Markers + reference

Asteropyrum

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 164–164 kb
Candidate markers 285
Primer pairs 110

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 10 remaining regions by MarkerSeek score (out of 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1342 0.0170 0.97 67.8 yes View details
petN-psbM LSC 1338 0.0161 0.97 63.2 yes View details
trnT-GGU-psbD LSC 1808 0.0219 0.99 60.0 yes View details
psaA-ycf3 LSC 812 0.0181 0.89 58.6 yes View details
trnT-UGU-trnL-UAA LSC 1569 0.0281 0.97 64.3 yes View details
ndhC-trnV-UAC LSC 1238 0.0265 0.94 64.1 yes View details
rbcL-accD LSC 823 0.0259 0.98 60.8 yes View details
ycf4-cemA LSC 755 0.0195 0.88 67.8 yes View details
petD LSC 1182 0.0119 0.99 55.5 yes View details
ycf1 IRb 798 0.0000 1.00 25.4 no View details
ndhA SSC 2117 0.0153 0.99 55.1 yes View details
rps15 SSC 228 0.0090 0.98 44.8 yes View details
ycf1 SSC 5292 0.0136 1.00 60.4 yes View details
rpoA-trnH-GUG LSC 548 0.0167 0.33 45.5 no View details
trnR-UCU-atpA LSC 131 0.0465 0.98 80.6 yes View details
ndhE-ndhG SSC 185 0.0465 0.93 76.4 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
rpl16-rps3 IRb 175 0.0294 0.97 72.1 yes View details
rps3-rpl16 IRa 175 0.0294 0.97 72.1 yes View details
ndhD-psaC SSC 127 0.0248 0.95 71.2 yes View details
atpF-atpH LSC 506 0.0201 0.98 70.0 yes View details
trnF-GAA-ndhJ LSC 739 0.0145 0.93 69.9 yes View details
petA-psbJ LSC 453 0.0163 0.95 69.8 yes View details
ccsA-ndhD SSC 206 0.0464 0.94 69.3 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1407–1436 1.000 82.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1386–1415 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1397–1426 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAACCGATCATGTCC GAGGTTCGAATCCTTCCGTC 1409–1438 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAACCGATCATGTCCTT TTCGGAGGTTCGAATCCTTC 1411–1440 1.000 77.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AAGACACTCACCGAAGAAGC 298–300 1.000 68.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT CGAAGAAGCGGAAGTCCTTT 287–289 1.000 68.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACACTCACCGAAGAAGC 238–240 1.000 67.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGAAGAAGCGGAAGTCCTTT 227–229 1.000 67.6
trnR-UCU-atpA_p5 trnR-UCU-atpA AGTAGGAATGAAAAGCGTCCA AAGACACTCACCGAAGAAGC 302–304 1.000 67.3
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTATGGACTGGTCGTGGC 601–619 1.000 81.9
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC ATTTATGGACTGGTCGTGGC 628–646 1.000 80.0
atpF-atpH_p3 atpF-atpH AGTGACCCAAGGAAACGAAA ATTTATGGACTGGTCGTGGC 600–618 1.000 76.4
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA GGTCGTGGCATTAGCACTTT 590–608 1.000 75.6
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GTCGTGGCATTAGCACTTTT 589–607 1.000 74.3
rpoC1-rpoB_p1 rpoC1-rpoB CCAACCATCTCTCCGTTAGG TTTGGCTCTGGAACTGAACC 200–205 1.000 75.4
rpoC1-rpoB_p2 rpoC1-rpoB CCCAACCATCTCTCCGTTAG TTTGGCTCTGGAACTGAACC 201–206 1.000 75.4
rpoC1-rpoB_p3 rpoC1-rpoB CCAACCATCTCTCCGTTAGG TTGCTCGTTCGAGAACTACG 223–228 1.000 75.2
rpoC1-rpoB_p4 rpoC1-rpoB CCCAACCATCTCTCCGTTAG TTGCTCGTTCGAGAACTACG 224–229 1.000 75.2
rpoC1-rpoB_p5 rpoC1-rpoB CCAACCATCTCTCCGTTAGG ACGATCTTTGGCTCTGGAAC 206–211 1.000 74.7
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1487–1493 1.000 71.8
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1493–1499 1.000 70.3
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTC 1487–1493 1.000 67.6
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTC 1493–1499 1.000 66.1
petN-psbM_p5 petN-psbM TTGCTTGGGCTGCTTTAATG TGCTACTGCACTGTTCATTCT 1485–1491 1.000 65.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TCTACCAAGGGCTATAGTCA 1901–1950 1.000 52.5
trnT-GGU-psbD_p2 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCTACCAAGGGCTATAGTCA 1864–1913 1.000 51.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ATCTACCAAGGGCTATAGTCA 1902–1951 1.000 49.6
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TCTACCAAGGGCTATAGTCAT 1901–1950 1.000 49.6
trnT-GGU-psbD_p5 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGTAAATCTACCAAGGGCTA 1907–1956 1.000 48.4

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
Asteropyrum cavaleriei NC_041530.1 163660 View on NCBI ↗
Asteropyrum peltatum NC_045850.1 164455 View on NCBI ↗