Markers + reference

Alseodaphne

3 species · Lauraceae · Laurales

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Species 3
Genome length 153–153 kb
Candidate markers 260
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 399 0.0168 1.00 66.0 yes View details
trnK-UUU-rps16 LSC 820 0.0041 1.00 50.4 yes View details
accD-psaI LSC 585 0.0068 1.00 62.8 yes View details
petA-psbJ LSC 1145 0.0178 1.00 70.2 yes View details
ycf1 IRb 1374 0.0000 1.00 27.2 no View details
ndhF SSC 2229 0.0048 1.00 59.4 yes View details
ndhF-rpl32 SSC 1234 0.0070 1.00 49.3 yes View details
rpl32-trnL-UAG SSC 1373 0.0058 1.00 61.6 yes View details
ccsA SSC 951 0.0021 1.00 51.6 yes View details
ycf1 SSC 5586 0.0027 1.00 54.2 yes View details
rpl2-rpl23 LSC 33 0.0444 0.91 75.9 yes View details
ccsA-ndhD SSC 236 0.0198 1.00 62.5 yes View details
trnS-GCU-trnG-UCC LSC 827 0.0040 1.00 61.7 yes View details
psaA-ycf3 LSC 639 0.0031 1.00 60.9 yes View details
rps19-rpl2 LSC 79 0.0307 0.96 60.8 yes View details
matK-trnK-UUU LSC 719 0.0028 1.00 60.7 yes View details
petN-psbM LSC 1069 0.0019 1.00 60.7 yes View details
cemA LSC 690 0.0019 1.00 60.0 yes View details
petB LSC 1437 0.0019 1.00 60.0 yes View details
atpH-atpI LSC 665 0.0010 1.00 59.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 464–470 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 478–484 1.000 80.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 477–483 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 479–485 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 467–473 1.000 80.6
matK-trnK-UUU_p1 matK-trnK-UUU TTGTTGCCGAAATCCATCCA GTCGGGCAATCGAATCTCTT 867–868 1.000 79.2
matK-trnK-UUU_p2 matK-trnK-UUU TGTTGCCGAAATCCATCCAT GTCGGGCAATCGAATCTCTT 866–867 1.000 78.8
matK-trnK-UUU_p3 matK-trnK-UUU TTGTTGCCGAAATCCATCCA AACGGTAGAGTACTCGGCTT 790–791 1.000 78.4
matK-trnK-UUU_p4 matK-trnK-UUU TTGTTGCCGAAATCCATCCA ACGGTAGAGTACTCGGCTTT 789–790 1.000 78.4
matK-trnK-UUU_p5 matK-trnK-UUU TTGTTGCCGAAATCCATCCA ATGGGTTGCTAACTCAACGG 805–806 1.000 78.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAGGTATTTAAGGAATTTCGAAT 902–905 1.000 40.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAGGTATTTAAGGAATTTCGAAT 901–904 1.000 40.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGACCATAGCCGCACTT GAGGTATTTAAGGAATTTCGAAT 923–926 1.000 40.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GAGGTATTTAAGGAATTTCGAAT 911–914 1.000 40.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAGGTATTTAAGGAATTTCGAATT 901–904 1.000 40.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACGCTTTTACCACT 898–901 1.000 70.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACGCTTTTACCAC 898–901 1.000 70.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACGCTTTTACCAC 899–902 1.000 68.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGAATCACGCTTTTACCACT 897–900 1.000 68.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACGCTTTTACCACT 884–887 1.000 67.5
trnG-UCC_p1 trnG-UCC TTGAAGCAGCAACAAGGCTA CGTTGAGAAATGGTCCCGAT 1645–1646 1.000 80.5
trnG-UCC_p2 trnG-UCC AACATGTCAGCACCCCAATT ATCGTTGAGAAATGGTCCCG 1213–1214 1.000 80.4
trnG-UCC_p3 trnG-UCC AACATGTCAGCACCCCAATT CGTTGAGAAATGGTCCCGAT 1211–1212 1.000 80.4
trnG-UCC_p4 trnG-UCC ACATGTCAGCACCCCAATTT ATCGTTGAGAAATGGTCCCG 1212–1213 1.000 80.4
trnG-UCC_p5 trnG-UCC ACATGTCAGCACCCCAATTT CGTTGAGAAATGGTCCCGAT 1210–1211 1.000 80.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 750–752 1.000 79.0
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCCGCAG 742–744 1.000 78.8
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 806–808 1.000 78.3
atpH-atpI_p4 atpH-atpI GATACCTTCTACGGCTTGGC TTTTGCAACTTTAGCCGCAG 835–837 1.000 78.2
atpH-atpI_p5 atpH-atpI CGATACCTTCTACGGCTTGG TTTTGCAACTTTAGCCGCAG 836–838 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Alseodaphne gracilis NC_037489.1 153099 View on NCBI ↗
Alseodaphne huanglianshanensis NC_037490.1 153070 View on NCBI ↗
Alseodaphne semecarpifolia NC_037491.1 153051 View on NCBI ↗