Markers + reference

Pleurospermum

8 species · Apiaceae · Apiales

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Species 8
Genome length 155–156 kb
Candidate markers 272
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 312 0.0398 1.00 70.0 yes View details
trnK-UUU-rps16 LSC 894 0.0295 0.99 68.7 yes View details
trnS-GCU-trnG-UCC LSC 751 0.0274 0.96 70.5 yes View details
rpoB-trnC-GCA LSC 1230 0.0210 1.00 72.0 yes View details
petN-psbM LSC 1091 0.0218 1.00 65.0 yes View details
trnT-GGU-psbD LSC 1430 0.0242 0.99 69.2 yes View details
trnL-UAA-trnF-GAA LSC 356 0.0169 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 684 0.0274 0.99 73.0 yes View details
psaJ-rpl33 LSC 458 0.0249 1.00 67.1 yes View details
ycf1 IRb 1878 0.0039 1.00 45.7 no View details
ndhF-rpl32 SSC 1189 0.0206 1.00 65.2 yes View details
rpl32-trnL-UAG SSC 920 0.0183 0.97 61.2 yes View details
ycf1 SSC 5445 0.0129 1.00 49.7 yes View details
ndhH-rps15 SSC 91 0.0387 1.00 70.5 yes View details
petA-psbJ LSC 1037 0.0164 0.98 70.2 yes View details
trnG-UCC-trnR-UCU LSC 226 0.0303 0.96 69.2 yes View details
trnF-GAA-ndhJ LSC 386 0.0281 0.98 67.4 yes View details
psaA-pafI LSC 678 0.0095 1.00 67.3 yes View details
rps19-rpl2 IRb 58 0.0365 1.00 67.3 yes View details
trnE-UUC-trnT-GGU LSC 804 0.0211 1.00 66.6 yes View details
pafI-trnS-GGA LSC 873 0.0198 1.00 66.4 yes View details
psbM-trnD-GUC LSC 691 0.0190 1.00 65.4 yes View details
psbE-petL LSC 1157 0.0145 1.00 65.0 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGCTTAGTTTCCGTCTGGG 991–1065 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 992–1066 1.000 83.4
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 993–1067 1.000 83.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 997–1071 1.000 83.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1005–1079 1.000 83.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TGCTGCCATTTTGGAAGGAT 1688–1729 1.000 84.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TGCTGCCATTTTGGAAGGAT 1687–1728 1.000 84.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AGGGATCCCAGAACAAGGAA 1619–1660 1.000 84.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGGGATCCCAGAACAAGGA 1619–1660 1.000 84.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGGGATCCCAGAACAAGGAA 1618–1659 1.000 84.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGGTTACTAGAACGAATCA 629–830 1.000 69.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGGTTACTAGAACGAATCAC 629–830 1.000 68.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGGTTACTAGAACGAATCA 624–825 1.000 68.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AGGGGGTTACTAGAACGAATCA 630–831 1.000 68.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGGTTACTAGAACGAATCAC 624–825 1.000 68.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 276–306 1.000 72.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 282–312 1.000 71.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT AGAAGACCTCTGTCCTATCCA 265–295 1.000 69.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU TAACGATGCGGGTTCGATTC AGAAGACCTCTGTCCTATCCA 264–294 1.000 69.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT AGGTTTAGAAGACCTCTGTCCT 271–301 1.000 68.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CTTACCACTCGGCCATATCG 1242–1276 1.000 86.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCGGATTTGAACTGGGGAAA 1282–1316 1.000 85.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA TTATTGATCAGGCGACACCC 1300–1334 1.000 83.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA AAAAGGATTTGCAGTCCCCC 1264–1298 1.000 83.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCTTACCACTCGGCCATATC 1243–1277 1.000 83.1
petN-psbM_p1 petN-psbM TTCCCGATCCCCCTCTATTC AAGTCTCCCCTTCTGACTCC 2021–2088 1.000 85.0
petN-psbM_p2 petN-psbM TTCCCGATCCCCCTCTATTC CTTTCCCTTTTCGTTTCGCC 2299–2366 0.875 79.6
petN-psbM_p3 petN-psbM CTTCCCGATCCCCCTCTATT CTTTCCCTTTTCGTTTCGCC 2300–2367 0.875 79.5
petN-psbM_p4 petN-psbM TTCCCGATCCCCCTCTATTC CCCTTTTCGTTTCGCCTTTC 2295–2336 0.750 73.4
petN-psbM_p5 petN-psbM CTTCCCGATCCCCCTCTATT CCCTTTTCGTTTCGCCTTTC 2296–2337 0.750 73.4

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
Pleurospermum astrantioideum NC_071798.1 155972 View on NCBI ↗
Pleurospermum camtschaticum NC_033343.1 155415 View on NCBI ↗
Pleurospermum cristatum OP425136.1 155672 View on NCBI ↗
Pleurospermum franchetianum NC_060749.1 155656 View on NCBI ↗
Pleurospermum gonocaulum NC_071802.1 155399 View on NCBI ↗
Pleurospermum rupestre NC_071807.1 155917 View on NCBI ↗
Pleurospermum szechenyii NC_071808.1 156023 View on NCBI ↗
Pleurospermum wrightianum PX091994.1 155856 View on NCBI ↗