Markers + reference

Aneura

2 species · Aneuraceae · Metzgeriales

Back to catalogue

Species 2
Genome length 121–121 kb
Candidate markers 269
Primer pairs 90

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpI Genome 783 0.0396 1.00 66.6 yes View details
trnH-GUG-ycf2 Genome 327 0.0767 1.00 74.5 yes View details
ycf2 Genome 5613 0.0589 1.00 68.3 yes View details
cysA-trnT-GGU Genome 752 0.1121 0.72 76.0 yes View details
psbZ-trnG-GCC Genome 248 0.1639 0.98 76.5 yes View details
psbE-petL Genome 684 0.1048 0.98 82.1 yes View details
rps15-ycf1 Genome 1756 0.0794 0.99 76.6 yes View details
ycf1 Genome 3255 0.0687 1.00 72.1 yes View details
trnV-GAC-rps12 Genome 708 0.0878 0.98 82.3 no View details
trnT-GGU-psbD Genome 725 0.0816 1.00 82.2 yes View details
rpl20-rps12 Genome 795 0.0502 0.93 81.7 yes View details
trnR-UCU-QU390_pgt004 Genome 95 0.1196 0.97 80.7 yes View details
trnW-CCA-trnP-UGG Genome 49 0.1458 0.98 80.0 yes View details
atpI-atpH Genome 424 0.0963 0.96 79.3 yes View details
trnfM-CAU-rps14 Genome 109 0.1376 1.00 78.6 yes View details
trnG-GCC-trnfM-CAU Genome 37 0.1622 1.00 78.0 yes View details
ccsA Genome 987 0.0598 1.00 77.2 yes View details
petN-trnC-GCA Genome 345 0.0849 0.92 77.0 yes View details
psbA-trnH-GUG Genome 184 0.1602 0.98 76.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petN-trnC-GCA_p1 petN-trnC-GCA TGCACCCCAAGCTATACTAGT TTCGAATCCGGGTGTCACTT 372–395 1.000 69.2
petN-trnC-GCA_p2 petN-trnC-GCA TGCACCCCAAGCTATACTAGT GTTCGAATCCGGGTGTCAC 373–396 1.000 67.3
petN-trnC-GCA_p3 petN-trnC-GCA TGCACCCCAAGCTATACTAGT TCGAATCCGGGTGTCACTT 371–394 1.000 66.6
petN-trnC-GCA_p4 petN-trnC-GCA TGCACCCCAAGCTATACTAGT TTCGAATCCGGGTGTCACT 372–395 1.000 66.6
petN-trnC-GCA_p5 petN-trnC-GCA TGCACCCCAAGCTATACTAG TTCGAATCCGGGTGTCACTT 372–395 1.000 66.3
atpI_p1 atpI ATTGCGATCCGAATGTGACA GCCGGGTCCTATAGAAGCTA 1567–1621 1.000 87.0
atpI_p2 atpI TGGCTGGGATTTTTGAACGA GCCGGGTCCTATAGAAGCTA 1771–1825 1.000 86.5
atpI_p3 atpI TGGCTGGGATTTTTGAACGA ACGGAAGCAGCAGAAATCAA 1725–1779 1.000 86.5
atpI_p4 atpI TGATGCCCGAGCCTCTATTA GCCGGGTCCTATAGAAGCTA 1578 0.500 59.3
atpI_p5 atpI TGATGCCCGAGCCTCTATTA ACGGAAGCAGCAGAAATCAA 1532 0.500 59.1
atpI-atpH_p1 atpI-atpH TTCGTGGGGACGATGTTTTT CACACACTCCCTTCCCAAAA 1520–1551 1.000 85.4
atpI-atpH_p2 atpI-atpH TTTCGTGGGGACGATGTTTT CACACACTCCCTTCCCAAAA 1521–1552 1.000 85.4
atpI-atpH_p3 atpI-atpH ACCCTGGCGAGTTTTGAAAT CACACACTCCCTTCCCAAAA 1495 0.500 59.4
atpI-atpH_p4 atpI-atpH ACCCTGGCGAGTTTTGAAAT GCCGGGTCCTATAGAAGCTA 899 0.500 59.3
atpI-atpH_p5 atpI-atpH ACCCTGGCGAGTTTTGAAAT ACGGAAGCAGCAGAAATCAA 853 0.500 59.1
trnR-UCU-QU390_pgt004_p1 trnR-UCU-QU390_pgt004 GGATTCGAACCTATACTCGAGG AGATGAGGCGTCGACTAGAA 225–234 1.000 65.2
trnR-UCU-QU390_pgt004_p2 trnR-UCU-QU390_pgt004 GGATTCGAACCTATACTCGAGG GATGAGGCGTCGACTAGAAC 224–233 1.000 64.7
trnR-UCU-QU390_pgt004_p3 trnR-UCU-QU390_pgt004 ACGTTCAATAGGATTCGAACCT AGATGAGGCGTCGACTAGAA 235–244 1.000 64.6
trnR-UCU-QU390_pgt004_p4 trnR-UCU-QU390_pgt004 GGATTCGAACCTATACTCGAGG CTAGAACCCCTAGCCTTCCA 211–220 1.000 64.4
trnR-UCU-QU390_pgt004_p5 trnR-UCU-QU390_pgt004 ACGTTCAATAGGATTCGAACCT GATGAGGCGTCGACTAGAAC 234–243 1.000 64.1
psbA-trnH-GUG_p1 psbA-trnH-GUG CCTCCGTCGAAGCTCCTG CTGCCTTAATCCACTTGGCT 245–247 1.000 59.8
psbA-trnH-GUG_p2 psbA-trnH-GUG CCTCCGTCGAAGCTCCTG GATCCACAATCCACTGCCTT 258–260 1.000 59.8
psbA-trnH-GUG_p3 psbA-trnH-GUG CCTCCGTCGAAGCTCCTG ACTGCCTTAATCCACTTGGC 246–248 1.000 59.6
psbA-trnH-GUG_p4 psbA-trnH-GUG CTCCGTCGAAGCTCCTGC CTGCCTTAATCCACTTGGCT 244–246 1.000 54.3
psbA-trnH-GUG_p5 psbA-trnH-GUG CTCCGTCGAAGCTCCTGC GATCCACAATCCACTGCCTT 257–259 1.000 54.2
trnH-GUG-ycf2_p1 trnH-GUG-ycf2 AAGGCAGTGGATTGTGGATC TGTACAAAGATTCCTTTCTTAGTGA 416–417 1.000 45.0
trnH-GUG-ycf2_p2 trnH-GUG-ycf2 AAGGCAGTGGATTGTGGATC ACAAAGATTCCTTTCTTAGTGA 413–414 1.000 45.0
trnH-GUG-ycf2_p3 trnH-GUG-ycf2 GCCAAGTGGATTAAGGCAGT TGTACAAAGATTCCTTTCTTAGTGA 428–429 1.000 44.9
trnH-GUG-ycf2_p4 trnH-GUG-ycf2 AAGGCAGTGGATTGTGGATC CACCCAAATCAAAAATTTTGTACA 434–435 1.000 44.8
trnH-GUG-ycf2_p5 trnH-GUG-ycf2 GCCAAGTGGATTAAGGCAGT CACCCAAATCAAAAATTTTGTACA 446–447 1.000 44.7

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
Aneura maxima NC_082503.1 120999 View on NCBI ↗
Aneura pinguis NC_035617.1 120698 View on NCBI ↗