Markers + reference

Halimocnemis

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 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
psbZ-trnG-UCC LSC 318 0.1980 0.94 83.1 yes View details
trnL-UAA-trnF-GAA LSC 355 0.0367 1.00 66.4 yes View details
trnM-CAU-atpE LSC 265 0.0711 0.95 75.2 yes View details
accD-psaI LSC 589 0.0520 0.98 75.0 yes View details
trnN-GUU-ndhF IRb 2112 0.0401 0.91 73.9 yes View details
rpl32-trnL-UAG SSC 787 0.0674 0.96 84.2 yes View details
ycf1 SSC 5451 0.0387 0.99 61.3 yes View details
trnP-UGG-psaJ LSC 457 0.0435 0.96 82.2 yes View details
trnG-GCC-trnR-UCU LSC 123 0.0678 0.96 81.4 yes View details
rps11-rpl36 LSC 156 0.0658 0.97 80.4 yes View details
trnT-UGU-trnL-UAA LSC 672 0.0269 0.94 78.6 yes View details
trnH-GUG-psbA LSC 229 0.0550 0.95 78.2 yes View details
trnG-UCC-trnfM-CAU LSC 230 0.0711 0.98 77.6 yes View details
psbE-petL LSC 1303 0.0332 0.97 76.9 yes View details
petN-psbM LSC 699 0.0418 0.99 75.2 yes View details
psbB-psbT LSC 176 0.0526 0.97 74.8 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 85 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 297–299 1.000 84.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 311–313 1.000 84.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 310–312 1.000 84.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 312–314 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 326–328 1.000 81.2
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATAAATTGCGTCCAATAGG 260–264 1.000 50.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATAAATTGCGTCCAATAGG 263–267 1.000 50.3
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATAAATTGCGTCCAA 260–264 1.000 49.8
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATAAATTGCGTCCAA 263–267 1.000 49.5
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 219–223 1.000 49.5
petN-psbM_p1 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAACGGTCAGCCAAAATGA 807–821 1.000 68.8
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTCAGCCAAAATGA 745–759 1.000 68.4
petN-psbM_p3 petN-psbM ATTGTAAGTCTCGCTTGGGC AAACGGTCAGCCAAAATGAT 806–820 1.000 67.0
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC AACGGTCAGCCAAAATGATT 805–819 1.000 67.0
petN-psbM_p5 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAAACGGTCAGCCAAAATGA 808–822 1.000 66.8
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 463–475 1.000 88.4
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 461–473 1.000 88.0
psbZ-trnG-UCC_p3 psbZ-trnG-UCC CTCCTGATGGTTGGTCAAGT CGTCTTCTCCTTGGCAAAGA 457–469 1.000 83.2
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TGCTTCTCCTGATGGTTGGT CGTCTTCTCCTTGGCAAAGA 462–474 1.000 82.6
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TCTCCTGATGGTTGGTCAAG CGTCTTCTCCTTGGCAAAGA 458–470 1.000 80.8
trnG-UCC-trnfM-CAU_p1 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG GTTCAAATCCTGTCTCCGCA 295–296 1.000 82.8
trnG-UCC-trnfM-CAU_p2 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG TAGCTCGCAAGGCTCATAAC 328–329 1.000 82.0
trnG-UCC-trnfM-CAU_p3 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG GTAGCTCGCAAGGCTCATAA 329–330 1.000 81.9
trnG-UCC-trnfM-CAU_p4 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG TCAAATCCTGTCTCCGCAAA 293–294 1.000 79.9
trnG-UCC-trnfM-CAU_p5 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG TTCAAATCCTGTCTCCGCAA 294–295 1.000 79.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGCCAATTAAGTCCGTAGCG 726–745 1.000 84.3
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT AGCCAATTAAGTCCGTAGCG 758–777 1.000 83.3
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 714–733 1.000 82.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GCCAATTAAGTCCGTAGCGT 725–744 1.000 82.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 746–765 1.000 81.9

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
Halimocnemis karelinii ON929838.1 152055 View on NCBI ↗
Halimocnemis longifolia ON929837.1 151507 View on NCBI ↗