Markers + reference

Laburnum

2 species · Fabaceae · Fabales

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Species 2
Genome length 153–153 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 267 0.0150 1.00 61.5 yes View details
ndhJ LSC 477 0.0021 1.00 47.0 yes View details
ndhJ-trnF-GAA LSC 605 0.0083 0.99 64.3 yes View details
rps2 LSC 711 0.0000 1.00 26.7 yes View details
rpoB LSC 3213 0.0009 1.00 55.8 yes View details
psbZ-trnG-GCC LSC 358 0.0056 1.00 56.9 yes View details
ycf4 LSC 555 0.0000 1.00 24.7 yes View details
psbE-petL LSC 1398 0.0022 1.00 60.3 yes View details
rpl33-rps18 LSC 216 0.0093 1.00 57.8 yes View details
rpl20-rps12 LSC 755 0.0026 1.00 60.3 yes View details
rps4 LSC 612 0.0016 1.00 59.7 yes View details
trnS-GCU-trnT-CGU LSC 804 0.0012 1.00 59.6 yes View details
trnK-UUU-rbcL LSC 808 0.0012 1.00 59.5 yes View details
atpI LSC 744 0.0013 1.00 59.5 yes View details
atpH-atpI LSC 1320 0.0008 1.00 59.3 yes View details
rps16 LSC 1091 0.0009 1.00 59.3 yes View details
petA LSC 963 0.0010 1.00 59.3 yes View details
trnL-CAA-ndhB IRb 577 0.0017 1.00 59.3 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 TTCCCTCTAGACCTAGCTGC 335–336 1.000 79.6
trnH-GUG-psbA_p2 trnH-GUG-psbA TTCAATTTCTGGGCGAACGA TTCCCTCTAGACCTAGCTGC 399–400 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 349–350 1.000 79.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 348–349 1.000 79.5
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 350–351 1.000 79.5
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AAAGCCGAGTACTCTACCGT AGTCCTGAATTAGCTGCTGC 917 1.000 78.5
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AAGCCGAGTACTCTACCGTT AGTCCTGAATTAGCTGCTGC 916 1.000 78.5
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AAAGCCGAGTACTCTACCGT GAGGCTTCCAAATGGAGTCC 932 1.000 76.8
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AAGCCGAGTACTCTACCGTT GAGGCTTCCAAATGGAGTCC 931 1.000 76.8
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TACCGTTGAGTTAGCAACCC AGTCCTGAATTAGCTGCTGC 903 1.000 76.1
ndhJ_p1 ndhJ AGACCGGATTCTTTTGTCCA CTGGGATTGTAGAAATGCGGA 629–630 1.000 61.5
ndhJ_p2 ndhJ AGACCGGATTCTTTTGTCCA TCTGGGATTGTAGAAATGCGG 630–631 1.000 61.5
ndhJ_p3 ndhJ AGACCGGATTCTTTTGTCCA TGGGATTGTAGAAATGCGGA 628–629 1.000 61.4
ndhJ_p4 ndhJ AGACCGGATTCTTTTGTCCAA CTGGGATTGTAGAAATGCGGA 629–630 1.000 59.5
ndhJ_p5 ndhJ AGACCGGATTCTTTTGTCCAA TCTGGGATTGTAGAAATGCGG 630–631 1.000 59.5
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GGGATAGCTCAGCTGGTAGA 741–746 1.000 80.5
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 705–710 1.000 80.1
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC TCAAATCTGGTTCCTGGCAC 690–695 1.000 79.9
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC AGAATGGTCGGGATAGCTCA 750–755 1.000 79.8
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCAAGAATGGTCGGGATAGC 753–758 1.000 79.6
rps4_p1 rps4 TGCTTGATTTATCATATTTGTCA ACTAGAAAAAGTGGGCAAGGA 794 1.000 40.1
rps4_p2 rps4 ACAATACTTTAGTAGATTTTGCTTGA ACTAGAAAAAGTGGGCAAGGA 813 1.000 40.1
rps4_p3 rps4 ACTTTAGTAGATTTTGCTTGATT ACTAGAAAAAGTGGGCAAGGA 808 1.000 40.1
rps4_p4 rps4 TTGCTTGATTTATCATATTTGTCA ACTAGAAAAAGTGGGCAAGGA 795 1.000 40.1
rps4_p5 rps4 TGCTTGATTTATCATATTTGTCA ACTAGAAAAAGTGGGCAAGGAA 794 1.000 40.1
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 917–936 1.000 74.5
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 916–935 1.000 74.4
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU GTCAGTAACGCGGAAAGAGA TGAATCAAACGAGGGATCCC 979–998 1.000 71.7
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU AGCAATCCGACGCTTTAGTC TGAATCAAACGAGGGATCCC 919–938 1.000 71.6
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU CAGTAACGCGGAAAGAGAGG TGAATCAAACGAGGGATCCC 977–996 1.000 71.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Laburnum alpinum PP203128.1 152944 View on NCBI ↗
Laburnum anagyroides PP203129.1 152942 View on NCBI ↗