Markers + reference

Pseudognaphalium

5 species · Asteraceae · Asterales

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Species 5
Genome length 153–154 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 411 0.0431 0.92 83.2 yes View details
rps16 LSC 1154 0.0118 0.99 63.4 yes View details
trnR-UCU-trnG-UCC LSC 258 0.0652 0.92 82.2 yes View details
trnG-UCC-trnT-GGU LSC 483 0.0704 0.95 82.4 yes View details
trnT-GGU-psbD LSC 1333 0.0227 0.98 72.7 yes View details
psbZ-trnG-UCC LSC 302 0.0099 1.00 44.2 yes View details
trnG-UCC-trnfM-CAU LSC 282 0.0447 0.97 88.0 yes View details
ndhC-trnV-UAC LSC 1220 0.0169 0.99 73.8 yes View details
psbE-petL LSC 1283 0.0148 0.99 64.6 yes View details
rpl16 LSC 1423 0.0125 0.99 67.1 yes View details
trnL-UAG-rpl32 SSC 813 0.0255 0.98 76.1 yes View details
rpl32-ndhF SSC 1101 0.0137 0.97 68.1 yes View details
atpB-rbcL LSC 651 0.0061 1.00 64.7 yes View details
ycf3-trnS-GGA LSC 925 0.0072 1.00 63.9 yes View details
trnT-UGU-trnL-UAA LSC 597 0.0132 1.00 62.0 yes View details
trnF-GAA-ndhJ LSC 677 0.0079 0.97 61.5 yes View details
ndhA-ndhI SSC 12 0.0333 1.00 60.5 yes View details
accD-psaI LSC 713 0.0055 0.99 59.8 yes View details
ndhD-ccsA SSC 271 0.0096 1.00 59.8 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 95 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 CCGTGCTAACCTTGGTATGG 506–604 1.000 84.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 520–618 1.000 84.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 519–617 1.000 84.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 521–619 1.000 84.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 507–605 1.000 84.3
rps16_p1 rps16 ACGAATAGAGCAAGAAAAGAAGG ACTGGTTCCAAATTCGAGGA 1270–1302 1.000 43.1
rps16_p2 rps16 ACGAATAGAGCAAGAAAAGAAGGA ACTGGTTCCAAATTCGAGGA 1270–1302 1.000 43.1
rps16_p3 rps16 CGAATAGAGCAAGAAAAGAAGGA ACTGGTTCCAAATTCGAGGA 1269–1301 1.000 43.1
rps16_p4 rps16 ACGAATAGAGCAAGAAAAGAAGG ACTGGTTCCAAATTCGAGGAA 1270–1302 1.000 43.1
rps16_p5 rps16 ACGAATAGAGCAAGAAAAGAAGGA ACTGGTTCCAAATTCGAGGAA 1270–1302 1.000 43.1
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 312–345 1.000 75.3
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 315–348 1.000 75.0
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 318–351 1.000 74.5
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 321–354 1.000 74.2
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 316–349 1.000 72.8
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ATTTGAACCGAGGGCTTACG 567–693 0.800 50.1
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT AGGGCTTACGCTTTACACTC 557–683 0.800 49.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GAGGGCTTACGCTTTACACT 558–684 0.800 49.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GGGCTTACGCTTTACACTCT 556–682 0.800 49.3
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GGATTTGAACCGAGGGCTTA 569–695 0.800 48.9
trnT-GGU-psbD_p1 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT GAAACGGTCCCTACGTAACC 1457–1647 0.800 74.2
trnT-GGU-psbD_p2 trnT-GGU-psbD TAAGCCCTCGGTTCAAATCC GAAACGGTCCCTACGTAACC 1455–1645 0.800 73.1
trnT-GGU-psbD_p3 trnT-GGU-psbD TGAACCAAGCCCTTTCCTTT GAAACGGTCCCTACGTAACC 1500–1690 0.800 72.5
trnT-GGU-psbD_p4 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT ACAAAAACGAAACGGTCCCT 1465–1655 0.800 72.3
trnT-GGU-psbD_p5 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT CGAAACGGTCCCTACGTAAC 1458–1648 0.800 71.2
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG ACTTCATTTTGGGCGGGTAG 493–496 1.000 78.2
psbZ-trnG-UCC_p2 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG GACTTCATTTTGGGCGGGTA 494–497 1.000 78.1
psbZ-trnG-UCC_p3 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC ACTTCATTTTGGGCGGGTAG 491–494 1.000 77.8
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC GACTTCATTTTGGGCGGGTA 492–495 1.000 77.7
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG ATGACTTCATTTTGGGCGGG 496–499 1.000 73.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Pseudognaphalium adnatum NC_087964.1 153292 View on NCBI ↗
Pseudognaphalium flavescens PP525147.1 152858 View on NCBI ↗
Pseudognaphalium hypoleucum NC_087965.1 153262 View on NCBI ↗
Pseudognaphalium luteoalbum NC_087966.1 153273 View on NCBI ↗
Pseudognaphalium thermale OR771721.1 153769 View on NCBI ↗