Markers + reference

Cedrela

2 species · Meliaceae · Sapindales

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Species 2
Genome length 159–159 kb
Candidate markers 271
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5352 0.3516 0.85 74.4 yes View details
ndhA SSC 2185 0.4782 0.85 79.4 yes View details
ndhD SSC 1527 0.4937 0.89 81.8 yes View details
ndhF SSC 2229 0.4619 0.86 79.7 yes View details
ycf1 IRa 1076 0.0000 1.00 25.0 no View details
rpl32-ndhF SSC 987 0.4345 0.90 82.3 yes View details
ccsA SSC 960 0.4499 0.88 81.7 yes View details
ndhI SSC 504 0.4339 0.90 80.2 yes View details
trnL-UAG-rpl32 SSC 1026 0.4400 0.82 79.9 yes View details
ndhH SSC 1197 0.4600 0.79 79.2 yes View details
ycf1-rps15 SSC 368 0.4495 0.89 77.0 yes View details
psaC-ndhD SSC 137 0.5079 0.92 76.6 yes View details
rps15-ndhH SSC 102 0.2935 0.90 76.0 yes View details
rpl32 SSC 159 0.4823 0.89 75.7 yes View details
rps15 SSC 273 0.4896 0.88 75.5 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1_p1 ycf1 AGGAGACAGAACACGAAGGA TTTCGGGGAGAACCAAAAGG 871 0.500 59.9
ycf1_p2 ycf1 AAGGACGTGTACCAGAGGAA TTTCGGGGAGAACCAAAAGG 856 0.500 59.9
ycf1_p3 ycf1 AAATCGGATTTTCGGCGAGA TTTCGGGGAGAACCAAAAGG 698 0.500 59.8
ycf1_p4 ycf1 AGGAGACAGAACACGAAGGA AACGTTGTTTTCGGGGAGAA 879 0.500 59.6
ycf1_p5 ycf1 AAGGACGTGTACCAGAGGAA AACGTTGTTTTCGGGGAGAA 864 0.500 59.6
ycf1-rps15_p1 ycf1-rps15 TGGCAGTCGTTTCAGTATGG ATGAGACGAAGAACACCGTG 902 0.500 58.7
ycf1-rps15_p2 ycf1-rps15 GGCAGTCGTTTCAGTATGGT ATGAGACGAAGAACACCGTG 901 0.500 58.7
ycf1-rps15_p3 ycf1-rps15 TGGCAGTCGTTTCAGTATGG AACCGATCCGCAGTTTTCTT 492 0.500 58.4
ycf1-rps15_p4 ycf1-rps15 GGCAGTCGTTTCAGTATGGT AACCGATCCGCAGTTTTCTT 491 0.500 58.4
ycf1-rps15_p5 ycf1-rps15 TGGCAGTCGTTTCAGTATGG CCAACGGGTTACATAAGGCA 1026 0.500 58.3
rps15_p1 rps15 TGGCAGTCGTTTCAGTATGG GAAAGGAGTCTGTGCACCAA 1209 0.500 59.0
rps15_p2 rps15 GGCAGTCGTTTCAGTATGGT GAAAGGAGTCTGTGCACCAA 1208 0.500 59.0
rps15_p3 rps15 TGGCAGTCGTTTCAGTATGG CATGAGGTAAATCAGCCGCT 1324 0.500 58.9
rps15_p4 rps15 GGCAGTCGTTTCAGTATGGT CATGAGGTAAATCAGCCGCT 1323 0.500 58.9
rps15_p5 rps15 TGGCAGTCGTTTCAGTATGG TCTGTGCACCAATATCTGCC 1201 0.500 58.9
rps15-ndhH_p1 rps15-ndhH TGGCAGTCGTTTCAGTATGG GAAAGGAGTCTGTGCACCAA 1209 0.500 59.0
rps15-ndhH_p2 rps15-ndhH GGCAGTCGTTTCAGTATGGT GAAAGGAGTCTGTGCACCAA 1208 0.500 59.0
rps15-ndhH_p3 rps15-ndhH TGGCAGTCGTTTCAGTATGG CTATTCCAGACGCTCGTAGC 1504 0.500 58.9
rps15-ndhH_p4 rps15-ndhH GGCAGTCGTTTCAGTATGGT CTATTCCAGACGCTCGTAGC 1503 0.500 58.9
rps15-ndhH_p5 rps15-ndhH TGGCAGTCGTTTCAGTATGG CATGAGGTAAATCAGCCGCT 1324 0.500 58.9
ndhH_p1 ndhH AAGAAAACTGCGGATCGGTT AAGAATTCCCAAAGGGCTGG 1746 0.500 58.7
ndhH_p2 ndhH AAACTGCGGATCGGTTGAAT AAGAATTCCCAAAGGGCTGG 1742 0.500 58.1
ndhH_p3 ndhH AACTGCGGATCGGTTGAATT AAGAATTCCCAAAGGGCTGG 1741 0.500 58.1
ndhH_p4 ndhH ACTGCGGATCGGTTGAATTT AAGAATTCCCAAAGGGCTGG 1740 0.500 58.1
ndhH_p5 ndhH TGCGGATCGGTTGAATTTCA AAGAATTCCCAAAGGGCTGG 1738 0.500 58.1
ndhA_p1 ndhA TCGGTGAAATGACGGAATCC GACAGACGCGAACACATACT 2879 0.500 59.7
ndhA_p2 ndhA AGCCCCAAAAGGAGAATTGG GACAGACGCGAACACATACT 2680 0.500 59.4
ndhA_p3 ndhA AAGAGTCGAAGCCCCAAAAG GACAGACGCGAACACATACT 2689 0.500 59.0
ndhA_p4 ndhA TCCGACTTTTGAATTGCCGA GACAGACGCGAACACATACT 2725 0.500 58.9
ndhA_p5 ndhA ATGGGGGAAGTTGATCGTTG GACAGACGCGAACACATACT 2511 0.500 58.8

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
Cedrela fissilis PP747016.1 158507 View on NCBI ↗
Cedrela odorata NC_037251.1 158558 View on NCBI ↗