Candidate markers 278
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 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps4-rps16 LSC 587 0.0907 0.93 82.9 yes View details
ycf3-psaA LSC 793 0.0606 0.94 86.8 yes View details
psbD-trnT-GGU LSC 1160 0.0622 0.92 87.6 yes View details
trnT-GGU-trnE-UUC LSC 641 0.0549 0.95 87.6 yes View details
trnD-GUC-psbM LSC 1172 0.0617 0.94 89.6 yes View details
psbM-petN LSC 1112 0.0661 0.95 84.0 yes View details
trnG-GCC-trnS-GCU LSC 390 0.2692 0.96 80.1 yes View details
ndhC-trnV-UAC LSC 925 0.0833 0.93 84.4 yes View details
psbE-petL LSC 1406 0.0543 0.94 83.2 yes View details
ycf1 IRb 2846 0.0320 0.99 55.9 yes View details
ycf1 IRa 5613 0.0351 0.99 62.9 no View details
psbA-trnH-GUG LSC 303 0.0923 0.90 84.0 yes View details
trnF-GAA-ndhJ LSC 519 0.0652 0.87 82.3 yes View details
accD-psaI LSC 619 0.0511 0.92 81.5 yes View details
trnR-UCU-trnG-GCC LSC 159 0.0730 0.96 81.3 yes View details
psbK-psbI LSC 415 0.0612 0.96 80.8 yes View details
trnC-GCA-rpoB LSC 1166 0.0467 0.96 80.7 yes View details
ndhF-trnL-UAG SSC 330 0.0579 0.98 80.7 yes View details
petA-psbJ LSC 419 0.0738 0.98 80.3 yes View details
ycf4-cemA LSC 592 0.0561 0.98 80.2 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
rps4-rps16_p1 rps4-rps16 CGCTCCGGAAAAAGATCTCA TGGCGGGAACATTTGAAGAA 1248 0.250 49.8
rps4-rps16_p2 rps4-rps16 ACGCTCCGGAAAAAGATCTC TGGCGGGAACATTTGAAGAA 1249 0.250 49.8
rps4-rps16_p3 rps4-rps16 CGCTCCGGAAAAAGATCTCA GCGGGAACATTTGAAGAAGC 1246 0.250 49.8
rps4-rps16_p4 rps4-rps16 ACGCTCCGGAAAAAGATCTC GCGGGAACATTTGAAGAAGC 1247 0.250 49.8
rps4-rps16_p5 rps4-rps16 CGCTCCGGAAAAAGATCTCA ATGGGGAAACGTAGGGAAGA 1456 0.250 49.6
psbA-trnH-GUG_p1 psbA-trnH-GUG TCTAGCGGCTGTTGAAGTTC CGAGATATAGTGGGCGAACG 411–429 1.000 91.1
psbA-trnH-GUG_p2 psbA-trnH-GUG TTCCCTCTAGATCTAGCGGC CGAGATATAGTGGGCGAACG 422–440 1.000 91.0
psbA-trnH-GUG_p3 psbA-trnH-GUG GGCTGTTGAAGTTCCATCCA CGAGATATAGTGGGCGAACG 405–423 1.000 91.0
psbA-trnH-GUG_p4 psbA-trnH-GUG CCTCTAGATCTAGCGGCTGT CGAGATATAGTGGGCGAACG 419–437 1.000 91.0
psbA-trnH-GUG_p5 psbA-trnH-GUG GCGAACCTTGGTATGGAAGT CGAGATATAGTGGGCGAACG 467–485 1.000 90.4
psbK-psbI_p1 psbK-psbI CAAGCGGCTGTAAGTTTTCG TCTTCACGTCCAGGATTACG 546–573 1.000 81.4
psbK-psbI_p2 psbK-psbI AGCGGCTGTAAGTTTTCGAT TCTTCACGTCCAGGATTACG 544–571 1.000 81.1
psbK-psbI_p3 psbK-psbI AAGCGGCTGTAAGTTTTCGA TCTTCACGTCCAGGATTACG 545–572 1.000 80.8
psbK-psbI_p4 psbK-psbI GCAAGCGGCTGTAAGTTTTC TCTTCACGTCCAGGATTACG 547–574 1.000 79.3
psbK-psbI_p5 psbK-psbI CAAGCGGCTGTAAGTTTTCG TTCTTCACGTCCAGGATTACG 547–574 1.000 79.0
ycf3-psaA_p1 ycf3-psaA TTGGTTGAAGATCACGAGGC GCCCATTCCTCGAAAGAAGT 864–904 1.000 88.9
ycf3-psaA_p2 ycf3-psaA TTGGTTGAAGATCACGAGGC GAGAAATGACCTGGTCTGGC 882–922 1.000 87.6
ycf3-psaA_p3 ycf3-psaA TCACGAGGCGGTTTGAATAA GCCCATTCCTCGAAAGAAGT 853–893 1.000 86.8
ycf3-psaA_p4 ycf3-psaA TCACGAGGCGGTTTGAATAA GAGAAATGACCTGGTCTGGC 871–911 1.000 85.5
ycf3-psaA_p5 ycf3-psaA GATCACGAGGCGGTTTGAAT GCCCATTCCTCGAAAGAAGT 855–895 1.000 85.4
psbD-trnT-GGU_p1 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GCCCTTTTAACTCAGCGGTA 1297–1366 1.000 88.8
psbD-trnT-GGU_p2 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GGCGTAAGTCATCGGTTCAA 1260–1329 1.000 87.6
psbD-trnT-GGU_p3 psbD-trnT-GGU GGTCTCTCCGTAACCAGTCA GCCCTTTTAACTCAGCGGTA 1301–1370 1.000 87.0
psbD-trnT-GGU_p4 psbD-trnT-GGU GGTCTCTCCGTAACCAGTCA GGCGTAAGTCATCGGTTCAA 1264–1333 1.000 85.7
psbD-trnT-GGU_p5 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GCCATGGTAAGGCGTAAGTC 1270–1339 1.000 84.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TTTCGTAGTACCCTACCCCC 644–782 1.000 89.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TGTCCTGAACCACTAGACGA 585–723 1.000 88.9
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TACCGCTGAGTTAAAAGGGC TTTCGTAGTACCCTACCCCC 609–747 1.000 88.8
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 606–744 1.000 88.8
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGAAAAAGCCCCTTATCGG TTTCGTAGTACCCTACCCCC 668–806 1.000 88.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Anemonastrum flaccidum NC_060982.1 157213 View on NCBI ↗
Anemonastrum narcissiflorum NC_045879.1 158557 View on NCBI ↗
Anemonastrum shikokianum NC_069812.1 159286 View on NCBI ↗
Anemonastrum trullifolium NC_039456.1 157096 View on NCBI ↗