Markers + reference

Huperzia

4 species · Lycopodiaceae · Lycopodiales

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Species 4
Genome length 154–162 kb
Candidate markers 272
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbJ-petA Genome 1347 0.0139 1.00 56.1 yes View details
trnF-GAA-trnL-UAA Genome 1495 0.0166 1.00 58.2 yes View details
rps4-trnS-GGA Genome 381 0.0232 0.99 61.1 yes View details
rps16 Genome 970 0.0151 1.00 54.5 yes View details
trnG-UCC-trnR-UCU Genome 1475 0.0181 1.00 61.9 yes View details
rpoC2 Genome 5217 0.0118 0.97 50.6 yes View details
trnL-CAA-ndhB Genome 989 0.0187 0.99 60.7 yes View details
ndhB Genome 2199 0.0106 1.00 51.2 yes View details
ndhD-ccsA Genome 249 0.0361 1.00 52.8 yes View details
trnP-GGG-rpl32 Genome 843 0.0194 1.00 59.6 yes View details
rrn23-trnA-UGC Genome 961 0.0245 1.00 81.0 yes View details
rpl23-rpl2 Genome 38 0.0614 1.00 77.2 yes View details
rpoC1-rpoB Genome 56 0.0655 1.00 76.8 yes View details
atpA-atpF Genome 45 0.0704 1.00 72.7 yes View details
rpl32-rpl21 Genome 141 0.0437 1.00 67.8 yes View details
ndhE-psaC Genome 344 0.0213 1.00 67.1 yes View details
psbN-psbT Genome 167 0.0180 1.00 65.1 yes View details
trnA-UGC-rrn23 Genome 961 0.0082 0.82 63.8 yes View details
rps12-rpl20 Genome 2284 0.0144 0.99 63.7 yes View details
trnfM-CAU-trnG-GCC Genome 127 0.0276 1.00 63.4 yes View details
rpl14-rps8 Genome 381 0.0189 0.99 62.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl23-rpl2_p1 rpl23-rpl2 TGCGGGTTCAATAGTAACACA GCGCCTGGAGTATAGTCTCT 170 1.000 67.5
rpl23-rpl2_p2 rpl23-rpl2 TGCGGGTTCAATAGTAACACA CAACTAATCGATCACGTGCG 187 1.000 65.6
rpl23-rpl2_p3 rpl23-rpl2 CATCGACCCCCAGGAAAAA GCGCCTGGAGTATAGTCTCT 196 1.000 65.2
rpl23-rpl2_p4 rpl23-rpl2 TGCGGGTTCAATAGTAACACA TGCGCCTGGAGTATAGTCTC 171 1.000 65.2
rpl23-rpl2_p5 rpl23-rpl2 CATCGACCCCCAGGAAAAA CAACTAATCGATCACGTGCG 213 1.000 63.3
rpl14-rps8_p1 rpl14-rps8 TTTTTGGTCCAGTTGCTCGA GCAATGGTGTCGTTACCCAT 464–547 1.000 80.0
rpl14-rps8_p2 rpl14-rps8 CGAGTTTTTGGTCCAGTTGC GCAATGGTGTCGTTACCCAT 468–551 1.000 79.4
rpl14-rps8_p3 rpl14-rps8 GTTTTTGGTCCAGTTGCTCG GCAATGGTGTCGTTACCCAT 465–548 1.000 79.4
rpl14-rps8_p4 rpl14-rps8 TTTTTGGTCCAGTTGCTCGA TTGGCAATGGTGTCGTTACC 467–550 1.000 78.2
rpl14-rps8_p5 rpl14-rps8 GTTTTTGGTCCAGTTGCTCG TTGGCAATGGTGTCGTTACC 468–551 1.000 77.6
psbN-psbT_p1 psbN-psbT TGGTTATGCCTTGTACACCG TTTCGCTATTTCTTCCCGGG 298 1.000 80.5
psbN-psbT_p2 psbN-psbT ACCCTGGTCGCTATCTTCAT TTTCGCTATTTCTTCCCGGG 342 1.000 79.5
psbN-psbT_p3 psbN-psbT TGGTTATGCCTTGTACACCG AACCACCCAAAGTTCCAAGT 278 1.000 76.6
psbN-psbT_p4 psbN-psbT ACCCTGGTCGCTATCTTCAT AACCACCCAAAGTTCCAAGT 322 1.000 75.5
psbN-psbT_p5 psbN-psbT TGGTTATGCCTTGTACACCG CGCTATTTCTTCCCGGGAAC 295 1.000 75.2
rps12-rpl20_p1 rps12-rpl20 GGAATCAAAGACAGCCGGTA CTGGTTACCGGTCCGAAAAA 2461–2484 1.000 78.7
rps12-rpl20_p2 rps12-rpl20 GGAATCAAAGACAGCCGGTA ACGTTTACGAGCTACAGAGC 2389–2412 1.000 77.7
rps12-rpl20_p3 rps12-rpl20 GGAATCAAAGACAGCCGGTA TATTTGCTGGTTACCGGTCC 2467–2490 1.000 76.4
rps12-rpl20_p4 rps12-rpl20 TAGGAATCAAAGACAGCCGG CTGGTTACCGGTCCGAAAAA 2463–2486 1.000 76.3
rps12-rpl20_p5 rps12-rpl20 ATAGAACCAAATCCCCTGCC CTGGTTACCGGTCCGAAAAA 2437–2460 1.000 75.8
psbJ-petA_p1 psbJ-petA GGTTCATACTCCGGATTGGG TCCATTACGTGTTCAAGGTCT 1498 1.000 63.6
psbJ-petA_p2 psbJ-petA GGTTCATACTCCGGATTGGG ACGTGTTCAAGGTCTTTTGT 1492 1.000 61.8
psbJ-petA_p3 psbJ-petA GGTTCATACTCCGGATTGGG TCCATTACGTGTTCAAGGTCTT 1498 1.000 61.2
psbJ-petA_p4 psbJ-petA GGTTCATACTCCGGATTGGG ACGTGTTCAAGGTCTTTTGTT 1492 1.000 60.1
psbJ-petA_p5 psbJ-petA GGTTCATACTCCGGATTGGG ATCCATTACGTGTTCAAGGTCT 1499 1.000 59.5
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TCTACCGACTGAGCTATCCC GGGTTCGAGTCCCTCTACC 1534–1544 1.000 68.7
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TCTACCGACTGAGCTATCCC GGTTCGAGTCCCTCTACCC 1533–1543 1.000 68.7
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA TCTACCGACTGAGCTATCCC GTTCGAGTCCCTCTACCCC 1532–1542 1.000 68.7
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA ATCCTCTGCTCTACCGACTG GGTTCGAGTCCCTCTACCC 1542–1552 1.000 68.4
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA ATCCTCTGCTCTACCGACTG GTTCGAGTCCCTCTACCCC 1541–1551 1.000 68.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Huperzia arctica NC_072340.1 153956 View on NCBI ↗
Huperzia crispata NC_064991.1 154320 View on NCBI ↗
Huperzia kunmingensis NC_085758.1 161404 View on NCBI ↗
Huperzia selago NC_085757.1 161519 View on NCBI ↗