Markers + reference

Filipendula

10 species · Rosaceae · Rosales

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Species 10
Genome length 154–155 kb
Candidate markers 261
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 940 0.0212 1.00 61.8 yes View details
rps16-trnQ-UUG LSC 779 0.0212 0.99 64.8 yes View details
rpoB-trnC-GCA LSC 1204 0.0166 1.00 53.9 yes View details
petN-ndhC LSC 1394 0.0172 0.99 63.0 yes View details
atpB-rbcL LSC 762 0.0171 1.00 60.6 yes View details
rps3-rpl22 LSC 415 0.0189 1.00 51.9 yes View details
rps12-trnV-GAC IRb 2949 0.0159 1.00 64.5 yes View details
ycf1 IRb 1947 0.0069 1.00 48.2 no View details
ndhF SSC 2292 0.0109 1.00 46.3 yes View details
ndhF-trnL-UAG SSC 1210 0.0207 1.00 64.8 yes View details
ycf1 SSC 5376 0.0108 1.00 47.9 yes View details
trnV-GAC-rps12 IRa 2949 0.0159 1.00 64.5 yes View details
trnE-UUC-trnT-GGU LSC 645 0.0180 1.00 73.4 yes View details
trnS-GCU-trnG-UCC LSC 601 0.0182 1.00 72.1 yes View details
ycf3-psaA LSC 741 0.0151 0.99 71.3 yes View details
trnR-UCU-atpA LSC 519 0.0179 0.96 69.9 yes View details
rpl22-rps19 LSC 611 0.0192 1.00 68.8 yes View details
rbcL-psbM LSC 820 0.0134 0.99 68.7 yes View details
rpl23-trnH-GUG IRa 934 0.0056 1.00 68.4 no View details
clpP-psbB LSC 755 0.0135 1.00 65.7 yes View details
trnS-GGA-ycf3 LSC 868 0.0150 1.00 65.6 yes View details
trnL-UAG-ccsA SSC 115 0.0230 1.00 64.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1092–1295 0.900 83.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 1186–1389 0.900 83.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CTCGACGAGAGGGAAGAGAT 1188–1391 0.900 83.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGATCTCGACGAGAGGGAAG 1209–1395 0.800 78.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ATCTCGACGAGAGGGAAGAG 1207–1393 0.800 78.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 859–873 1.000 84.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 838–852 1.000 84.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 849–863 1.000 84.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TTCGGAGGTTCGAATCCTTC 863–877 1.000 80.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAACGGATCATGTCCTT TAAGGCAACGGGTTTTGGTC 889–903 1.000 79.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGTTGTAGAACGAATCGCA 455–686 1.000 87.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGTTGTAGAACGAATCGCA 454–685 1.000 87.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGGTTGTAGAACGAATCGCA 509–740 1.000 85.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGAAAACGGAAAGAGAGGG GGGTTGTAGAACGAATCGCA 515–746 1.000 85.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC GGGTTGTAGAACGAATCGCA 457–688 1.000 84.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCAAGGAAGCAGAAACCCTT 595–629 0.900 70.7
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CCAAGGAAGCAGAAACCCTT 630–664 0.900 67.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TACCAAGGAAGCAGAAACCC 597–631 0.900 66.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA CCAAGGAAGCAGAAACCCTT 594–628 0.900 65.1
trnR-UCU-atpA_p5 trnR-UCU-atpA ATGGATAGGACAGAGGTCTTCT CCAAGGAAGCAGAAACCCTT 631–665 0.900 63.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTTCCTCATTCCCACCCCC CCGGATTTGAACTGGGGAAA 1292–1306 1.000 73.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTTCCTCATTCCCACCCCC TTTCGTGATTAGGCGACACC 1311–1325 1.000 71.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTTCCTCATTCCCACCCCC AAAAGGATTTGCAGTCCCCC 1274–1288 1.000 71.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTTCCTCATTCCCACCCCC CCGGATTTGAACTGGGGAAA 1291–1305 1.000 69.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTTCCTCATTCCCACCCCC TTTCGTGATTAGGCGACACC 1310–1324 1.000 67.3
petN-ndhC_p1 petN-ndhC TCTTGCTTGGGCTGCTTTAA TCATATTCGTAAAGCAGAAGCA 1296–1493 1.000 56.3
petN-ndhC_p2 petN-ndhC ATCTTGCTTGGGCTGCTTTA TCATATTCGTAAAGCAGAAGCA 1297–1494 1.000 54.6
petN-ndhC_p3 petN-ndhC TAAATCTTGCTTGGGCTGCT TCATATTCGTAAAGCAGAAGCA 1300–1497 1.000 54.6
petN-ndhC_p4 petN-ndhC GTAAATCTTGCTTGGGCTGC TCATATTCGTAAAGCAGAAGCA 1301–1498 1.000 54.1
petN-ndhC_p5 petN-ndhC ATGGGGAAGAAGTGGACTCT TCATATTCGTAAAGCAGAAGCA 1242–1439 1.000 53.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Filipendula angustiloba NC_072629.1 154624 View on NCBI ↗
Filipendula auriculata NC_072622.1 153781 View on NCBI ↗
Filipendula camtschatica NC_073010.1 154205 View on NCBI ↗
Filipendula intermedia NC_072626.1 154610 View on NCBI ↗
Filipendula multijuga NC_072623.1 154633 View on NCBI ↗
Filipendula nuda NC_072627.1 154622 View on NCBI ↗
Filipendula palmata NC_072624.1 154624 View on NCBI ↗
Filipendula ulmaria NC_072628.1 154464 View on NCBI ↗
Filipendula vestita NC_072625.1 154524 View on NCBI ↗
Filipendula vulgaris PP336747.1 154593 View on NCBI ↗