Markers + reference

Helichrysum

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–153 kb
Candidate markers 264
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl16 LSC 1402 0.0057 1.00 56.8 yes View details
psbJ-petA LSC 801 0.0175 1.00 60.1 yes View details
psaI-accD LSC 714 0.0129 0.98 68.0 yes View details
atpE-trnM-CAU LSC 214 0.0140 1.00 52.9 yes View details
trnS-GGA-pafI LSC 925 0.0130 1.00 62.2 yes View details
psbD-trnG-UCC LSC 1664 0.0074 0.97 65.1 yes View details
trnG-UCC-trnR-UCU LSC 231 0.0315 0.96 70.7 yes View details
psbA-trnH-GUG LSC 408 0.0354 0.97 77.8 yes View details
rpl32-trnL-UAG SSC 817 0.0162 0.98 59.3 yes View details
atpH-atpI LSC 1123 0.0056 0.96 66.0 yes View details
ndhJ-trnF-GAA LSC 601 0.0116 1.00 65.4 yes View details
rpoB-trnE-UUC LSC 747 0.0094 1.00 64.1 yes View details
psbM-petN LSC 501 0.0081 0.98 63.3 yes View details
trnQ-UUG-rps16 LSC 915 0.0066 1.00 62.5 yes View details
trnV-UAC-ndhC LSC 1251 0.0041 0.99 62.4 yes View details
infA-rpl36 LSC 122 0.0164 1.00 61.9 yes View details
rbcL-atpB LSC 740 0.0054 1.00 61.9 yes View details
rpl33-psaJ LSC 446 0.0069 0.98 61.4 yes View details
trnL-UAG-ccsA SSC 113 0.0177 1.00 61.4 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
rpl16_p1 rpl16 GTCGAGGGAATTGCACGTAT CGCACCAAAAACTCGAGTTC 2463–2465 1.000 80.1
rpl16_p2 rpl16 GTCGAGGGAATTGCACGTAT ACACATCAATTCTCGAGCCC 2223–2225 1.000 80.1
rpl16_p3 rpl16 GTCGAGGGAATTGCACGTAT TCGACGATTGCTAGCTCCTA 2253–2255 1.000 80.0
rpl16_p4 rpl16 GTCGAGGGAATTGCACGTAT GCGTCTTTGATCACAGCAAC 2297–2299 1.000 80.0
rpl16_p5 rpl16 GCAAATTGCAGGACGTATCG CGCACCAAAAACTCGAGTTC 2146–2148 1.000 79.9
infA-rpl36_p1 infA-rpl36 ACTCCGCAACAAAGATTCGA TTTTACGAACGGAAGCTCTT 178 1.000 58.3
infA-rpl36_p2 infA-rpl36 TCGACTCCGCAACAAAGATT TTTTACGAACGGAAGCTCTT 181 1.000 58.3
infA-rpl36_p3 infA-rpl36 ACTCCGCAACAAAGATTCGA ACAAATTTTACGAACGGAAGCT 183 1.000 57.0
infA-rpl36_p4 infA-rpl36 TCGACTCCGCAACAAAGATT ACAAATTTTACGAACGGAAGCT 186 1.000 57.0
infA-rpl36_p5 infA-rpl36 ACTCCGCAACAAAGATTCGA CACAAATTTTACGAACGGAAGC 184 1.000 56.7
rpl33-psaJ_p1 rpl33-psaJ AGAACCGGTATTCGCACATC TGTGGCACCGGTACTAAGTA 581–590 1.000 80.5
rpl33-psaJ_p2 rpl33-psaJ GAACCGGTATTCGCACATCT TGTGGCACCGGTACTAAGTA 580–589 1.000 80.5
rpl33-psaJ_p3 rpl33-psaJ TTTCGAACACAAGCGGTACA TGTGGCACCGGTACTAAGTA 608–617 1.000 80.4
rpl33-psaJ_p4 rpl33-psaJ TCGCACATCTTTACCCTTGG TGTGGCACCGGTACTAAGTA 570–579 1.000 80.2
rpl33-psaJ_p5 rpl33-psaJ TCGAACACAAGCGGTACATT TGTGGCACCGGTACTAAGTA 606–615 1.000 79.7
psbJ-petA_p1 psbJ-petA ATTCCGGATTGGGTTCATCC CGAGAAGGTTCAATTGTCCG 861–869 1.000 69.1
psbJ-petA_p2 psbJ-petA ATTCCGGATTGGGTTCATCC CGAGAAGGTTCAATTGTCCGA 861–869 1.000 67.8
psbJ-petA_p3 psbJ-petA ATTCCGGATTGGGTTCATCC TCGAGAAGGTTCAATTGTCCG 862–870 1.000 67.8
psbJ-petA_p4 psbJ-petA TGTGATCGGTTTAGTAGGCG CGAGAAGGTTCAATTGTCCG 899–907 1.000 67.4
psbJ-petA_p5 psbJ-petA GTGATCGGTTTAGTAGGCGT CGAGAAGGTTCAATTGTCCG 898–906 1.000 67.4
psaI-accD_p1 psaI-accD TTGCGATTGCCGGAAATACT TCCAGAAGGGCTTATTCGATC 871–885 1.000 66.0
psaI-accD_p2 psaI-accD TTGCGATTGCCGGAAATACT CCAGAAGGGCTTATTCGATCT 870–884 1.000 66.0
psaI-accD_p3 psaI-accD TTGCGATTGCCGGAAATACT TTCCAGAAGGGCTTATTCGA 872–886 1.000 66.0
psaI-accD_p4 psaI-accD AGGCCTACTAAAGGGACCAA TCCAGAAGGGCTTATTCGATC 851–865 1.000 65.3
psaI-accD_p5 psaI-accD AGGCCTACTAAAGGGACCAA CCAGAAGGGCTTATTCGATCT 850–864 1.000 65.2
rbcL-atpB_p1 rbcL-atpB CACCTGCTTTGAATCCAACAC ATACGCCCCAGGTCATTTTC 839–848 1.000 72.7
rbcL-atpB_p2 rbcL-atpB CACCTGCTTTGAATCCAACAC GATACGCCCCAGGTCATTTT 840–849 1.000 72.7
rbcL-atpB_p3 rbcL-atpB ACCTGCTTTGAATCCAACACT ATACGCCCCAGGTCATTTTC 838–847 1.000 72.4
rbcL-atpB_p4 rbcL-atpB ACCTGCTTTGAATCCAACACT GATACGCCCCAGGTCATTTT 839–848 1.000 72.4
rbcL-atpB_p5 rbcL-atpB TGCTTTGAATCCAACACTTGC ATACGCCCCAGGTCATTTTC 835–844 1.000 72.0

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
Helichrysum italicum subsp. picardii ON641295.1 152407 View on NCBI ↗
Helichrysum nuratavicum PQ328025.1 152585 View on NCBI ↗