Markers + reference

Weigela

3 species · Caprifoliaceae · Dipsacales

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Species 3
Genome length 157–158 kb
Candidate markers 261
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 344 0.0489 0.99 71.4 yes View details
accD LSC 1787 0.0101 1.00 56.3 yes View details
rpoA LSC 996 0.0141 1.00 53.9 yes View details
trnN-GUU-ndhF IRb 2167 0.0476 0.95 86.0 yes View details
ycf1 SSC 5270 0.0122 1.00 45.3 yes View details
ycf1-trnN-GUU IRa 540 0.1020 0.70 73.3 yes View details
rps18 LSC 474 0.0091 1.00 66.5 yes View details
rpl22 LSC 492 0.0149 1.00 65.2 yes View details
trnI-CAU-ycf2 IRb 277 0.0169 1.00 63.6 yes View details
ycf2-trnI-CAU IRa 276 0.0170 1.00 63.6 yes View details
trnI-CAU-trnH-GUG IRa 286 0.0070 1.00 63.2 no View details
rpoB-trnC-GCA LSC 1275 0.0026 1.00 61.7 yes View details
ycf4-cemA LSC 815 0.0033 0.99 61.6 yes View details
trnT-GGU-psbD LSC 849 0.0039 1.00 61.3 yes View details
petA-psbJ LSC 1054 0.0016 0.99 61.0 yes View details
trnK-UUU-rps16 LSC 869 0.0015 0.99 60.9 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1046–1049 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGAGCTTAGTTTCCGTCTGG 1047–1050 1.000 81.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGGAGCTTAGTTTCCGTCTG 1048–1051 1.000 81.1
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGTGGGAGCTTAGTTTCCG 1052–1055 1.000 81.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GAGCTTAGTTTCCGTCTGGG 1047–1050 1.000 81.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTGAAAAAGGTGCTCAGCCT 1055–1065 1.000 79.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTGAAAAAGGTGCTCAGCCT 1054–1064 1.000 79.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGTGCTCAGCCT 994–1004 1.000 79.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGTGCTCAGCCT 993–1003 1.000 79.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAAGGTGCTCAGCCTACAG 1050–1060 1.000 78.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA CCGGATTTGAACTGGGGAAA 1349–1373 1.000 78.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCATCAAGCCCTGA CCGGATTTGAACTGGGGAAA 1428–1452 1.000 76.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCCATCAAGCCCTG CCGGATTTGAACTGGGGAAA 1429–1453 1.000 76.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA AAAAGGATTTGCAGTCCCCC 1331–1355 1.000 76.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCCATCAAGCCCTGATCA CCGGATTTGAACTGGGGAAA 1425–1449 1.000 74.6
trnT-GGU-psbD_p1 trnT-GGU-psbD CAAAGAGGCCCCTTTAGCTC GGACCAGCCTACAAAAACGA 1036–1039 1.000 77.5
trnT-GGU-psbD_p2 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 992–995 1.000 77.2
trnT-GGU-psbD_p3 trnT-GGU-psbD CAAAGAGGCCCCTTTAGCTC TCTCCGTAACCAGTCATCCA 1009–1012 1.000 76.6
trnT-GGU-psbD_p4 trnT-GGU-psbD AATCCGATAAGGGGCTTTGG GGACCAGCCTACAAAAACGA 973–976 1.000 76.6
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCTCCGTAACCAGTCATCCA 965–968 1.000 76.3
accD_p1 accD GCTCGAATTCAAATGAGCGG TAAGGCGGGAGGAGGAAATT 2018–2284 1.000 81.0
accD_p2 accD CCCCTCTGCTCGAATTCAAA TAAGGCGGGAGGAGGAAATT 2025–2291 1.000 80.8
accD_p3 accD TCAAATGAGCGGGAAGAAGG TAAGGCGGGAGGAGGAAATT 2010–2276 1.000 80.8
accD_p4 accD GATTACAACGAGGCCCAGAG TAAGGCGGGAGGAGGAAATT 2275 0.333 49.6
accD_p5 accD GATTACAACGAGGCCCAGAG GCGGGAGGAGGAAATTTGTT 2271 0.333 49.2
ycf4-cemA_p1 ycf4-cemA TTGGCCTATTTCTTGCGTGT GAGAAATCCACCAGGGCAAA 919–927 1.000 79.7
ycf4-cemA_p2 ycf4-cemA ACAAAAAGCTGCCGAATTGG GAGAAATCCACCAGGGCAAA 935–943 1.000 79.2
ycf4-cemA_p3 ycf4-cemA TTGGCCTATTTCTTGCGTGT CAGGGCAAAAAGACGAGAGA 908–916 1.000 78.9
ycf4-cemA_p4 ycf4-cemA ACAAAAAGCTGCCGAATTGG CAGGGCAAAAAGACGAGAGA 924–932 1.000 78.5
ycf4-cemA_p5 ycf4-cemA TTGGCCTATTTCTTGCGTGT ATCCACCAGGGCAAAAAGAC 914–922 1.000 77.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Weigela floribunda OR881377.1 157146 View on NCBI ↗
Weigela japonica NC_040937.1 156600 View on NCBI ↗
Weigela subsessilis OR881380.1 157840 View on NCBI ↗