Markers + reference

Sabulina

2 species · Caryophyllaceae · Caryophyllales

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Species 2
Genome length 153–154 kb
Candidate markers 263
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

15 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 570 0.1277 0.98 81.8 yes View details
trnS-GCU-trnG-UCC LSC 691 0.1129 0.99 83.8 yes View details
atpH-atpI LSC 709 0.0809 0.78 76.3 yes View details
rpoB-trnC-GCA LSC 1016 0.0814 0.96 81.2 yes View details
psbM-trnD-GUC LSC 687 0.0797 0.97 84.3 yes View details
trnD-GUC-trnY-GUA LSC 420 0.1037 0.96 86.2 yes View details
trnE-UUC-trnT-GGU LSC 583 0.1123 0.96 87.7 yes View details
trnT-GGU-psbD LSC 1198 0.0707 0.92 84.0 yes View details
psaA-pafI LSC 1189 0.0665 0.59 70.1 yes View details
pafI-trnS-GGA LSC 777 0.0889 0.95 85.7 yes View details
psbE-petL LSC 1276 0.0718 0.68 73.8 yes View details
ycf1 IRb 1896 0.0148 1.00 51.9 no View details
ndhF-rpl32 SSC 697 0.1139 0.63 72.1 yes View details
rpl32-trnL-UAG SSC 785 0.1047 0.99 80.6 yes View details
ycf1 SSC 5589 0.0489 0.99 68.8 yes View details
trnF-GAA-ndhJ LSC 751 0.0723 0.96 83.3 yes View details
trnT-UGU-trnL-UAA LSC 733 0.0775 0.99 81.8 yes View details
trnC-GCA-petN LSC 574 0.0676 0.98 81.4 yes View details
rps16-trnQ-UUG LSC 633 0.0925 0.91 80.9 yes View details
trnG-GCC-trnfM-CAU LSC 191 0.1183 0.97 80.4 yes View details
pafII-cemA LSC 709 0.0797 0.94 80.1 yes View details
ndhC-trnV-UAC LSC 1106 0.0710 0.94 79.9 yes View details
psbC-trnS-UGA LSC 219 0.1553 1.00 79.8 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CACGATAAAGGCTTCCGGAA 1328–1386 1.000 86.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGATAAAGGCTTCCGGAACA 1326–1384 1.000 86.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ACGATAAAGGCTTCCGGAAC 1327–1385 1.000 86.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA CACGATAAAGGCTTCCGGAA 1281–1339 1.000 86.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA CGATAAAGGCTTCCGGAACA 1279–1337 1.000 86.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GAGAACTAGCCCACCTTTCG CTTACAGCAGCTTGCCAAAC 1377–1392 1.000 87.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GAGAACTAGCCCACCTTTCG GGATAATGCGGGTTGTGTCT 1543 0.500 59.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGTTCCGGAAGCCTTTATCG GGATAATGCGGGTTGTGTCT 1853 0.500 59.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCCGGAAGCCTTTATCGTG GGATAATGCGGGTTGTGTCT 1851 0.500 59.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTTCCGGAAGCCTTTATCGT GGATAATGCGGGTTGTGTCT 1852 0.500 59.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG ACGAATCACACTTTTACCACT 815–911 1.000 59.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 814–910 1.000 58.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AGAACGAATCACACTTTTACCAC 818–914 1.000 58.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG GAACGAATCACACTTTTACCACT 817–913 1.000 58.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 816–912 1.000 57.4
atpH-atpI_p1 atpH-atpI GCGGCAGAAATCAGTGGATT TTTTGCAACTTTAGCCGCAG 668–787 1.000 80.7
atpH-atpI_p2 atpH-atpI GCGGCAGAAATCAGTGGATT CGAATCCATGGAGGGTCATC 638–757 1.000 80.5
atpH-atpI_p3 atpH-atpI GCGGCAGAAATCAGTGGATT TACCTGTCATGTTCCTCGGA 717–836 1.000 79.6
atpH-atpI_p4 atpH-atpI CGGCAGAAATCAGTGGATTC TTTTGCAACTTTAGCCGCAG 667–786 1.000 78.9
atpH-atpI_p5 atpH-atpI CGGCAGAAATCAGTGGATTC CGAATCCATGGAGGGTCATC 637–756 1.000 78.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TGGTTTGTTCTTGCCTCTCC CCGGATTTGAACTGGGGAAT 1344–1374 1.000 86.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGGTTTGTTCTTGCCTCTCC AGCACGTATCAAGAGACCCT 1453–1484 1.000 86.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCCTACACAAGCAAACTGT CCGGATTTGAACTGGGGAAT 1752–1782 1.000 84.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCTACACAAGCAAACTGT ATTACCCCACACCGAATTGG 2044 0.500 58.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TGGTTTGTTCTTGCCTCTCC ATTACCCCACACCGAATTGG 1636 0.500 58.7
trnC-GCA-petN_p1 trnC-GCA-petN ATTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACAAT 624–629 1.000 83.1
trnC-GCA-petN_p2 trnC-GCA-petN ATTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 686–691 1.000 81.9
trnC-GCA-petN_p3 trnC-GCA-petN ATTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 633–638 1.000 77.9
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC GCCCAAGCGAGACTTACAAT 619–624 1.000 77.7
trnC-GCA-petN_p5 trnC-GCA-petN ATTCCCCAGTTCAAATCCGG GACTACCATTAAAGCAGCCCA 640–645 1.000 77.1

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
Sabulina glaucina subsp. leptophylla PX275705.1 154065 View on NCBI ↗
Sabulina tenuifolia NC_087611.1 152715 View on NCBI ↗