Markers + reference

Viburnum

25 species · Adoxaceae · Dipsacales

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Species 25
Genome length 157–159 kb
Candidate markers 268
Primer pairs 100

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 874 0.0184 1.00 60.9 yes View details
rps16-trnQ-UUG LSC 1521 0.0148 0.98 69.9 yes View details
trnC-GCA-petN LSC 495 0.0221 0.99 64.9 yes View details
ndhC-trnV-UAC LSC 1056 0.0160 0.99 62.6 yes View details
psbE-petL LSC 1284 0.0207 0.99 78.9 yes View details
ycf1 IRb 1413 0.0082 0.99 46.9 no View details
ndhF SSC 2238 0.0071 1.00 44.2 yes View details
ndhF-rpl32 SSC 1256 0.0243 0.99 71.1 yes View details
psaC-ndhE SSC 264 0.0165 0.98 54.8 yes View details
rps15-ycf1 SSC 405 0.0248 1.00 58.9 yes View details
ycf1 SSC 5685 0.0100 1.00 43.8 yes View details
trnE-UUC-trnT-GGU LSC 811 0.0157 1.00 68.7 yes View details
ndhD-psaC SSC 127 0.0689 0.94 68.1 yes View details
petN-psbM LSC 1171 0.0107 0.97 65.4 yes View details
atpH-atpI LSC 1117 0.0083 1.00 64.6 yes View details
trnH-GUG-psbA LSC 382 0.0181 1.00 63.3 yes View details
ycf1-ndhF SSC 7 0.1976 1.00 60.8 yes View details
petL-petG LSC 175 0.0156 1.00 60.3 yes View details
rpl16 LSC 1468 0.0124 1.00 60.2 yes View details
trnP-UGG-psaJ LSC 389 0.0197 1.00 59.8 yes View details
rps8-rpl14 LSC 199 0.0157 1.00 59.5 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 100 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 439–461 1.000 90.1
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 452–474 1.000 89.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 453–475 1.000 89.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 454–476 1.000 89.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 488–510 1.000 87.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGGTATGTTGCTGCCA 1682–1705 1.000 87.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1681–1704 1.000 87.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGACCCAACTTGCAATTGA AAAAGGGTATGTTGCTGCCA 1813–1836 1.000 87.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCATTCGACCCAACTTGCAA AAAAGGGTATGTTGCTGCCA 1817–1833 0.920 82.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CACACGCATTTCCATTGCAT AAAAGGGTATGTTGCTGCCA 2036–2059 0.920 82.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1564–1622 0.960 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1579–1637 0.960 82.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1578–1636 0.960 82.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1568–1626 1.000 81.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1594–1652 1.000 81.7
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 996–1221 0.960 80.5
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 981–1206 0.960 80.3
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 995–1220 0.960 80.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 965–1190 0.960 79.9
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 980–1205 0.920 79.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC ACGAGCGAAAGGGAAAATGT 639–1021 1.000 86.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CCATACTACGAGCGAAAGGG 646–1028 1.000 86.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CCCATACTACGAGCGAAAGG 647–1029 1.000 86.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CCCCATACTACGAGCGAAAG 648–1030 1.000 86.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACGAGCGAAAGGGAAAATGT 583–965 0.960 84.5
petN-psbM_p1 petN-psbM ACATTTTCCCTTTCGCTCGT TGCTACTGCACTGTTCATTCT 596–1305 1.000 76.7
petN-psbM_p2 petN-psbM CCCTTTCGCTCGTAGTATGG TGCTACTGCACTGTTCATTCT 589–1298 1.000 76.5
petN-psbM_p3 petN-psbM CCTTTCGCTCGTAGTATGGG TGCTACTGCACTGTTCATTCT 588–1297 1.000 76.5
petN-psbM_p4 petN-psbM CTTTCGCTCGTAGTATGGGG TGCTACTGCACTGTTCATTCT 587–1296 1.000 76.5
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 634–1343 1.000 76.2

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
Viburnum acerifolium NC_084405.1 158517 View on NCBI ↗
Viburnum amplificatum NC_086696.1 159015 View on NCBI ↗
Viburnum betulifolium NC_037951.1 158023 View on NCBI ↗
Viburnum brachybotryum NC_045062.1 157433 View on NCBI ↗
Viburnum burejaeticum NC_050741.1 158383 View on NCBI ↗
Viburnum carlesii MN985820.2 158378 View on NCBI ↗
Viburnum carlesii x Viburnum macrocephalum NC_048464.1 158377 View on NCBI ↗
Viburnum chinshanense NC_072570.1 158391 View on NCBI ↗
Viburnum dentatum NC_086692.1 157964 View on NCBI ↗
Viburnum dilatatum NC_057163.1 158392 View on NCBI ↗
Viburnum erosum MN641480.1 158587 View on NCBI ↗
Viburnum fordiae MN524625.1 157627 View on NCBI ↗
Viburnum furcatum PX673848.1 158192 View on NCBI ↗
Viburnum grandiflorum NC_086697.1 158151 View on NCBI ↗
Viburnum japonicum NC_072552.1 158606 View on NCBI ↗
Viburnum lentago NC_086695.1 158314 View on NCBI ↗
Viburnum molle NC_086516.1 158501 View on NCBI ↗
Viburnum mongolicum PX111644.1 158347 View on NCBI ↗
Viburnum opulus var. sargentii MW788538.1 158481 View on NCBI ↗
Viburnum plicatum NC_086694.1 158595 View on NCBI ↗
Viburnum rhytidophyllum MT374829.1 158390 View on NCBI ↗
Viburnum schensianum NC_056104.1 158408 View on NCBI ↗
Viburnum setigerum PX530810.1 158611 View on NCBI ↗
Viburnum sympodiale PP078695.1 158185 View on NCBI ↗
Viburnum tinus NC_086693.1 158062 View on NCBI ↗