Markers + reference

Actaea

10 species · Ranunculaceae · Ranunculales

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Species 10
Genome length 159–160 kb
Candidate markers 269
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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 319 0.0546 0.97 85.4 yes View details
trnK-UUU-rps16 LSC 777 0.0283 0.99 73.6 yes View details
rps16-trnQ-UUG LSC 1890 0.0242 0.97 70.7 yes View details
trnD-GUC-trnY-GUA LSC 441 0.0343 0.96 74.9 yes View details
trnT-UGU-trnL-UAA LSC 700 0.0248 0.93 76.8 yes View details
ndhC-trnV-UAC LSC 1392 0.0210 0.96 63.1 yes View details
ycf1 IRb 1082 0.0090 1.00 52.9 no View details
ndhF SSC 2250 0.0122 1.00 52.8 yes View details
ndhF-trnL-UAG SSC 1143 0.0263 0.99 72.4 yes View details
ndhG-ndhI SSC 399 0.0277 0.96 63.4 yes View details
ycf1 SSC 5601 0.0141 1.00 49.7 yes View details
ycf1-ndhF SSC 83 0.2210 0.90 72.4 yes View details
ndhH-rps15 SSC 161 0.0427 0.91 71.9 yes View details
ycf3-trnS-GGA LSC 930 0.0186 0.99 71.4 yes View details
rpl14-rpl16 LSC 137 0.0516 0.96 70.8 yes View details
petD-rpoA LSC 196 0.0363 1.00 70.7 yes View details
petN-psbM LSC 1241 0.0143 0.98 68.5 yes View details
psaJ-rpl33 LSC 435 0.0246 0.97 68.2 yes View details
ndhJ-ndhK LSC 148 0.0316 1.00 67.6 yes View details
ccsA-ndhD SSC 237 0.0340 0.97 67.0 yes View details
rps19-trnH-GUG LSC 44 0.1132 1.00 66.3 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 95 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 420–465 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 434–479 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 433–478 1.000 90.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 435–480 1.000 90.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TATCATCAACCGCGCTAACC 431–476 1.000 89.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGCATTAATATTAATTACACGAAA 838–843 0.200 8.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGCATTAATATTAATTACACGAAA 837–842 0.200 8.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CGCATTAATATTAATTACACGAAA 852–857 0.200 8.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGCATTAATATTAATTACACGAAA 847–852 0.200 8.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC CGCATTAATATTAATTACACGAAA 824–829 0.200 8.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACCGATCATGTCCTTCAAGC GAGGTTCGAATCCTTCCGTC 1921–2038 1.000 88.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1926–2043 1.000 87.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACCGATCATGTCCTTCAAGC CTCGGAGGTTCGAATCCTTC 1925–2042 1.000 87.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTCGGAGGTTCGAATCCTTC 1930–2047 1.000 86.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAACCGATCATGTCC GAGGTTCGAATCCTTCCGTC 1928–2045 1.000 85.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCACTGTTCATTCTAGTCCC 1337–1390 1.000 76.6
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1343–1396 1.000 76.0
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCACTGTTCATTCTAGTCCC 1343–1396 1.000 75.1
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1349–1402 1.000 74.5
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA GCACTGTTCATTCTAGTCCCT 1336–1389 1.000 74.3
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT TGGCAATATGTCTACGCTGG 489–513 1.000 87.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT GGCAATATGTCTACGCTGGT 488–512 1.000 87.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA AGTCATCGGGTACTAGGTCG TGGCAATATGTCTACGCTGG 553–577 1.000 86.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA AGTCATCGGGTACTAGGTCG GGCAATATGTCTACGCTGGT 552–576 1.000 86.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA AGTCATCGGGTACTAGGTCG GGGGACGGACTGTAAATTCG 574–598 1.000 85.4
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 988–1029 1.000 78.6
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 1009–1050 1.000 78.0
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTGAA 959–1000 1.000 78.0
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA GACGGAAAGAGAGGGATTCG 1010–1051 1.000 77.5
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 989–1030 1.000 76.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Actaea asiatica NC_041525.1 159638 View on NCBI ↗
Actaea biternata NC_081474.1 159761 View on NCBI ↗
Actaea cimicifuga NC_077574.1 159761 View on NCBI ↗
Actaea dahurica NC_041533.1 159370 View on NCBI ↗
Actaea heracleifolia NC_042253.1 159578 View on NCBI ↗
Actaea japonica NC_081475.1 159736 View on NCBI ↗
Actaea purpurea NC_081476.1 159497 View on NCBI ↗
Actaea simplex PQ675799.1 159635 View on NCBI ↗
Actaea spicata PP316505.1 159753 View on NCBI ↗
Actaea vaginata NC_041543.1 159110 View on NCBI ↗