Markers + reference

Geranium

2 species · Geraniaceae · Geraniales

Back to catalogue

Species 2
Genome length 154–155 kb
Candidate markers 235
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 13 remaining regions by MarkerSeek score (out of 235 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-psbK Genome 3816 0.0533 0.99 78.0 yes View details
rpl23-rps12 Genome 863 0.1356 0.93 83.5 yes View details
trnI-rrn16S Genome 2621 0.0669 0.99 79.3 yes View details
trnQ-rpl23 Genome 3396 0.0815 0.99 74.7 yes View details
trnE-rps11 Genome 1622 0.0581 0.97 77.2 yes View details
ndhC-trnM Genome 4094 0.0755 0.93 86.3 yes View details
rps12-trnI Genome 1533 0.0824 0.98 82.4 yes View details
rps11 Genome 951 0.0535 0.98 89.5 yes View details
rps11 Genome 282 0.0952 0.97 84.9 yes View details
trnI-rpl16 Genome 733 0.0569 0.98 81.0 yes View details
rpl14-rps8 Genome 87 0.0706 0.98 80.4 yes View details
rrn16S-trnV Genome 812 0.0511 0.92 79.1 yes View details
rps15 Genome 285 0.0573 0.98 77.1 yes View details
rpl23 Genome 1550 0.0739 0.99 76.9 yes View details
rps18 Genome 474 0.0566 0.97 75.0 yes View details
rps11-rpoA Genome 70 0.0781 0.91 74.6 yes View details
petA-psbJ Genome 1246 0.0238 0.98 74.5 yes View details
rpl23 Genome 192 0.0535 0.97 69.7 no View details
rpl23 Genome 222 0.0415 0.98 64.1 no View details
rps11 Genome 432 0.0305 0.99 60.1 no 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
psbA-psbK_p1 psbA-psbK TTTTTCCACCCTTAGCACCC GAAGGCGGGAATTTTTGCTC 572 0.500 59.9
psbA-psbK_p2 psbA-psbK TGAATGACCCGCTTAACTCG GAAGGCGGGAATTTTTGCTC 833 0.500 59.9
psbA-psbK_p3 psbA-psbK TTTTTCCACCCTTAGCACCC GGGGTGCACTATTTTTGGGA 830 0.500 59.4
psbA-psbK_p4 psbA-psbK TGAATGACCCGCTTAACTCG GGGGTGCACTATTTTTGGGA 1091 0.500 59.4
psbA-psbK_p5 psbA-psbK GCCTTTGGCGTCGTATCTTA GAAGGCGGGAATTTTTGCTC 356 0.500 59.4
trnI-rpl16_p1 trnI-rpl16 GTTGGGCGCTTTAACCATTC AATACGACTGCCTTGAGAGG 844–846 1.000 77.3
trnI-rpl16_p2 trnI-rpl16 GTTGGGCGCTTTAACCATTC CCGAAAGAAATACGACTGCC 852–854 1.000 76.3
trnI-rpl16_p3 trnI-rpl16 GTTGGGCGCTTTAACCATTC AAATACGACTGCCTTGAGAGG 845–847 1.000 75.0
trnI-rpl16_p4 trnI-rpl16 AGTTGGGCGCTTTAACCATT AATACGACTGCCTTGAGAGG 845–847 1.000 74.4
trnI-rpl16_p5 trnI-rpl16 TTGGGCGCTTTAACCATTCA AATACGACTGCCTTGAGAGG 843–845 1.000 74.3
rpl14-rps8_p1 rpl14-rps8 AATTTCCCTAGCGCCTGAAG AACCGTCTCTTTGTTAGCCA 185–187 1.000 75.7
rpl14-rps8_p2 rpl14-rps8 GTGCAATCACCCACGAATTG AACCGTCTCTTTGTTAGCCA 228–230 1.000 75.3
rpl14-rps8_p3 rpl14-rps8 TGCAATCACCCACGAATTGA AACCGTCTCTTTGTTAGCCA 227–229 1.000 74.6
rpl14-rps8_p4 rpl14-rps8 AATCCAAAAGGAACTCGCGT AACCGTCTCTTTGTTAGCCA 253–255 1.000 74.3
rpl14-rps8_p5 rpl14-rps8 ATCCAAAAGGAACTCGCGTT AACCGTCTCTTTGTTAGCCA 252–254 1.000 74.3
rps11-rpoA_p1 rps11-rpoA AACCCCTATGCCACATAACG GACTCTTACTTTTTCTCGAATCA 140–146 1.000 46.2
rps11-rpoA_p2 rps11-rpoA AACCCCTATGCCACATAACG ACTCTTACTTTTTCTCGAATCA 139–145 1.000 46.2
rps11-rpoA_p3 rps11-rpoA AACCCCTATGCCACATAACG GACTCTTACTTTTTCTCGAATCAT 140–146 1.000 46.2
rps11-rpoA_p4 rps11-rpoA AACCCCTATGCCACATAACG ACTCTTACTTTTTCTCGAATCAT 139–145 1.000 46.2
rps11-rpoA_p5 rps11-rpoA CGGGATATAACCCCTATGCC GACTCTTACTTTTTCTCGAATCA 148–154 1.000 45.8
rpl23-rps12_p1 rpl23-rps12 ATGGGACCGGACCTAGTATG CGAATACGGCTTTCCACAGA 1620 0.500 59.9
rpl23-rps12_p2 rpl23-rps12 ATGGGACCGGACCTAGTATG TCGAATACGGCTTTCCACAG 1621 0.500 59.9
rpl23-rps12_p3 rpl23-rps12 ATGGGACCGGACCTAGTATG TACTCCGACAGCATCTAGGG 1118 0.500 59.8
rpl23-rps12_p4 rpl23-rps12 ATGGGACCGGACCTAGTATG TCTACAACGCACTAGAACGC 1155 0.500 59.7
rpl23-rps12_p5 rpl23-rps12 AAAGAATGGGACCGGACCTA CGAATACGGCTTTCCACAGA 1625 0.500 59.7
rps15_p1 rps15 ACGAAACTAAATTTATCCAAATGCA AAAGATGGGTAGGAGGCCC 421–427 1.000 44.2
rps15_p2 rps15 ACGAAACTAAATTTATCCAAATGCA AAAAAGATGGGTAGGAGGCC 423–429 1.000 44.1
rps15_p3 rps15 ACGAAACTAAATTTATCCAAATGCA AAAAGATGGGTAGGAGGCCC 422–428 1.000 44.1
rps15_p4 rps15 AACGAAACTAAATTTATCCAAATGCA AAAAAGATGGGTAGGAGGCC 424–430 1.000 44.1
rps15_p5 rps15 ACGAAACTAAATTTATCCAAATGCAA AAAAAGATGGGTAGGAGGCC 423–429 1.000 44.1

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
Geranium koreanum NC_063552.1 154493 View on NCBI ↗
Geranium thunbergii NC_063551.1 155144 View on NCBI ↗