Markers + reference

Lindera

25 species · Lauraceae · Laurales

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Species 25
Genome length 153–153 kb
Candidate markers 264
Primer pairs 95

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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 370 0.0355 1.00 78.0 yes View details
psbK-psbI LSC 384 0.0147 1.00 55.6 yes View details
psbM-trnD-GUC LSC 973 0.0125 1.00 66.8 yes View details
petA-psbJ LSC 1138 0.0191 1.00 73.0 yes View details
ycf2 LSC 6837 0.0058 1.00 58.1 yes View details
ycf1 IRb 1372 0.0005 1.00 27.9 no View details
ndhF-rpl32 SSC 1109 0.0146 1.00 79.6 yes View details
rpl32-trnL-UAG SSC 1398 0.0150 0.99 74.3 yes View details
ndhD SSC 1509 0.0057 1.00 44.6 yes View details
ycf1 SSC 5568 0.0079 1.00 57.7 yes View details
ycf2 IRa 3162 0.0009 1.00 33.8 no View details
trnG-GCC-trnfM-CAU LSC 156 0.0211 1.00 74.6 yes View details
atpH-atpI LSC 676 0.0095 0.98 72.5 yes View details
trnK-UUU-rps16 LSC 820 0.0109 1.00 71.8 yes View details
trnT-UGU-trnL-UAA LSC 567 0.0111 0.96 71.0 yes View details
ycf1-ndhF SSC 25 0.0794 0.84 69.5 yes View details
ndhC-trnV-UAC LSC 1859 0.0080 1.00 67.5 yes View details
trnT-GGU-psbD LSC 1443 0.0080 1.00 66.5 yes View details
trnS-GGA-rps4 LSC 287 0.0228 0.98 65.2 yes View details
rps16-trnQ-UUG LSC 1877 0.0097 1.00 64.2 yes View details
petN-psbM LSC 1065 0.0048 1.00 62.6 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 95 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 426–470 1.000 90.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 440–484 1.000 90.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 439–483 1.000 90.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 441–485 1.000 90.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 429–473 1.000 90.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 938–974 1.000 85.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 937–973 1.000 85.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGACCATAGCCGCACTT AAAAAGGCGCTCAACCTACA 959–995 1.000 85.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 947–983 1.000 84.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 941–977 1.000 84.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1939–1981 1.000 86.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGGTACAAGAATCCACAGCC GAGGTTCGAATCCTTCCGTC 1972–2014 1.000 85.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1943–1985 1.000 85.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGGTACAAGAATCCACAGCC CTCGGAGGTTCGAATCCTTC 1976–2018 1.000 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGTACAAGAATCCACAGCCA GAGGTTCGAATCCTTCCGTC 1971–2013 1.000 83.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTGAGAGTAAGCA 429–443 1.000 66.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAGAGTTTGAGAGTAAGCA 426–440 1.000 64.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAGAGTTTGAGAGTAAGCA 427–441 1.000 64.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAAGAGTTTGAGAGTAAGCA 428–442 1.000 64.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACGAAGAGTTTGAGAGTAAGCA 430–444 1.000 62.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 747–766 1.000 85.5
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 803–822 1.000 84.5
atpH-atpI_p3 atpH-atpI GATACCTTCTACGGCTTGGC TTTTGCAACTTTAGCCGCAG 832–851 1.000 84.1
atpH-atpI_p4 atpH-atpI CGATACCTTCTACGGCTTGG TTTTGCAACTTTAGCCGCAG 833–852 1.000 84.0
atpH-atpI_p5 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCCGCAG 739–758 0.920 81.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTCT 1223–1243 1.000 71.8
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTC 1223–1243 1.000 71.7
petN-psbM_p3 petN-psbM GGGACACGATTCACATGGAT TGCTACTGCGTTGTTCATTCT 1244–1264 1.000 70.4
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTCT 1162–1182 1.000 70.3
petN-psbM_p5 petN-psbM GGGACACGATTCACATGGAT TGCTACTGCGTTGTTCATTC 1244–1264 1.000 70.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (25)

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

Species Accession Length (bp) Link
Lindera aggregata NC_045252.1 152664 View on NCBI ↗
Lindera angustifolia NC_045253.1 152832 View on NCBI ↗
Lindera chienii NC_063700.1 152744 View on NCBI ↗
Lindera chunii NC_045254.1 152694 View on NCBI ↗
Lindera communis NC_045255.1 152668 View on NCBI ↗
Lindera erythrocarpa NC_045256.1 152920 View on NCBI ↗
Lindera floribunda NC_045257.1 152551 View on NCBI ↗
Lindera glauca NC_035953.1 152780 View on NCBI ↗
Lindera latifolia PV217815.1 152779 View on NCBI ↗
Lindera limprichtii PP346660.1 152696 View on NCBI ↗
Lindera megaphylla NC_045258.1 152762 View on NCBI ↗
Lindera metcalfiana NC_045259.1 152893 View on NCBI ↗
Lindera nacusua NC_045260.1 152762 View on NCBI ↗
Lindera neesiana NC_045261.1 152502 View on NCBI ↗
Lindera obtusiloba NC_045262.1 152772 View on NCBI ↗
Lindera obtusiloba var. heterophylla MT621623.1 152687 View on NCBI ↗
Lindera praecox NC_045263.1 152728 View on NCBI ↗
Lindera pulcherrima PP346659.1 152693 View on NCBI ↗
Lindera reflexa NC_045264.1 153006 View on NCBI ↗
Lindera rubronervia NC_045265.1 152885 View on NCBI ↗
Lindera sericea NC_045266.1 153028 View on NCBI ↗
Lindera setchuenensis PV217816.1 152851 View on NCBI ↗
Lindera thomsonii var. velutina MT621636.1 152651 View on NCBI ↗
Lindera tienchuanensis PV217817.1 152708 View on NCBI ↗
Lindera villipes MT621624.1 152718 View on NCBI ↗