Markers + reference

Limonium

5 species · Plumbaginaceae · Caryophyllales

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Species 5
Genome length 155–155 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC-GCA LSC 1346 0.0167 1.00 68.6 yes View details
trnE-UUC-trnT-GGU LSC 791 0.0191 0.96 68.0 yes View details
ycf4-cemA LSC 534 0.0202 1.00 55.4 yes View details
petA-psbJ LSC 842 0.0204 1.00 65.9 yes View details
psaJ-rpl33 LSC 515 0.0221 1.00 64.7 yes View details
ndhF SSC 2220 0.0126 1.00 52.1 yes View details
ndhF-rpl32 SSC 924 0.0275 0.99 68.1 yes View details
rpl32-trnL-UAG SSC 807 0.0295 1.00 71.3 yes View details
ndhA SSC 2001 0.0120 1.00 44.5 yes View details
trnL-UAG-ccsA SSC 133 0.0346 1.00 72.0 yes View details
rps16-trnQ-UUG LSC 347 0.0290 0.98 71.5 yes View details
psbM-trnD-GUC LSC 877 0.0115 0.99 62.7 yes View details
trnS-GCU-trnG-UCC LSC 799 0.0168 1.00 62.0 yes View details
petN-psbM LSC 1061 0.0115 1.00 62.0 yes View details
atpH-atpI LSC 756 0.0130 0.98 60.5 yes View details
trnT-UGU-trnL-UAA LSC 660 0.0146 1.00 60.5 yes View details
rbcL-accD LSC 674 0.0160 1.00 60.1 yes View details
trnG-UCC-trnR-UCU LSC 155 0.0361 1.00 59.5 yes View details
ndhH-rps15 SSC 88 0.0352 1.00 59.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCACACCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 408–442 1.000 86.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 386–420 1.000 86.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 397–431 1.000 85.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACACCAGATCATGTCCT ATATTTTAGTGGGGCGTGGC 465–499 1.000 84.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ATATTTTAGTGGGGCGTGGC 443–477 1.000 83.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCCTCGGTACAAATCACTCG ACGAATCACACTTTTACCACT 899–933 1.000 54.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 920–954 1.000 53.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCCTCGGTACAAATCACTCG AGAACGAATCACACTTTTACCAC 902–936 1.000 53.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCCTCGGTACAAATCACTCG GAACGAATCACACTTTTACCACT 901–935 1.000 53.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 922–956 1.000 52.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG GCATATGGAAATAAATTGCGTCC 287–296 1.000 51.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA GCATATGGAAATAAATTGCGTCC 293–302 1.000 50.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATAAATTGCGTCCAATAGG 282–291 1.000 50.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA TGGAAATAAATTGCGTCCAATAGG 288–297 1.000 50.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGCATATGGAAATAAATTGCGTCC 288–297 1.000 49.8
atpH-atpI_p1 atpH-atpI ATAACAGAAGCGGCCGAAAT TTTTGCAACTTTAGCCGCAG 805–843 1.000 84.9
atpH-atpI_p2 atpH-atpI ATAACAGAAGCGGCCGAAAT CGAATCCATGGAGGGTCATC 775–813 1.000 84.6
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 861–899 1.000 84.1
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 821–859 1.000 83.9
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 831–869 1.000 83.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CTTACCACTCGGCCATATCG 1423–1468 1.000 85.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CCAGATTTGAACCGGGGAAA 1464–1509 1.000 84.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA GGGATTTCGGGTCTGTTGTT 1497–1542 1.000 84.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AAAGGATTTGCAGTCCTCCG 1444–1489 1.000 84.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA TCTGTTGTTGATCAGGCGAC 1486–1531 1.000 83.9
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAACGGTCAGCCAAAATGA 1158–1161 1.000 70.2
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG AAAACGGTCAGCCAAAATGA 1164–1167 1.000 68.7
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA AAACGGTCAGCCAAAATGAT 1157–1160 1.000 68.3
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA AACGGTCAGCCAAAATGATT 1156–1159 1.000 68.3
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAAACGGTCAGCCAAAATGA 1159–1162 1.000 68.2

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
Limonium aureum NC_045399.1 154661 View on NCBI ↗
Limonium bicolor NC_059915.1 154617 View on NCBI ↗
Limonium franchetii NC_085143.1 154673 View on NCBI ↗
Limonium otolepis NC_065861.1 154520 View on NCBI ↗
Limonium tetragonum NC_059914.1 154691 View on NCBI ↗