Markers + reference

Diarthron

2 species · Thymelaeaceae · Malvales

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Species 2
Genome length 172–173 kb
Candidate markers 287
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 9 remaining regions by MarkerSeek score (out of 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 319 0.0450 0.91 69.0 yes View details
rps16-trnQ-UUG LSC 1267 0.0393 0.94 75.5 yes View details
psbK-psbI LSC 444 0.0375 0.84 70.7 yes View details
atpF-atpH LSC 511 0.0407 0.96 72.5 yes View details
petN-psbM LSC 1070 0.0314 0.69 66.3 yes View details
psbM-trnD-GUC LSC 748 0.0430 1.00 77.7 yes View details
trnT-GGU-psbD LSC 1237 0.0297 0.82 68.6 yes View details
trnL-UAA-trnF-GAA LSC 378 0.0511 0.98 71.8 yes View details
trnF-GAA-ndhJ LSC 460 0.0286 0.99 65.3 yes View details
psbE-petL LSC 1196 0.0293 1.00 69.3 yes View details
trnP-UGG-psaJ LSC 373 0.0539 0.99 70.8 yes View details
ndhF SSC 2253 0.0337 1.00 62.3 yes View details
ndhF-trnL-UAG IRa 1698 0.0336 0.95 67.9 yes View details
psbZ-trnG-GCC LSC 590 0.0281 0.97 73.2 yes View details
atpH-atpI LSC 1168 0.0288 0.98 73.1 yes View details
trnG-UCC-trnR-UCU LSC 152 0.0592 1.00 73.0 yes View details
psbI-trnS-GCU LSC 85 0.0952 0.99 72.9 yes View details
psbC-trnS-UGA LSC 278 0.0323 0.89 72.9 yes View details
rps14-psaB LSC 126 0.0476 1.00 70.2 yes View details
psaI-ycf4 LSC 414 0.0387 1.00 69.1 yes View details
rpl33-rps18 LSC 331 0.0350 0.95 68.5 yes View details
trnT-UGU-trnL-UAA LSC 712 0.0306 0.96 67.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGAAGCTCCATCTACAAATGG 373–381 1.000 58.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGAAGCTCCATCTACAAATGG 374–382 1.000 58.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TGAAGCTCCATCTACAAATGG 366–374 1.000 57.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTGAAGCTCCATCTACAAATGG 374–382 1.000 56.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTGAAGCTCCATCTACAAATGG 375–383 1.000 56.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGCTATTCGAAG 1342–1357 1.000 85.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG TTTGGTCCCGCTATTCGAAG 1322–1337 1.000 84.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCAAATCGACCATGTCCT TTTGGTCCCGCTATTCGAAG 1364–1379 1.000 84.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTTTGGTCCCGCTATTCGA 1344–1359 1.000 83.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACCACATCGCTTCAAACGAA TTTGGTCCCGCTATTCGAAG 1323–1338 1.000 83.4
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG TCCGAAGATGAAGAGCGAAA 463–534 1.000 77.6
psbK-psbI_p2 psbK-psbI CAAGCCGCTGTAAGTTTTCG CCGAAGATGAAGAGCGAAAC 462–533 1.000 77.3
psbK-psbI_p3 psbK-psbI AGCCGCTGTAAGTTTTCGAT TCCGAAGATGAAGAGCGAAA 461–532 1.000 77.3
psbK-psbI_p4 psbK-psbI CAAGCCGCTGTAAGTTTTCG GAATCCGAAGATGAAGAGCGA 466–537 1.000 77.2
psbK-psbI_p5 psbK-psbI AAGCCGCTGTAAGTTTTCGA TCCGAAGATGAAGAGCGAAA 462–533 1.000 77.0
psbI-trnS-GCU_p1 psbI-trnS-GCU CAAGCCGCTGTAAGTTTTCG TGGACTAAAGCGTCGGATTG 669–737 1.000 86.3
psbI-trnS-GCU_p2 psbI-trnS-GCU ACTTAGACTTGGAGTCCCCC TGGACTAAAGCGTCGGATTG 504 0.500 59.6
psbI-trnS-GCU_p3 psbI-trnS-GCU ACTTAGACTTGGAGTCCCCC GTGGACTAAAGCGTCGGATT 505 0.500 59.6
psbI-trnS-GCU_p4 psbI-trnS-GCU CTTAGACTTGGAGTCCCCCA TGGACTAAAGCGTCGGATTG 503 0.500 59.6
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTAGACTTGGAGTCCCCCA GTGGACTAAAGCGTCGGATT 504 0.500 59.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 232–242 1.000 66.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 235–245 1.000 66.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 238–248 1.000 65.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 241–251 1.000 65.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 236–246 1.000 63.9
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA GGTTGTAGCATTGGCCCTTT 592–595 1.000 79.2
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA AGCATTGGCCCTTTTATTTGC 586–589 1.000 77.1
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GGTTGTAGCATTGGCCCTT 592–595 1.000 76.9
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA GCCCTTTTATTTGCCAATCCC 579–582 1.000 76.6
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GGCCCTTTTATTTGCCAATCC 580–583 1.000 76.5

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
Diarthron linifolium NC_058916.1 172644 View on NCBI ↗
Diarthron tianschanicum NC_063827.1 172119 View on NCBI ↗