Markers + reference

Drummondita

3 species · Rutaceae · Sapindales

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Species 3
Genome length 157–157 kb
Candidate markers 270
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0013 1.00 34.1 yes View details
psbA-trnK-UUU LSC 267 0.0262 1.00 67.4 yes View details
trnC-GCA-petN LSC 737 0.0077 1.00 57.6 yes View details
trnD-GUC-trnY-GUA LSC 466 0.0100 1.00 56.4 yes View details
psbC-trnS-UGA LSC 253 0.0397 1.00 79.9 yes View details
psbZ-trnG-GCC LSC 520 0.0237 1.00 72.3 yes View details
psaI-ycf4 LSC 450 0.0105 0.99 51.4 yes View details
petA-psbJ LSC 1084 0.0080 1.00 64.8 yes View details
psbE-petL LSC 1370 0.0044 1.00 57.5 yes View details
psbB LSC 1527 0.0035 1.00 48.6 yes View details
rrn16-trnI-GAU IRb 294 0.0249 1.00 55.9 yes View details
trnN-GUU-rpl32 SSC 4259 0.0036 1.00 47.1 yes View details
ndhH SSC 1182 0.0023 1.00 50.4 yes View details
psbT-psbN LSC 71 0.0282 1.00 67.0 yes View details
ycf4-cemA LSC 501 0.0094 0.99 63.2 yes View details
petN-psbM LSC 1277 0.0063 1.00 62.8 yes View details
trnR-ACG-trnN-GUU IRb 631 0.0011 1.00 62.7 yes View details
trnN-GUU-trnR-ACG IRa 631 0.0011 1.00 62.7 yes View details
trnT-GGU-psbD LSC 1243 0.0064 1.00 62.4 yes View details
rbcL-accD LSC 557 0.0060 1.00 61.7 yes View details
psbM-trnD-GUC LSC 586 0.0046 1.00 61.4 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACTCGTCTACACAAAAACCA GATGATTAAATAAACCAAGATTTTACC 1114 1.000 40.1
psbA_p2 psbA AACTCGTCTACACAAAAACCA GATGATTAAATAAACCAAGATTTTACC 1115 1.000 40.1
psbA_p3 psbA ACTCGTCTACACAAAAACCAA GATGATTAAATAAACCAAGATTTTACC 1114 1.000 40.1
psbA_p4 psbA AACTCGTCTACACAAAAACCAA GATGATTAAATAAACCAAGATTTTACC 1115 1.000 40.1
psbA_p5 psbA ACTCGTCTACACAAAAACCAAA GATGATTAAATAAACCAAGATTTTACC 1114 1.000 40.1
psbA-trnK-UUU_p1 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT TGCAATGAAAAATGCGTGCA 462–464 1.000 80.0
psbA-trnK-UUU_p2 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT GCAATGAAAAATGCGTGCAC 461–463 1.000 79.4
psbA-trnK-UUU_p3 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT GTGCAATGAAAAATGCGTGC 463–465 1.000 79.4
psbA-trnK-UUU_p4 psbA-trnK-UUU ACCATCCAATGTAAAGGCGG TGCAATGAAAAATGCGTGCA 470–472 1.000 78.9
psbA-trnK-UUU_p5 psbA-trnK-UUU CCATCCAATGTAAAGGCGGT TGCAATGAAAAATGCGTGCA 469–471 1.000 78.9
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT ACGAGCGAAAGGGAAAATGT 855–859 1.000 77.4
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCATACTACGAGCGAAAGGG 862–866 1.000 77.2
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCCATACTACGAGCGAAAGG 863–867 1.000 77.2
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCCCATACTACGAGCGAAAG 864–868 1.000 77.2
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 817–821 1.000 77.1
petN-psbM_p1 petN-psbM ACATTTTCCCTTTCGCTCGT TCGTTCTAGTTCCTACTGCCT 1386–1387 1.000 71.2
petN-psbM_p2 petN-psbM CCCTTTCGCTCGTAGTATGG TCGTTCTAGTTCCTACTGCCT 1379–1380 1.000 71.0
petN-psbM_p3 petN-psbM CCTTTCGCTCGTAGTATGGG TCGTTCTAGTTCCTACTGCCT 1378–1379 1.000 71.0
petN-psbM_p4 petN-psbM CTTTCGCTCGTAGTATGGGG TCGTTCTAGTTCCTACTGCCT 1377–1378 1.000 71.0
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TCGTTCTAGTTCCTACTGCCT 1424–1425 1.000 70.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCAGTAGGAACTAGAACGA TTTTACTTGCCCGGGATTGT 733–749 1.000 69.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGCAGTAGGAACTAGAACGA TACTTGCCCGGGATTGTAGT 730–746 1.000 68.5
psbM-trnD-GUC_p3 psbM-trnD-GUC AGCAAAAAGGCAGTAGGAACT TTTTACTTGCCCGGGATTGT 740–756 1.000 68.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGCAGTAGGAACTAGAACGA TTCAATTGGTCAGAGCACCG 711–727 1.000 68.1
psbM-trnD-GUC_p5 psbM-trnD-GUC AGCAAAAAGGCAGTAGGAACT TACTTGCCCGGGATTGTAGT 737–753 1.000 67.3
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 536–538 1.000 75.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 535–537 1.000 75.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA TTTGATTTGGCTCCATCGGG TGGCAATATGTCTACGCTGG 596–598 1.000 74.8
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA TTTGATTTGGCTCCATCGGG GGCAATATGTCTACGCTGGT 595–597 1.000 74.8
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 557–559 1.000 74.4

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
Drummondita calida NC_081873.1 157438 View on NCBI ↗
Drummondita fulva NC_081874.1 157286 View on NCBI ↗
Drummondita hassellii NC_081875.1 157416 View on NCBI ↗