Markers + reference

Pimpinella

26 species · Apiaceae · Apiales

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Species 26
Genome length 146–166 kb
Candidate markers 287
Primer pairs 85

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 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 896 0.0641 0.58 70.6 yes View details
rps16-trnQ-UUG LSC 1349 0.0491 0.63 67.5 yes View details
trnE-UUC-trnT-GGU LSC 896 0.0592 0.82 77.7 yes View details
ndhC-trnV-UAC LSC 741 0.0699 0.98 78.0 yes View details
petA-psbJ LSC 971 0.0593 0.85 75.6 yes View details
ndhF-rpl32 SSC 1163 0.0510 0.78 74.7 yes View details
rpl32-trnL-UAG SSC 662 0.0739 0.78 69.1 yes View details
rpl36-trnH-GUG LSC 5269 0.0732 0.02 60.1 no View details
trnC-GCA-petN LSC 696 0.0429 0.96 80.4 yes View details
trnT-UGU-trnL-UAA LSC 762 0.0409 0.95 77.3 yes View details
rpoB-trnC-GCA LSC 1253 0.0433 0.97 76.6 yes View details
atpH-atpI LSC 1142 0.0446 0.98 74.1 yes View details
psbA-trnK-UUU LSC 213 0.0501 0.95 73.0 yes View details
trnT-GGU-psbD LSC 1416 0.0389 0.98 72.6 yes View details
rps4-trnT-UGU LSC 373 0.0496 0.91 72.4 yes View details
trnS-GCU-trnG-UCC LSC 567 0.0445 0.92 71.5 yes View details
ycf3-trnS-GGA LSC 867 0.0423 0.89 71.3 yes View details
atpB-rbcL LSC 764 0.0336 0.96 71.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU GCTTTCGCGTCTCTCTAAAA CTAGTTCCGGGTTCGAATCC 260–297 1.000 75.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TCGCGTCTCTCTAAAATAGCAG CTAGTTCCGGGTTCGAATCC 256–293 1.000 73.9
psbA-trnK-UUU_p3 psbA-trnK-UUU TCGCGTCTCTCTAAAATAGCA CTAGTTCCGGGTTCGAATCC 256–293 1.000 73.8
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTTTCGCGTCTCTCTAAAA ACTCCATCCGACTAGTTCCG 271–308 1.000 72.8
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTTCGCGTCTCTCTAAAAT CTAGTTCCGGGTTCGAATCC 260–297 1.000 72.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TCTATCCCAATGAGCCGTCT 836–1244 1.000 91.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 835–1243 1.000 91.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AGCCGTCTATCGAATCGTTG 824–1232 1.000 90.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGCCGTCTATCGAATCGTTG 823–1231 1.000 90.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG TCTATCCCAATGAGCCGTCT 988–1192 0.346 64.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CTTACAGCAGCTTGCCAAAC 1616–2159 1.000 90.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACTTTCTACCCGAGCTCCAT CTTACAGCAGCTTGCCAAAC 1619–2162 1.000 90.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT TTTGCCCTGGAATTGACCAA 1157–1700 0.231 54.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CCCAGCTATCCAACGAAGAC 1754–2297 0.231 54.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACTTTCTACCCGAGCTCCAT CCCAGCTATCCAACGAAGAC 1757–2300 0.231 53.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 575–662 1.000 63.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 624–711 1.000 62.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 576–663 1.000 61.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 625–712 1.000 60.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 561–648 1.000 60.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TGCTTTGGCTTTACTCACGT 846–1537 1.000 91.4
atpH-atpI_p2 atpH-atpI CTCGCGATACCTTCTACAGC TGCTTTGGCTTTACTCACGT 936–1627 1.000 91.4
atpH-atpI_p3 atpH-atpI CTTGGACTACGAACGGGAAG TGCTTTGGCTTTACTCACGT 1253–1942 0.885 86.4
atpH-atpI_p4 atpH-atpI CTTGGACTACGAACGGGAAG TTCGGAACCCACAAACCATT 1494–2183 0.885 85.6
atpH-atpI_p5 atpH-atpI TACTCATCCGCAAATCAGCC TGCTTTGGCTTTACTCACGT 1208–1897 0.231 54.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1784–1851 1.000 90.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CCGGATTTGAACTGGGGAAA 1976–2043 1.000 90.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CTTACCACTCGGCCATATCG 1764–1811 0.885 84.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CTTACCACTCGGCCATATCG 1956–2003 0.885 84.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CGGAATTCAAGACTCAGCCA 2223–2291 0.308 59.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (26)

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

Species Accession Length (bp) Link
Pimpinella acuminata PQ551036.1 165871 View on NCBI ↗
Pimpinella alpina OR896890.1 152816 View on NCBI ↗
Pimpinella candolleana NC_070341.1 153199 View on NCBI ↗
Pimpinella caudata PV794573.1 165877 View on NCBI ↗
Pimpinella chungdienensis PV794574.1 153023 View on NCBI ↗
Pimpinella cnidioides PV794575.1 152443 View on NCBI ↗
Pimpinella coriacea PV794576.1 153106 View on NCBI ↗
Pimpinella diversifolia NC_070342.1 153135 View on NCBI ↗
Pimpinella fargesii PV794580.1 151868 View on NCBI ↗
Pimpinella flaccida PV794581.1 152943 View on NCBI ↗
Pimpinella grisea PV794582.1 152637 View on NCBI ↗
Pimpinella helosciadoidea PV794585.1 147204 View on NCBI ↗
Pimpinella henryi PV794584.1 152089 View on NCBI ↗
Pimpinella kingdon-wardii PV794587.1 153074 View on NCBI ↗
Pimpinella major OR896889.1 152412 View on NCBI ↗
Pimpinella purpurea NC_070343.1 165666 View on NCBI ↗
Pimpinella renifolia PV794594.1 153133 View on NCBI ↗
Pimpinella rhomboidea NC_070344.1 153297 View on NCBI ↗
Pimpinella rockii PV794596.1 153105 View on NCBI ↗
Pimpinella rubescens NC_070345.1 152236 View on NCBI ↗
Pimpinella silvatica PV794598.1 152285 View on NCBI ↗
Pimpinella smithii NC_061043.1 146350 View on NCBI ↗
Pimpinella thellungiana NC_070347.1 152558 View on NCBI ↗
Pimpinella tibetanica PV794600.1 153151 View on NCBI ↗
Pimpinella valleculosa NC_070348.1 146432 View on NCBI ↗
Pimpinella yunnanensis PV794603.1 153126 View on NCBI ↗