Markers + reference

Halerpestes

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 156–157 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 764 0.1588 0.63 75.0 yes View details
rps16-trnQ-UUG LSC 1333 0.2056 0.80 83.5 yes View details
trnC-GCA-petN LSC 882 0.1249 0.96 87.3 yes View details
ndhC-trnV-UAC LSC 466 0.3091 0.97 83.6 yes View details
trnN-GUU-ndhF SSC 2514 0.2612 0.30 67.9 yes View details
ndhF-rpl32 SSC 784 0.2052 0.93 83.3 yes View details
rpl32-trnL-UAG SSC 760 0.1795 0.89 82.3 yes View details
trnT-UGU-trnL-UAA LSC 674 0.1008 0.93 88.5 yes View details
trnE-UUC-trnT-GGU LSC 730 0.1335 0.90 88.3 yes View details
psbE-petL LSC 1188 0.1046 0.95 85.9 yes View details
trnD-GUC-trnY-GUA LSC 438 0.1410 0.89 84.8 yes View details
trnF-GAA-ndhJ LSC 732 0.0931 0.91 84.4 yes View details
rbcL-accD LSC 746 0.1060 0.94 84.0 yes View details
petN-psbM LSC 1223 0.1333 0.95 83.7 yes View details
psbZ-trnG-GCC LSC 445 0.1149 0.86 83.3 yes View details
trnL-UAA-trnF-GAA LSC 404 0.0873 0.94 83.2 yes View details
rpoB-trnC-GCA LSC 1043 0.1098 0.89 82.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG TGAAACGATTCGGGATCACC 1936 0.500 59.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCTTGGGCCAGCAAATGAT TGAAACGATTCGGGATCACC 2163 0.500 59.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TGAAACGATTCGGGATCACC 1539 0.500 59.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATTCACTCGACCCAACCATG TGAAACGATTCGGGATCACC 1705 0.500 58.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CACTCGACCCAACCATGAAT TGAAACGATTCGGGATCACC 1702 0.500 58.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1206–1398 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG CTCGGAGGTTCGAATCCTTC 1210–1402 1.000 84.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1209–1401 1.000 82.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG ACTCGGAGGTTCGAATCCTT 1211–1403 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA CTCGGAGGTTCGAATCCTTC 1213–1405 1.000 81.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTTCCGCCAATCCTTGATCA CCGGATTTGAACTGGGGAAA 1123–1205 1.000 90.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG CCGGATTTGAACTGGGGAAA 1415–1497 1.000 89.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GAAAATACCGGATCCCCACC CCGGATTTGAACTGGGGAAA 1742–1824 1.000 88.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCACCTACACAAGCAAAT CCGGATTTGAACTGGGGAAA 1729–1811 1.000 88.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATTAATCCCGCGGACACA CCGGATTTGAACTGGGGAAA 1367 0.500 58.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 945–962 1.000 90.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 939–956 1.000 88.6
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 963–980 1.000 87.8
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 957–974 1.000 86.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CATTAAAGCAGCCCAAGCAA 947–964 1.000 84.1
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA GTCAAGAGTTGTGGAGTGGG 1882–1961 1.000 91.0
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TCAAGAGTTGTGGAGTGGGA 1881–1960 1.000 90.4
petN-psbM_p3 petN-psbM TTGACTCTGCGGCATTGATT GTCAAGAGTTGTGGAGTGGG 1984–2057 1.000 89.4
petN-psbM_p4 petN-psbM TTTGACTCTGCGGCATTGAT GTCAAGAGTTGTGGAGTGGG 1985–2058 1.000 89.4
petN-psbM_p5 petN-psbM ATCCCTTTTTGACTCTGCGG GTCAAGAGTTGTGGAGTGGG 2065 0.500 57.7
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA TATTAGGTCGGGACTGACGG TGGCAATATGTCTACGCTGG 533–560 1.000 87.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA TATTAGGTCGGGACTGACGG GGCAATATGTCTACGCTGGT 532–559 1.000 87.5
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA TATTAGGTCGGGACTGACGG GGGGACGGACTGTAAATTCG 554–581 1.000 86.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 481–508 1.000 86.3
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TATTAGGTCGGGACTGACGG GGGACGGACTGTAAATTCGT 553–580 1.000 86.2

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
Halerpestes sarmentosa PV621857.1 157319 View on NCBI ↗
Halerpestes tricuspis PP234556.1 156033 View on NCBI ↗