Markers + reference

Sambucus

10 species · Adoxaceae · Dipsacales

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Species 10
Genome length 158–159 kb
Candidate markers 248
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 248 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 395 0.0163 0.99 60.8 yes View details
trnE-UUC-trnT-GGU LSC 838 0.0219 0.97 73.8 yes View details
trnM-CAU-psbD LSC 1429 0.0186 0.94 64.0 yes View details
ycf3-trnS-GGA LSC 865 0.0385 0.84 75.7 yes View details
trnF-GAA-ndhJ LSC 695 0.0149 0.98 58.6 yes View details
trnN-GUU-nad5 IRb 1558 0.0332 0.99 88.7 yes View details
nad5-rpl32 SSC 1163 0.0119 0.99 66.7 yes View details
ycf1 SSC 5700 0.0090 0.99 47.2 yes View details
petA-psbJ LSC 1033 0.0036 0.98 67.1 yes View details
ndhC-trnV-UAC LSC 1191 0.0080 0.98 66.5 yes View details
trnK-UUU-rps16 LSC 916 0.0094 0.99 65.2 yes View details
trnT-UGU-trnL-UAA LSC 788 0.0100 0.98 64.0 yes View details
rpl32-trnL-UAG SSC 933 0.0108 0.99 64.0 yes View details
psbC-trnS-UGA LSC 231 0.0199 0.99 63.8 yes View details
psaA-ycf3 LSC 740 0.0056 0.99 63.1 yes View details
atpF-atpH LSC 374 0.0155 0.98 63.0 yes View details
rps2-rpoC2 LSC 233 0.0237 1.00 61.0 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 CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 464–635 1.000 85.5
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 465–636 1.000 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 457–628 1.000 83.9
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 513–684 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 514–685 1.000 82.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG TTGAAAAAGGTGCTCAGCCT 1054–1098 1.000 85.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAAAGGTGCTCAGCCTACC 1051–1095 1.000 85.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTGAAAAAGGTGCTCAGCCT 1071–1115 1.000 85.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTGAAAAAGGTGCTCAGCCT 1070–1114 1.000 85.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAAAGGTGCTCAGCCTACC 1067–1111 1.000 84.8
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA GCCTGGTTGTAGCATTAGCA 452–491 1.000 81.7
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG GCCTGGTTGTAGCATTAGCA 453–492 1.000 81.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 483–522 1.000 81.0
atpF-atpH_p4 atpF-atpH TGGCCCAAAGAAACGAAAGA TGGCCTGGTTGTAGCATTAG 454–493 1.000 80.3
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA CAGAGGGCAAAATACGAGGT 518–557 1.000 80.1
rps2-rpoC2_p1 rps2-rpoC2 ATCGTTCGCTGGAATCGAAA GGTTGAGGGTTGGAACGAAT 1518–1523 1.000 80.7
rps2-rpoC2_p2 rps2-rpoC2 TCGTTCGCTGGAATCGAAAT GGTTGAGGGTTGGAACGAAT 1517–1522 1.000 80.7
rps2-rpoC2_p3 rps2-rpoC2 ATCGTTCGCTGGAATCGAAA CTCGAAAAGAGGGTTGAGGG 1529–1534 1.000 80.6
rps2-rpoC2_p4 rps2-rpoC2 TCGTTCGCTGGAATCGAAAT CTCGAAAAGAGGGTTGAGGG 1528–1533 1.000 80.6
rps2-rpoC2_p5 rps2-rpoC2 CGAGATCGGGGTCACAATTT GGTTGAGGGTTGGAACGAAT 1492–1497 1.000 80.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC GAACCGATGACTTACGCCTT 953–994 1.000 88.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 887–928 1.000 88.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC CCGATGACTTACGCCTTACC 950–991 1.000 87.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCGATGACTTACGCCTTACC 884–925 1.000 87.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC TTGAACCGATGACTTACGCC 955–996 1.000 86.3
trnM-CAU-psbD_p1 trnM-CAU-psbD GGCGTAAGTCATCGGTTCAA TTTACCAAGGGCTATAGTCA 1209–1483 1.000 47.8
trnM-CAU-psbD_p2 trnM-CAU-psbD GGCGTAAGTCATCGGTTCAA TTACCAAGGGCTATAGTCAT 1208–1482 1.000 47.8
trnM-CAU-psbD_p3 trnM-CAU-psbD GGCGTAAGTCATCGGTTCAA TTTACCAAGGGCTATAGTCAT 1209–1483 1.000 47.8
trnM-CAU-psbD_p4 trnM-CAU-psbD CCCCTTTAACTCAGCGGTAG TTTACCAAGGGCTATAGTCA 1245–1519 1.000 47.7
trnM-CAU-psbD_p5 trnM-CAU-psbD CCCCTTTAACTCAGCGGTAG TTACCAAGGGCTATAGTCAT 1244–1518 1.000 47.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Sambucus adnata NC_051521.1 158756 View on NCBI ↗
Sambucus ebulus NC_066018.1 158399 View on NCBI ↗
Sambucus javanica NC_051520.1 158624 View on NCBI ↗
Sambucus javanica subsp. chinensis ON006402.1 158705 View on NCBI ↗
Sambucus mexicana NC_086590.1 158242 View on NCBI ↗
Sambucus nigra NC_045061.1 158205 View on NCBI ↗
Sambucus racemosa subsp. kamtschatica PZ239382.1 158338 View on NCBI ↗
Sambucus racemosa subsp. pubens PZ239385.1 158320 View on NCBI ↗
Sambucus sieboldiana PZ239387.1 158392 View on NCBI ↗
Sambucus williamsii NC_033878.1 158305 View on NCBI ↗