Markers + reference

Paraquilegia

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 164–164 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 699 0.0219 0.98 73.2 yes View details
rps16-trnQ-UUG LSC 775 0.0133 0.97 69.4 yes View details
trnE-UUC-trnT-GGU LSC 670 0.0060 0.99 57.6 yes View details
rps4-trnT-UGU LSC 404 0.0255 0.97 71.9 yes View details
trnT-UGU-trnL-UAA LSC 710 0.0198 1.00 63.0 yes View details
ycf4-cemA LSC 769 0.0235 1.00 65.8 yes View details
petB LSC 1492 0.0054 1.00 52.4 yes View details
rpoA LSC 1014 0.0039 1.00 46.4 yes View details
rps12-trnV-GAC IRb 6343 0.0017 1.00 53.7 yes View details
ycf1 IRb 1066 0.0009 0.99 46.5 yes View details
ndhF SSC 2229 0.0056 0.96 54.6 yes View details
ccsA SSC 984 0.0031 0.99 53.2 yes View details
ycf1 SSC 5574 0.0027 1.00 51.4 no View details
trnV-GAC-rps12 IRa 6343 0.0017 1.00 53.7 yes View details
rps19-trnH-GUG LSC 75 0.0556 0.96 85.5 no View details
ccsA-ndhD SSC 149 0.0365 0.92 77.1 yes View details
psbC-trnS-UGA LSC 196 0.0255 1.00 67.2 yes View details
atpB-rbcL LSC 715 0.0056 1.00 62.0 yes View details
ycf3-trnS-GGA LSC 605 0.0034 0.96 61.3 yes View details
rpl16 LSC 1349 0.0030 0.99 61.3 yes View details
atpH-atpI LSC 963 0.0031 0.99 61.2 yes View details
petN-psbM LSC 1156 0.0043 1.00 61.2 yes View details
cemA LSC 690 0.0043 1.00 61.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTACCAACGGTATGGACGA CCTTGAAAAAGGCGCTCAAC 892–910 1.000 79.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCTACCAACGGTATGGACGA CTTGAAAAAGGCGCTCAACC 891–909 1.000 79.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 826–844 1.000 79.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 825–843 1.000 79.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTACCAACGGTATGGACGA TGAAAAAGGCGCTCAACCTA 889–907 1.000 79.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACCGATCATGTCCTTCAAGC GAGGTTCGAATCCTTCCGTC 840–864 1.000 82.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 845–869 1.000 81.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACCGATCATGTCCTTCAAGC CTCGGAGGTTCGAATCCTTC 844–868 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTCGGAGGTTCGAATCCTTC 849–873 1.000 80.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAACCGATCATGTCC GAGGTTCGAATCCTTCCGTC 847–871 1.000 79.9
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA ATAGGGGAATCCATGGAGGG 1068 1.000 79.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1025 1.000 79.9
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1081 1.000 79.2
atpH-atpI_p4 atpH-atpI GATACCTTCTACGGCTTGGC ATAGGGGAATCCATGGAGGG 1110 1.000 79.1
atpH-atpI_p5 atpH-atpI CGATACCTTCTACGGCTTGG ATAGGGGAATCCATGGAGGG 1111 1.000 79.0
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1311–1323 1.000 69.0
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1317–1329 1.000 67.5
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1257–1269 1.000 66.3
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTC 1311–1323 1.000 64.8
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTC 1317–1329 1.000 63.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU ACACGATCAACCTCCTTTCG GAACCGATGACTTACGCCTT 818–826 1.000 80.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CACGATCAACCTCCTTTCGT GAACCGATGACTTACGCCTT 817–825 1.000 80.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 803–811 1.000 79.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU ACACGATCAACCTCCTTTCG TGGAAAAAGCCCCTTATCGG 842–850 1.000 79.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CACGATCAACCTCCTTTCGT TGGAAAAAGCCCCTTATCGG 841–849 1.000 79.4
psbC-trnS-UGA_p1 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GAGAGATGGCTGAGTGGTTG 357 1.000 79.9
psbC-trnS-UGA_p2 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GTCTTTCGGAGAGATGGCTG 365 1.000 79.5
psbC-trnS-UGA_p3 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG ATAGCCCCGGTCTTGAAAAC 337 1.000 79.2
psbC-trnS-UGA_p4 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG TCTTTCGGAGAGATGGCTGA 364 1.000 78.9
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGGTTCGAATCCCTCTCTCT 288 1.000 78.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Paraquilegia anemonoides NC_041479.1 164383 View on NCBI ↗
Paraquilegia microphylla NC_067755.1 164390 View on NCBI ↗