Markers + reference

Pulsatilla

8 species · Ranunculaceae · Ranunculales

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Species 8
Genome length 162–164 kb
Candidate markers 273
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnK-UUU LSC 838 0.0300 0.94 64.2 yes View details
trnY-GUA-trnD-GUC LSC 596 0.0614 0.93 87.6 yes View details
ndhC-trnV-UAC LSC 1123 0.0350 0.89 74.4 yes View details
petA-psbJ LSC 561 0.0509 0.82 84.2 yes View details
trnN-GUU-ndhF IRb 2231 0.0285 0.99 68.1 yes View details
ndhF-trnL-UAG SSC 1278 0.0649 0.95 85.4 yes View details
ccsA-ndhD SSC 499 0.1146 0.82 80.2 yes View details
rps15 SSC 273 0.0009 1.00 22.9 yes View details
ndhH-rps15 SSC 196 0.1092 0.96 72.6 yes View details
atpH-atpF LSC 489 0.0126 0.98 66.7 yes View details
trnS-GCU-trnL-UAA LSC 728 0.0252 0.91 65.2 yes View details
trnM-CAU-atpE LSC 268 0.0204 0.98 61.8 yes View details
psbZ-trnS-UGA LSC 374 0.0118 0.94 58.8 yes View details
psbD-trnT-GGU LSC 1300 0.0111 0.97 57.8 yes View details
rps4-rps16 LSC 687 0.0225 0.97 57.6 yes View details
trnP-UGG-psaJ LSC 427 0.0268 0.87 57.0 yes View details
psbM-petN LSC 1227 0.0052 0.97 56.3 yes View details
rps16 LSC 1118 0.0056 0.99 55.8 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
rps4-rps16_p1 rps4-rps16 AGTCGTAGAATATTATTCCCGTCA ATTCCTTCAAGTCGCACGTT 698–1040 1.000 47.5
rps4-rps16_p2 rps4-rps16 AGTCGTAGAATATTATTCCCGTCA AAGTCGCACGTTGCTTTCTA 690–1032 1.000 47.5
rps4-rps16_p3 rps4-rps16 GTCGTAGAATATTATTCCCGTCA ATTCCTTCAAGTCGCACGTT 697–1039 1.000 47.5
rps4-rps16_p4 rps4-rps16 GTCGTAGAATATTATTCCCGTCA AAGTCGCACGTTGCTTTCTA 689–1031 1.000 47.5
rps4-rps16_p5 rps4-rps16 AGTCGTAGAATATTATTCCCGTCAA ATTCCTTCAAGTCGCACGTT 698–1040 1.000 47.5
rps16_p1 rps16 CCCATACCGGTTCCAAACAA AATTTGATTTCGCGTAACGT 1187–1194 1.000 54.8
rps16_p2 rps16 TCAATCCCATACCGGTTCCA AATTTGATTTCGCGTAACGT 1192–1199 1.000 52.2
rps16_p3 rps16 CAATCCCATACCGGTTCCAA AATTTGATTTCGCGTAACGT 1191–1198 1.000 52.0
rps16_p4 rps16 ATCCCATACCGGTTCCAAAC AATTTGATTTCGCGTAACGT 1189–1196 1.000 52.0
rps16_p5 rps16 CCCATACCGGTTCCAAACAA TTTGATTTCGCGTAACGTAA 1186–1192 0.750 39.6
rps16-trnK-UUU_p1 rps16-trnK-UUU GCTCAACCTACGGAAACTGT AAAGCCGAGTACTCTACCGT 916–1096 1.000 85.8
rps16-trnK-UUU_p2 rps16-trnK-UUU GCTCAACCTACGGAAACTGT AAGCCGAGTACTCTACCGTT 915–1095 1.000 85.8
rps16-trnK-UUU_p3 rps16-trnK-UUU GCTCAACCTACGGAAACTGT CCGCACTTAAAAGCCGAGTA 925–1105 1.000 84.9
rps16-trnK-UUU_p4 rps16-trnK-UUU GCTCAACCTACGGAAACTGT TACCGTTGAGTTAGCAACCC 902–1082 1.000 83.6
rps16-trnK-UUU_p5 rps16-trnK-UUU GCTCAACCTACGGAAACTGT CGAATCCGTTGCTTCATCCA 964–1144 1.000 81.9
psbZ-trnS-UGA_p1 psbZ-trnS-UGA CCAACCGTCAGAAGAAGCAA CAACCACTCAGCCATCTCTC 470–494 1.000 82.6
psbZ-trnS-UGA_p2 psbZ-trnS-UGA CCAACCGTCAGAAGAAGCAA GAGCTATCAACCACTCAGCC 477–501 1.000 82.3
psbZ-trnS-UGA_p3 psbZ-trnS-UGA CCAACCGTCAGAAGAAGCAA GGAGCTATCAACCACTCAGC 478–502 1.000 82.3
psbZ-trnS-UGA_p4 psbZ-trnS-UGA CCAACCGTCAGAAGAAGCAA CAAGACCGGAGCTATCAACC 485–509 1.000 82.2
psbZ-trnS-UGA_p5 psbZ-trnS-UGA TGACCAACCGTCAGAAGAAG CAACCACTCAGCCATCTCTC 473–497 1.000 81.6
psbD-trnT-GGU_p1 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GCCCTTTTAACTCAGCGGTA 1431–1575 1.000 82.3
psbD-trnT-GGU_p2 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA ATGGGCCCTTTTAACTCAGC 1435–1579 1.000 81.9
psbD-trnT-GGU_p3 psbD-trnT-GGU TCTCCGTAACCAGTCATCCA GGCGTAAGTCATCGGTTCAA 1394–1538 1.000 81.0
psbD-trnT-GGU_p4 psbD-trnT-GGU GGTCTCTCCGTAACCAGTCA GCCCTTTTAACTCAGCGGTA 1435–1579 1.000 80.4
psbD-trnT-GGU_p5 psbD-trnT-GGU GGTCTCTCCGTAACCAGTCA ATGGGCCCTTTTAACTCAGC 1439–1583 1.000 80.0
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC TGGCAATATGTCTACGCTGG GTGCTCTGACCGATTGAACT 568–883 1.000 89.4
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGCAATATGTCTACGCTGGT GTGCTCTGACCGATTGAACT 567–882 1.000 89.4
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GTGCTCTGACCGATTGAACT 589–904 1.000 88.5
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT GTGCTCTGACCGATTGAACT 588–903 1.000 88.3
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC GATTCTTCCTGGGTCGATGC GTGCTCTGACCGATTGAACT 622–937 1.000 88.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Pulsatilla campanella NC_061038.1 162322 View on NCBI ↗
Pulsatilla cernua MK860684.1 162481 View on NCBI ↗
Pulsatilla cernua var. koreana NC_045908.1 162709 View on NCBI ↗
Pulsatilla chinensis f. alba OR085847.1 163654 View on NCBI ↗
Pulsatilla chinensis var. kissii MK860683.1 163756 View on NCBI ↗
Pulsatilla dahurica MK860685.1 162450 View on NCBI ↗
Pulsatilla saxatilis OP729488.1 162659 View on NCBI ↗
Pulsatilla tongkangensis NC_061398.1 163442 View on NCBI ↗