Markers + reference

Erodium

5 species · Geraniaceae · Geraniales

Back to catalogue

Species 5
Genome length 116–118 kb
Candidate markers 230
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 230 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnG-UCC Genome 1038 0.2655 0.78 76.8 yes View details
rps12-clpP Genome 1336 0.1898 0.75 76.2 yes View details
rpl14-rpl16 Genome 688 0.1457 0.95 83.7 yes View details
trnA-UGC-ErcaC_r002 Genome 860 0.2834 0.87 78.2 yes View details
rpl32-rps15 Genome 1421 0.0806 0.74 76.4 yes View details
psaI-rpl20 Genome 1561 0.0608 0.99 79.8 yes View details
trnD-GUC-trnY-GUA Genome 343 0.0446 1.00 77.2 yes View details
trnL-CAA-ndhB Genome 597 0.0382 1.00 75.2 yes View details
rpoB-trnC-GCA Genome 1133 0.0268 1.00 74.3 yes View details
rps18-trnG-UCC Genome 127 0.2181 0.99 74.1 yes View details
psbB-psbT Genome 262 0.0487 0.88 73.4 yes View details
ErcaC_r001-trnI-GAU Genome 305 0.0410 1.00 73.1 yes View details
trnQ-UUG Genome 69 0.0551 1.00 72.7 yes View details
ErcaC_r004-trnR-ACG Genome 240 0.0521 0.98 71.7 yes View details
trnT-UGU-trnL-UAA Genome 988 0.0272 0.99 71.4 yes View details
trnQ-UUG Genome 72 0.0000 1.00 18.8 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-UUG_p1 trnQ-UUG CCACCTTTTGAAGAGCCCTT TGTTGACAAAGACCCATCGG 1045–1164 1.000 87.5
trnQ-UUG_p2 trnQ-UUG CCACCTTTTGAAGAGCCCTT GAATCCTTTCGTCCCAGGTC 795–827 0.600 65.6
trnQ-UUG_p3 trnQ-UUG CCACCTTTTGAAGAGCCCTT CTGTTCTGTATTGGTGCCGA 736–768 0.600 65.1
trnQ-UUG_p4 trnQ-UUG CCACCTTTTGAAGAGCCCTT TGTTCTGTATTGGTGCCGAG 735–767 0.600 65.1
trnQ-UUG_p5 trnQ-UUG TGAACAGTTCCTGTGGGTTG GAATCCTTTCGTCCCAGGTC 889–921 0.600 65.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GCCCAGGTATTACAGCCATT AAAGGGGATTTCGCGTCTTT 1274–1340 1.000 83.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCCCAGGTATTACAGCCATT AAGGGGATTTCGCGTCTTTT 1273–1339 1.000 83.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCCCTGATCAACGAACCTAC AAAAGGGGATTTCGCGTCTT 1322–1388 1.000 83.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCCCTGATCAACGAACCTAC AAAGGGGATTTCGCGTCTTT 1321–1387 1.000 83.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCCTGATCAACGAACCTAC AAGGGGATTTCGCGTCTTTT 1320–1386 1.000 83.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CTGGTTCAAATCCAGCTCGA 397–412 1.000 82.8
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGTTCAAATCCAGCTCGAC 396–411 1.000 82.0
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 413–428 1.000 81.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 412–427 1.000 81.4
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 434–449 1.000 80.1
trnE-UUC-trnG-UCC_p1 trnE-UUC-trnG-UCC TGGAGATTCCAATCGCTGTG GCCTTCCCAAAATGAAAGGC 1840–2031 0.600 75.0
trnE-UUC-trnG-UCC_p2 trnE-UUC-trnG-UCC GGAGATTCCAATCGCTGTGT GCCTTCCCAAAATGAAAGGC 1839–2030 0.600 75.0
trnE-UUC-trnG-UCC_p3 trnE-UUC-trnG-UCC TGGAGATTCCAATCGCTGTG GCCTTTCATTTTGGGAAGGC 1645 0.200 47.0
trnE-UUC-trnG-UCC_p4 trnE-UUC-trnG-UCC GGAGATTCCAATCGCTGTGT GCCTTTCATTTTGGGAAGGC 1644 0.200 47.0
trnE-UUC-trnG-UCC_p5 trnE-UUC-trnG-UCC TGGAGATTCCAATCGCTGTG TTGCCCCCAAAATGAAAGGA 1688 0.200 46.9
rps18-trnG-UCC_p1 rps18-trnG-UCC GCCTTCCCAAAATGAAAGGC TTCAATAAAAGTCCCCCGCC 1101 0.200 45.9
rps18-trnG-UCC_p2 rps18-trnG-UCC TCCTTTCATTTTGGGGGCAA TTCAATAAAAGTCCCCCGCC 1058 0.200 45.9
rps18-trnG-UCC_p3 rps18-trnG-UCC TCAATCGAGTCACCCGTCTA TTCAATAAAAGTCCCCCGCC 908 0.200 45.8
rps18-trnG-UCC_p4 rps18-trnG-UCC ACTATATCCGCAAAAGGCCG TTCAATAAAAGTCCCCCGCC 1136 0.200 45.8
rps18-trnG-UCC_p5 rps18-trnG-UCC GCCTTCCCAAAATGAAAGGC AACGAAAAATGGGAGGGAGG 1065 0.200 45.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GTTGCGTCTACCAATTTCGC 1012–1121 1.000 85.6
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTTGCGTCTACCAATTTCG 1013–1122 1.000 85.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TCCAATTAAGTCCGTTGCGT 1025–1134 1.000 85.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TCCGTTGCGTCTACCAATTT 1015–1124 1.000 85.2
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GACCGTCGCATTACAAATGC GTTGCGTCTACCAATTTCGC 1030–1139 1.000 85.1

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
Erodium carvifolium NC_015083.1 116935 View on NCBI ↗
Erodium cicutarium PP328802.1 118380 View on NCBI ↗
Erodium foetidum subsp. foetidum KF771022.1 115794 View on NCBI ↗
Erodium manescavi NC_030720.1 116810 View on NCBI ↗
Erodium rupestre NC_030719.1 116810 View on NCBI ↗