Markers + reference

Daphniphyllum

5 species · Daphniphyllaceae · Saxifragales

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Species 5
Genome length 160–160 kb
Candidate markers 274
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 390 0.0092 1.00 44.0 yes View details
trnS-GCU-trnG-GCC LSC 738 0.0046 0.99 56.1 yes View details
trnE-UUC-trnT-GGU LSC 827 0.0082 0.99 51.9 yes View details
trnT-UGU-trnL-UAA LSC 1041 0.0054 0.97 48.0 yes View details
psbE-petL LSC 1272 0.0072 1.00 50.4 yes View details
ycf1 IRb 1125 0.0005 1.00 25.7 no View details
ycf1-ndhF SSC 813 0.0139 0.99 71.5 yes View details
ndhF-rpl32 SSC 1124 0.0085 1.00 52.8 yes View details
rpl32-trnL-UAG SSC 1208 0.0073 0.99 46.1 yes View details
ycf1 SSC 5577 0.0044 1.00 55.6 yes View details
ccsA SSC 966 0.0034 1.00 62.2 yes View details
rbcL-accD LSC 649 0.0018 1.00 60.7 yes View details
trnH-GUG-psbA LSC 409 0.0103 0.95 58.6 yes View details
ndhD-psaC SSC 124 0.0250 0.99 57.6 yes View details
rpoC1 LSC 2829 0.0018 0.99 55.6 yes View details
ycf4-cemA LSC 897 0.0038 1.00 55.5 yes View details
trnF-GAA-ndhJ LSC 734 0.0054 0.93 55.1 yes View details
atpH-atpI LSC 1023 0.0018 0.99 55.0 yes View details
rpoC2 LSC 4179 0.0014 1.00 55.0 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 90 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 455–476 1.000 83.8
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 458–479 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 469–490 1.000 83.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 468–489 1.000 83.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 470–491 1.000 83.6
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 526–534 1.000 73.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 523–531 1.000 71.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 524–532 1.000 71.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 525–533 1.000 71.3
psbK-psbI_p5 psbK-psbI AAATTACCAGAGGCCTACGC TCTTCACGTCCAGGATTACG 610–618 1.000 71.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 799–817 1.000 53.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 798–816 1.000 53.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 802–820 1.000 52.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 801–819 1.000 52.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 800–818 1.000 52.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1090–1111 1.000 77.7
atpH-atpI_p2 atpH-atpI CGCAATCCCTTCTACAGCTT TTTTTGCAACTTTAGCCGCG 1178–1199 1.000 77.6
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1146–1167 1.000 77.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCTATGGAGGGTC 1062–1083 1.000 76.6
atpH-atpI_p5 atpH-atpI CGCAATCCCTTCTACAGCTT AGGCGAATCTATGGAGGGTC 1150–1171 1.000 76.5
rpoC2_p1 rpoC2 CCTGAATCTGAATGGGGCAT TCTCTTTCTGTCGAACGAAGA 284 1.000 59.5
rpoC2_p2 rpoC2 CCTGAATCTGAATGGGGCAT ACCTCTCAGTGACTGATGATCA 253 1.000 59.3
rpoC2_p3 rpoC2 CCTGAATCTGAATGGGGCAT CCTCTCAGTGACTGATGATCA 252 1.000 58.1
rpoC2_p4 rpoC2 CCTGAATCTGAATGGGGCAT ACCTCTCAGTGACTGATGATC 253 1.000 58.0
rpoC2_p5 rpoC2 CCTGAATCTGAATGGGGCAT AACCTCTCAGTGACTGATGA 254 1.000 57.6
rpoC1_p1 rpoC1 AGAAGACCGAATTCACACCG TTGCTCGTTCGAGAACTACG 2956–2980 1.000 80.0
rpoC1_p2 rpoC1 AGAAGACCGAATTCACACCG ACGATCTTTGGCTCTGGAAC 2939–2963 1.000 79.5
rpoC1_p3 rpoC1 GAAGACCGAATTCACACCGT TTGCTCGTTCGAGAACTACG 2955–2979 1.000 78.9
rpoC1_p4 rpoC1 GAAGACCGAATTCACACCGT ACGATCTTTGGCTCTGGAAC 2938–2962 1.000 78.5
rpoC1_p5 rpoC1 AGAAGACCGAATTCACACCG CGATCTTTGGCTCTGGAACT 2938–2962 1.000 77.1

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
Daphniphyllum calycinum NC_071199.1 160100 View on NCBI ↗
Daphniphyllum chartaceum NC_071195.1 159745 View on NCBI ↗
Daphniphyllum longeracemosum NC_071208.1 159977 View on NCBI ↗
Daphniphyllum macropodum ON729386.1 159750 View on NCBI ↗
Daphniphyllum oldhamii NC_037883.1 160137 View on NCBI ↗