Markers + reference

Anemone

11 species · Ranunculaceae · Ranunculales

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Species 11
Genome length 159–163 kb
Candidate markers 281
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps4-rps16 LSC 585 0.0504 0.98 86.7 yes View details
rps16-trnK-UUU LSC 825 0.0662 0.95 84.3 yes View details
trnG-UCC-trnS-GCU LSC 1173 0.1240 0.98 84.6 yes View details
trnS-GCU-trnL-UAA LSC 700 0.0325 0.99 76.3 yes View details
ndhC-trnV-UAC LSC 1129 0.0473 0.97 84.2 yes View details
ycf1 IRb 1842 0.0105 1.00 56.6 no View details
ndhF SSC 2232 0.0178 1.00 60.8 yes View details
ndhF-rpl32 SSC 1659 0.0446 0.98 77.0 yes View details
ndhE-ndhG SSC 260 0.0870 0.93 75.8 yes View details
ycf1 SSC 5637 0.0218 1.00 60.7 yes View details
ccsA-ndhD SSC 255 0.0794 1.00 85.3 yes View details
ndhG-ndhI SSC 374 0.0499 1.00 81.9 yes View details
rps12-clpP LSC 166 0.0446 0.96 78.4 yes View details
trnD-GUC-psbM LSC 1078 0.0283 1.00 78.2 yes View details
trnS-GGA-ycf3 LSC 874 0.0244 0.97 76.3 yes View details
trnT-GGU-trnE-UUC LSC 685 0.0197 0.99 76.3 yes View details
petL-petG LSC 175 0.0362 0.98 75.2 yes View details
infA-rps4 IRa 120 0.0359 1.00 75.1 no 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps4-rps16_p1 rps4-rps16 GTAAGTGGGTCGGTTTGGAA AAGTCGCACGTTGCTTTCTA 608–989 1.000 88.8
rps4-rps16_p2 rps4-rps16 AAGTGGGTCGGTTTGGAAAT AAGTCGCACGTTGCTTTCTA 606–987 1.000 87.9
rps4-rps16_p3 rps4-rps16 AGTAAGTGGGTCGGTTTGGA AAGTCGCACGTTGCTTTCTA 609–990 1.000 86.3
rps4-rps16_p4 rps4-rps16 GTAAGTGGGTCGGTTTGGAA CGTTGCTTTCTACCACATCG 600–981 1.000 83.6
rps4-rps16_p5 rps4-rps16 GTAAGTGGGTCGGTTTGGAA AGTCGCACGTTGCTTTCTAC 607–988 1.000 83.0
rps16-trnK-UUU_p1 rps16-trnK-UUU CATTAATTACGCGAAATCAAAT AAAGCCGAGTACTCTACCGT 791–963 0.818 44.7
rps16-trnK-UUU_p2 rps16-trnK-UUU CATTAATTACGCGAAATCAAAT AAGCCGAGTACTCTACCGTT 790–962 0.818 44.7
rps16-trnK-UUU_p3 rps16-trnK-UUU CATTAATTACGCGAAATCAAATT AAAGCCGAGTACTCTACCGT 791–963 0.818 44.7
rps16-trnK-UUU_p4 rps16-trnK-UUU CATTAATTACGCGAAATCAAATT AAGCCGAGTACTCTACCGTT 790–962 0.818 44.7
rps16-trnK-UUU_p5 rps16-trnK-UUU CATTAATTACGCGAAATCAAAT TACCGTTGAGTTAGCAACCC 777–949 0.818 44.7
trnS-GGA-ycf3_p1 trnS-GGA-ycf3 CCCTCGGTAAACAAAAGCCT CATTTATCCGCGATCTAGGCA 912–963 1.000 80.6
trnS-GGA-ycf3_p2 trnS-GGA-ycf3 ACGGAAAGAGAGGGATTCGA CATTTATCCGCGATCTAGGCA 933–984 1.000 80.0
trnS-GGA-ycf3_p3 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA CATTTATCCGCGATCTAGGCA 883–934 1.000 80.0
trnS-GGA-ycf3_p4 trnS-GGA-ycf3 ACCCTCGGTAAACAAAAGCC CATTTATCCGCGATCTAGGCA 913–964 1.000 78.2
trnS-GGA-ycf3_p5 trnS-GGA-ycf3 CCCTCGGTAAACAAAAGCCT TTTATCCGCGATCTAGGCAT 910–961 1.000 77.6
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT AGCCTCCTTTCCTAGTACCC 814–874 1.000 87.2
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCCTCCTTTCCTAGTACCCT 813–873 1.000 87.2
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 769–829 1.000 86.8
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC TACCGCTGAGTTAAAAGGGC AGCCTCCTTTCCTAGTACCC 779–839 1.000 86.6
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TACCGCTGAGTTAAAAGGGC GCCTCCTTTCCTAGTACCCT 778–838 1.000 86.6
trnD-GUC-psbM_p1 trnD-GUC-psbM GTTCGAGCCCCGTCAGTC AGAATGAACAGTGCAGTAGC 869–1204 1.000 51.3
trnD-GUC-psbM_p2 trnD-GUC-psbM GTTCGAGCCCCGTCAGTC TCGTTTTGACTGACCGTTTT 923–1258 1.000 51.0
trnD-GUC-psbM_p3 trnD-GUC-psbM GTTCGAGCCCCGTCAGTC AATCGTTTTGACTGACCGTT 925–1260 1.000 51.0
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCGAGCCCCGTCAGTC ATCGTTTTGACTGACCGTTT 924–1259 1.000 51.0
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCGAGCCCCGTCAGTC TCGTTTTGACTGACCGTTTTT 923–1258 1.000 51.0
trnG-UCC_p1 trnG-UCC TCACATTAATGATACACGCATCA TCTTGTTCGACAAATGGTCCA 865–928 0.909 46.1
trnG-UCC_p2 trnG-UCC TTCACATTAATGATACACGCATCA TCTTGTTCGACAAATGGTCCA 866–929 0.909 46.1
trnG-UCC_p3 trnG-UCC CACATTAATGATACACGCATCA TCTTGTTCGACAAATGGTCCA 864–927 0.909 46.1
trnG-UCC_p4 trnG-UCC TCACATTAATGATACACGCATCA CTTGTTCGACAAATGGTCCA 864–927 0.909 46.1
trnG-UCC_p5 trnG-UCC TCACATTAATGATACACGCATCAT TCTTGTTCGACAAATGGTCCA 865–928 0.909 46.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Anemone altaica NC_064389.1 160806 View on NCBI ↗
Anemone amurensis PX705446.1 160564 View on NCBI ↗
Anemone coronaria NC_082177.1 159564 View on NCBI ↗
Anemone hortensis NC_066445.1 158962 View on NCBI ↗
Anemone montana subsp. montana PP541875.1 162635 View on NCBI ↗
Anemone nemorosa NC_066446.1 160895 View on NCBI ↗
Anemone reflexa NC_054280.1 160910 View on NCBI ↗
Anemone sylvestris PQ178993.1 161033 View on NCBI ↗
Anemone thomsonii var. thomsonii OR251126.1 160058 View on NCBI ↗
Anemone trifolia subsp. trifolia PP316516.1 160856 View on NCBI ↗
Anemone turczaninovii MK860686.1 162795 View on NCBI ↗