Markers + reference

Diplolaena

2 species · Rutaceae · Sapindales

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Species 2
Genome length 156–157 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 381 0.1373 0.27 64.6 yes View details
trnK-UUU-rps16 LSC 555 0.0330 0.98 63.5 yes View details
rpoB-trnC-GCA LSC 1229 0.0149 0.98 54.0 yes View details
trnS-UGA-psbZ LSC 355 0.0085 1.00 50.4 yes View details
psbZ-trnG-GCC LSC 379 0.0449 1.00 68.3 yes View details
psbE-petL LSC 1383 0.0116 1.00 64.6 yes View details
rps3-rpl22 LSC 343 0.2553 0.96 89.6 yes View details
trnN-GUU-rpl32 SSC 4186 0.0065 1.00 54.3 yes View details
ccsA SSC 954 0.0126 1.00 55.3 yes View details
psaC SSC 246 0.0041 1.00 45.2 yes View details
atpA-atpF LSC 61 0.0492 1.00 80.8 yes View details
ndhD-psaC SSC 195 0.1031 0.99 74.3 yes View details
rpl22-trnH-GUG IRa 105 0.0370 0.77 72.6 no View details
trnG-UCC-trnR-UCU LSC 187 0.0214 1.00 64.8 yes View details
trnM-CAU-atpE LSC 234 0.0214 1.00 64.8 yes View details
trnF-GAA-ndhJ LSC 465 0.0134 0.96 64.0 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 63.4 yes View details
petA-psbJ LSC 1026 0.0078 1.00 63.2 yes View details
rps2-rpoC2 LSC 224 0.0179 1.00 62.8 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 90 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 451 0.500 58.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 465 0.500 58.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 464 0.500 58.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 466 0.500 58.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 480 0.500 55.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 660–675 1.000 83.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AATTGGAACCCTAGGGCTCT ATTTCAAAGAAAGCGGGGGT 908–923 1.000 82.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CCCAATGAGCCGTTTATCGA 833–848 1.000 82.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCCCAATGAGCCGTTTATCG 834–849 1.000 82.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGTAAGGAAGTTAGTGGGCG ATTTCAAAGAAAGCGGGGGT 1348–1364 1.000 81.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATCAATTGCGTCCAA 314 1.000 66.6
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATCAATTGCGTCCAA 317 1.000 66.3
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ATGGAAATCAATTGCGTCCA 315 1.000 64.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG ATGGAAATCAATTGCGTCCA 318 1.000 64.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGGAAATCAATTGCGTCCAA 318 1.000 64.1
atpA-atpF_p1 atpA-atpF GTCGCCTACTTGAAGTACGG ATTGGCATATTTGGGGCGAT 211–218 1.000 80.3
atpA-atpF_p2 atpA-atpF CCGTCGCCTACTTGAAGTAC ATTGGCATATTTGGGGCGAT 213–220 1.000 80.2
atpA-atpF_p3 atpA-atpF ATTGCTCGATACGTTCACGG ATTGGCATATTTGGGGCGAT 158–165 1.000 77.8
atpA-atpF_p4 atpA-atpF TCGCCTACTTGAAGTACGGT ATTGGCATATTTGGGGCGAT 210–217 1.000 77.3
atpA-atpF_p5 atpA-atpF CGTCGCCTACTTGAAGTACG ATTGGCATATTTGGGGCGAT 212–219 1.000 77.3
rps2-rpoC2_p1 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC ACAGGGAATTTATTCGGGGG 376–379 1.000 65.7
rps2-rpoC2_p2 rps2-rpoC2 CATTTCCGAGTACCATGACCA ACAGGGAATTTATTCGGGGG 406–409 1.000 64.7
rps2-rpoC2_p3 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC AACAGGGAATTTATTCGGGGG 377–380 1.000 63.4
rps2-rpoC2_p4 rps2-rpoC2 CCATTTCCGAGTACCATGACC ACAGGGAATTTATTCGGGGG 407–410 1.000 63.3
rps2-rpoC2_p5 rps2-rpoC2 TCCGAGTACCATGACCAAAA ACAGGGAATTTATTCGGGGG 402–405 1.000 62.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC GATCAAGCGACACCCAGATT 1308–1330 1.000 82.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC ACCAGCCAAGCAGAATAAGG 1351–1373 1.000 81.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC AAGCGACACCCAGATTTGAA 1304–1326 1.000 80.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC AAAAGGATTTGCAGTCCCCC 1277–1299 1.000 79.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCATTTCCATCTCCGAGCAT GATCAAGCGACACCCAGATT 1302–1324 1.000 79.1

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
Diplolaena drummondii NC_081871.1 156653 View on NCBI ↗
Diplolaena obovata NC_081872.1 156211 View on NCBI ↗