Markers + reference

Clausena

5 species · Rutaceae · Sapindales

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Species 5
Genome length 160–161 kb
Candidate markers 265
Primer pairs 105

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 455 0.0971 0.98 83.9 yes View details
psbK-psbI LSC 413 0.0415 0.96 73.3 yes View details
trnS-GCU-trnS-CGA LSC 867 0.0322 0.97 75.5 yes View details
trnS-CGA-trnR-UCU LSC 189 0.0700 0.95 79.2 yes View details
trnR-UCU-atpA LSC 225 0.0484 0.96 80.3 yes View details
petN-psbM LSC 1335 0.0379 0.96 80.6 yes View details
trnT-UGU-trnL-UAA LSC 1089 0.0314 0.97 74.4 yes View details
petA-psbJ LSC 1101 0.0305 0.98 74.5 yes View details
rps3 LSC 660 0.0145 1.00 54.9 yes View details
rps3-rps19 IRb 515 0.0413 0.95 76.0 yes View details
ndhF-trnL-UAG SSC 1643 0.0432 0.97 78.5 yes View details
ndhA SSC 2227 0.0217 0.99 62.6 yes View details
ycf1 SSC 4338 0.0260 0.99 59.5 yes View details
trnD-GUC-trnY-GUA LSC 486 0.0384 0.97 81.8 yes View details
atpF-atpH LSC 64 0.0516 1.00 78.7 yes View details
ccsA-ndhD SSC 311 0.0463 1.00 78.0 yes View details
rps16-trnQ-UUG LSC 1281 0.0286 0.98 74.3 yes View details
trnK-UUU-rps16 LSC 564 0.0361 0.98 73.3 yes View details
trnG-GCC-trnM-CAU LSC 177 0.0354 0.99 73.0 yes View details
trnF-GAA-ndhJ LSC 385 0.0336 0.98 72.3 yes View details
ndhK-ndhC LSC 66 0.0364 1.00 72.3 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 105 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 511–579 0.800 82.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 525–593 0.800 82.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 524–592 0.800 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 526–594 0.800 82.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 540–608 0.800 79.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG GGTGTGTTGCTGCCATTTTT 1237–1409 1.000 88.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGGTCTTACAAACTCTCCCG GGTGTGTTGCTGCCATTTTT 1304–1476 1.000 88.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TGCCTAAGGATTTTCGGACG 1119 0.200 47.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGGTCTTACAAACTCTCCCG TGCCTAAGGATTTTCGGACG 1186 0.200 47.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AATTGGAACCCTAGGGCTCT TGCCTAAGGATTTTCGGACG 1368 0.200 47.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1325–1372 1.000 88.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1323–1370 1.000 88.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1307–1354 1.000 87.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1318–1365 1.000 86.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGCGGATCATGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1324–1371 1.000 85.8
psbK-psbI_p1 psbK-psbI AGAGGGTTGCTCAAAAAGGG TGAGTGGATTAAAGCGTCGG 1371–1396 1.000 86.5
psbK-psbI_p2 psbK-psbI GAGGGTTGCTCAAAAAGGGA TGAGTGGATTAAAGCGTCGG 1370–1395 1.000 86.5
psbK-psbI_p3 psbK-psbI AGAGGGTTGCTCAAAAAGGG AGGCCCTGTTGAACGAAATT 1726–1762 0.800 78.1
psbK-psbI_p4 psbK-psbI AGAGGGTTGCTCAAAAAGGG AAGGCCCTGTTGAACGAAAT 1727–1763 0.800 78.0
psbK-psbI_p5 psbK-psbI GAGGGTTGCTCAAAAAGGGA AGGCCCTGTTGAACGAAATT 1725–1761 0.800 78.0
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CCGACGCTTTAATCCACTCA TGAACGAATCACACTTTTACCAC 895–935 1.000 62.2
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA CCGACGCTTTAATCCACTCA ACGAATCACACTTTTACCACT 892–932 1.000 61.2
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA TGAACGAATCACACTTTTACCAC 953–993 1.000 60.7
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AACGAAACGGAAAGAGAGGG TGAACGAATCACACTTTTACCAC 959–999 1.000 60.5
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CCGACGCTTTAATCCACTCA GAACGAATCACACTTTTACCACT 894–934 1.000 60.1
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU ACGATGCGGGTTCGATTC AGAAGACCTCTGTCCTATCCA 244–258 1.000 58.8
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU ACGATGCGGGTTCGATTC AGGTTTAGAAGACCTCTGTCCT 250–264 1.000 57.9
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU GATGCGGGTTCGATTCCC AGAAGACCTCTGTCCTATCCA 242–256 1.000 57.4
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU GATGCGGGTTCGATTCCC AGGTTTAGAAGACCTCTGTCCT 248–262 1.000 56.7
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU GTTCGATTCCCGCTACCC AGAAGACCTCTGTCCTATCCA 235–249 1.000 56.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Clausena anisata PQ310231.1 159769 View on NCBI ↗
Clausena anisum-olens MZ460583.1 159753 View on NCBI ↗
Clausena excavata NC_032685.1 161172 View on NCBI ↗
Clausena harmandiana LC794894.1 159508 View on NCBI ↗
Clausena lansium NC_061742.1 159787 View on NCBI ↗