Markers + reference

Alseodaphnopsis

6 species · Lauraceae · Laurales

Back to catalogue

Species 6
Genome length 153–153 kb
Candidate markers 258
Primer pairs 85

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 10 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA Genome 406 0.0207 0.99 74.2 yes View details
rpoC2 Genome 4158 0.0019 1.00 48.3 yes View details
petA-psbJ Genome 1150 0.0172 1.00 71.8 yes View details
ndhF-rpl32 Genome 1227 0.0092 1.00 65.8 yes View details
rpl32-trnL-UAG Genome 1383 0.0083 0.99 64.4 yes View details
ccsA-ndhD Genome 234 0.0157 1.00 55.7 yes View details
ycf1 Genome 5565 0.0052 1.00 44.1 yes View details
rpoC2-rpoC1 Genome 161 0.0613 0.96 72.7 yes View details
rps16-trnQ-UUG Genome 1914 0.0037 0.99 64.5 yes View details
trnK-UUU-rps16 Genome 821 0.0042 1.00 62.0 yes View details
psbM-trnD-GUC Genome 972 0.0061 1.00 62.0 yes View details
ycf3-trnS-GGA Genome 813 0.0055 0.99 59.4 yes View details
trnS-GCU-trnG-UCC Genome 824 0.0046 0.99 56.7 yes View details
ycf4-cemA Genome 911 0.0044 1.00 55.1 yes View details
psbE-petL Genome 1250 0.0028 0.99 55.1 yes View details
ycf2 Genome 6858 0.0022 1.00 54.7 yes View details
trnE-UUC-trnT-GGU Genome 724 0.0043 1.00 54.4 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 85 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 TTCCCTCTAGACCTAGCTGC 444–475 1.000 85.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 458–489 1.000 85.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 457–488 1.000 85.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 459–490 1.000 85.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 473–504 1.000 82.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 943–956 1.000 80.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 942–955 1.000 80.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGACCATAGCCGCACTT AAAAAGGCGCTCAACCTACA 964–977 1.000 80.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 952–965 1.000 79.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 946–959 1.000 79.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1850–1987 1.000 83.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGGTACAAGAATCCACAGCC GAGGTTCGAATCCTTCCGTC 1883–2020 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1854–1991 1.000 81.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCCGATAATGTCCTT GAGGTTCGAATCCTTCCGTC 1871–2008 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTACAAGAATCCACAGCCGA GAGGTTCGAATCCTTCCGTC 1881–2018 1.000 81.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACGCTTTTACCACT 892–898 1.000 71.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACGCTTTTACCAC 892–898 1.000 71.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACGCTTTTACCAC 893–899 1.000 68.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGAATCACGCTTTTACCACT 891–897 1.000 68.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACGCTTTTACCACT 878–884 1.000 68.3
rpoC2_p1 rpoC2 AATCGTGAGGGAGAAAGCAC TTCGTTGGGTCCTTTAGGGA 245 1.000 78.0
rpoC2_p2 rpoC2 AATCGTGAGGGAGAAAGCAC GATCCCGCGATTCCCATTAG 268 1.000 77.9
rpoC2_p3 rpoC2 GTGAGGGAGAAAGCACCAAT TTCGTTGGGTCCTTTAGGGA 241 1.000 77.2
rpoC2_p4 rpoC2 GTGAGGGAGAAAGCACCAAT GATCCCGCGATTCCCATTAG 264 1.000 77.1
rpoC2_p5 rpoC2 AATCGTGAGGGAGAAAGCAC ATTCGTTGGGTCCTTTAGGG 246 1.000 73.8
rpoC2-rpoC1_p1 rpoC2-rpoC1 GGTGTGCGATGTATATGCCA AGGCCTACTCATACGGTACC 298 1.000 85.7
rpoC2-rpoC1_p2 rpoC2-rpoC1 GGTGTGCGATGTATATGCCA GGCCTACTCATACGGTACCT 297 1.000 85.7
rpoC2-rpoC1_p3 rpoC2-rpoC1 AGGGTGTGCGATGTATATGC GGCCTACTCATACGGTACCT 299 1.000 85.3
rpoC2-rpoC1_p4 rpoC2-rpoC1 AGGGTGTGCGATGTATATGC AGGCCTACTCATACGGTACC 300 1.000 85.2
rpoC2-rpoC1_p5 rpoC2-rpoC1 GGTGTGCGATGTATATGCCA AGAAGAAGCCATACAGGGGT 324 1.000 85.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Alseodaphnopsis andersonii NC_058706.1 152795 View on NCBI ↗
Alseodaphnopsis maguanensis MT621590.1 152760 View on NCBI ↗
Alseodaphnopsis petiolaris NC_058707.1 152773 View on NCBI ↗
Alseodaphnopsis rugosa MT621582.1 152762 View on NCBI ↗
Alseodaphnopsis sichourensis NC_058708.1 152920 View on NCBI ↗
Alseodaphnopsis ximengensis MT621617.1 152870 View on NCBI ↗