Markers + reference

Caryodaphnopsis

12 species · Lauraceae · Laurales

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Species 12
Genome length 140–149 kb
Candidate markers 253
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF Genome 2232 0.2234 0.85 76.3 yes View details
ndhF-rpl32 Genome 346 0.2645 1.00 62.7 yes View details
rpl32-trnL-UAG Genome 1176 0.2040 0.78 75.7 yes View details
ccsA Genome 951 0.2369 0.88 70.7 yes View details
ndhA Genome 2186 0.2262 0.88 74.0 yes View details
ndhH Genome 1182 0.2152 0.85 65.0 yes View details
ycf1 Genome 5526 0.1467 0.83 74.1 yes View details
ndhD Genome 1536 0.1799 0.69 73.1 yes View details
rps15-ycf1 Genome 382 0.2264 0.88 72.6 yes View details
petA-psbJ Genome 1165 0.0135 1.00 70.0 yes View details
rps15 Genome 267 0.1967 0.80 65.1 yes View details
trnL-UAG-ccsA Genome 99 0.2212 0.95 64.8 yes View details
ndhI Genome 543 0.1747 0.77 64.8 yes View details
rps19-rpl2 Genome 67 0.0231 1.00 64.3 yes View details
ndhG-ndhI Genome 356 0.2037 0.91 61.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petA-psbJ_p1 petA-psbJ ACGTGTCCAAGGTTTGTTGT ATTCCGGATTGGGATCATCC 1300–1339 1.000 74.5
petA-psbJ_p2 petA-psbJ ACGTGTCCAAGGTTTGTTGT ACTGGTATTCCTGTGATCGG 1349–1388 1.000 71.3
petA-psbJ_p3 petA-psbJ ACGTGTCCAAGGTTTGTTGT CTGGTATTCCTGTGATCGGT 1348–1387 1.000 71.3
petA-psbJ_p4 petA-psbJ ACGTGTCCAAGGTTTGTTGT GGTTCATATTCCGGATTGGGA 1307–1346 1.000 69.6
petA-psbJ_p5 petA-psbJ ACGTGTCCAAGGTTTGTTGT ACTGGTATTCCTGTGATCGGT 1349–1388 1.000 69.3
rps19-rpl2_p1 rps19-rpl2 GCCCGGGACCAAGTTACTAT GTTATCCTGCGCTTGGAAGA 250–256 1.000 74.6
rps19-rpl2_p2 rps19-rpl2 GCCCGGGACCAAGTTACTAT CACAACCCCTTGGGGTTATC 264–270 1.000 73.3
rps19-rpl2_p3 rps19-rpl2 GCCCGGGACCAAGTTACTAT GGCCCCGATTGGTAGAAAAA 288–294 1.000 73.0
rps19-rpl2_p4 rps19-rpl2 CCCGGGACCAAGTTACTATT GTTATCCTGCGCTTGGAAGA 249–255 1.000 72.8
rps19-rpl2_p5 rps19-rpl2 GCCCGGGACCAAGTTACTAT TATCCTGCGCTTGGAAGAAG 248–254 1.000 72.3
ndhF_p1 ndhF TTTCACGCATGTCCAGTTGA GTACGTTTCTTTGGAACCGC 2963–2978 0.417 54.5
ndhF_p2 ndhF ACGAAGGGGACTAAACAGGA AATAAGGGCTGGTGAATCGG 2934–2946 0.417 54.2
ndhF_p3 ndhF TTTCACGCATGTCCAGTTGA AATAAGGGCTGGTGAATCGG 2658–2670 0.417 54.1
ndhF_p4 ndhF ACAGGAACAAGAGGGATCCA AATAAGGGCTGGTGAATCGG 2920–2932 0.417 54.0
ndhF_p5 ndhF AAGAGGGATCCACCGAAGAA AATAAGGGCTGGTGAATCGG 2912–2924 0.417 54.0
ndhF-rpl32_p1 ndhF-rpl32 CGGAACAAACAGAAGTCCCA ACCGGATATCCCCTTTCCTT 511–520 0.500 59.3
ndhF-rpl32_p2 ndhF-rpl32 ACAAACAGAAGTCCCAACCC ACCGGATATCCCCTTTCCTT 507–516 0.500 59.0
ndhF-rpl32_p3 ndhF-rpl32 AATAGGGAGGCACACAGAGT ACCGGATATCCCCTTTCCTT 1119–1128 0.500 58.7
ndhF-rpl32_p4 ndhF-rpl32 AAGGGGAAATTGTGCGGATT ACCGGATATCCCCTTTCCTT 1159–1168 0.500 58.5
ndhF-rpl32_p5 ndhF-rpl32 AGGGGAAATTGTGCGGATTT ACCGGATATCCCCTTTCCTT 1158–1167 0.500 58.5
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CGGAACAAACAGAAGTCCCA ACAGAAAAAGGCAGCCATCA 2117–2141 0.500 60.7
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CGGAACAAACAGAAGTCCCA AGCGTGTCTACCGATTTCAC 1814–1838 0.500 60.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CGGAACAAACAGAAGTCCCA CAGCGTGTCTACCGATTTCA 1815–1839 0.500 60.7
rpl32-trnL-UAG_p4 rpl32-trnL-UAG ACAAACAGAAGTCCCAACCC ACAGAAAAAGGCAGCCATCA 2113–2137 0.500 60.5
rpl32-trnL-UAG_p5 rpl32-trnL-UAG ACAAACAGAAGTCCCAACCC AGCGTGTCTACCGATTTCAC 1810–1834 0.500 60.5
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT ACAGAAAAAGGCAGCCATCA 323 0.500 60.9
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG ACAGAAAAAGGCAGCCATCA 322 0.500 60.9
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT CAATAAGACCCCCATGCCTC 910 0.500 60.2
trnL-UAG-ccsA_p4 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG CAATAAGACCCCCATGCCTC 909 0.500 60.2
trnL-UAG-ccsA_p5 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT ACTGGGATTGTAGAGCAGGT 573 0.500 60.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Caryodaphnopsis baviensis NC_085617.1 149000 View on NCBI ↗
Caryodaphnopsis bilocellata NC_085763.1 148972 View on NCBI ↗
Caryodaphnopsis cangyuanensis OR979503.1 149029 View on NCBI ↗
Caryodaphnopsis hekouensis OR979506.1 148535 View on NCBI ↗
Caryodaphnopsis henryi NC_085764.1 139585 View on NCBI ↗
Caryodaphnopsis laotica NC_085765.1 148982 View on NCBI ↗
Caryodaphnopsis latifolia NC_085766.1 148824 View on NCBI ↗
Caryodaphnopsis malipoensis NC_085767.1 149299 View on NCBI ↗
Caryodaphnopsis metallica NC_086962.1 148977 View on NCBI ↗
Caryodaphnopsis poilanei NC_085768.1 148552 View on NCBI ↗
Caryodaphnopsis rubrinervis PP413757.1 148824 View on NCBI ↗
Caryodaphnopsis tonkinensis NC_050345.1 149016 View on NCBI ↗