Markers + reference

Gaultheria

2 species · Ericaceae · Ericales

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Species 2
Genome length 176–176 kb
Candidate markers 283
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-GAC-rps12 Genome 1465 0.0110 1.00 54.1 yes View details
rpl22 Genome 465 0.0151 1.00 50.0 yes View details
rpoA-rpoB Genome 6523 0.0097 0.99 58.7 yes View details
trnT-GGU-petD Genome 2919 0.0099 1.00 52.2 yes View details
psbB-psbJ Genome 3422 0.0077 0.98 61.3 yes View details
ycf3-trnK-UUU Genome 1458 0.0082 1.00 49.8 yes View details
rpl32-ndhF Genome 1915 0.0177 0.97 61.6 yes View details
ndhF Genome 2238 0.0107 1.00 49.8 yes View details
trnE-UUC-petA Genome 1476 0.0102 1.00 64.7 yes View details
petN-psbM Genome 1169 0.0043 0.98 62.8 yes View details
psbM-trnD-GUC Genome 1541 0.0065 1.00 62.4 yes View details
trnL-UAA-trnT-UGU Genome 681 0.0059 1.00 62.3 yes View details
trnH-GUG-rpl23 Genome 281 0.0179 1.00 62.2 yes View details
rpl23-trnH-GUG Genome 281 0.0179 1.00 62.2 yes View details
atpI-trnfM-CAU Genome 419 0.0120 1.00 62.1 yes View details
atpB-rbcL Genome 800 0.0088 1.00 61.8 yes View details
rps12-trnC-GCA Genome 1636 0.0055 1.00 61.7 yes View details
trnL-UAG-rpl32 Genome 505 0.0060 0.99 61.4 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnV-GAC-rps12_p1 trnV-GAC-rps12 GATGACTTCCACCACGTCAA TGGCAACTTTACGTAAGGCA 1561–1596 1.000 77.7
trnV-GAC-rps12_p2 trnV-GAC-rps12 AACTGATGACTTCCACCACG TGGCAACTTTACGTAAGGCA 1565–1600 1.000 77.6
trnV-GAC-rps12_p3 trnV-GAC-rps12 ATGACTTCCACCACGTCAAG TGGCAACTTTACGTAAGGCA 1560–1595 1.000 77.6
trnV-GAC-rps12_p4 trnV-GAC-rps12 CTGATGACTTCCACCACGTC TGGCAACTTTACGTAAGGCA 1563–1598 1.000 76.7
trnV-GAC-rps12_p5 trnV-GAC-rps12 GGCTCGAACTGATGACTTCC TGGCAACTTTACGTAAGGCA 1571–1606 1.000 76.2
rpl22_p1 rpl22 TCCCGGGCATCTACCATTAT GAACCCGACCCTTTCTGATC 1233 1.000 80.5
rpl22_p2 rpl22 CGCCGTCGTAAATAGGAGAG GAACCCGACCCTTTCTGATC 1403 1.000 80.4
rpl22_p3 rpl22 CTCAAAACTGCTCAGCAACG GAACCCGACCCTTTCTGATC 1666 1.000 80.3
rpl22_p4 rpl22 CGCCGTCGTAAATAGGAGAG CAGCCTGAAACCAAGTGGAT 877 1.000 80.1
rpl22_p5 rpl22 CTCAAAACTGCTCAGCAACG CAGCCTGAAACCAAGTGGAT 1140 1.000 79.9
rpoA-rpoB_p1 rpoA-rpoB CTCTTCTTTGATCTCCGCGA ATCTTCTAGAGTCTCGGGCC 258 1.000 78.8
rpoA-rpoB_p2 rpoA-rpoB TCTCTTCTTTGATCTCCGCG ATCTTCTAGAGTCTCGGGCC 259 1.000 78.8
rpoA-rpoB_p3 rpoA-rpoB TCTTTGATCTCCGCGATTGC ATCTTCTAGAGTCTCGGGCC 254 1.000 77.7
rpoA-rpoB_p4 rpoA-rpoB CTCTTCTTTGATCTCCGCGA TTCTTCGCCTTCATCGAGAC 231 1.000 77.0
rpoA-rpoB_p5 rpoA-rpoB TCTCTTCTTTGATCTCCGCG TTCTTCGCCTTCATCGAGAC 232 1.000 77.0
atpI-trnfM-CAU_p1 atpI-trnfM-CAU TTTTGCAACTTTAGCTGCGG AAGGTTATGAGCCTTGCGAG 513–514 1.000 79.6
atpI-trnfM-CAU_p2 atpI-trnfM-CAU TTTTGCAACTTTAGCTGCGG TTGCGAGCTACCAGACTACT 500–501 1.000 78.6
atpI-trnfM-CAU_p3 atpI-trnfM-CAU TTTTGCAACTTTAGCTGCGG CTTGCGAGCTACCAGACTAC 501–502 1.000 78.3
atpI-trnfM-CAU_p4 atpI-trnfM-CAU TTTTGCAACTTTAGCTGCGG GTTATGAGCCTTGCGAGCTA 510–511 1.000 78.1
atpI-trnfM-CAU_p5 atpI-trnfM-CAU TTTTGCAACTTTAGCTGCGG TTATGAGCCTTGCGAGCTAC 509–510 1.000 78.1
trnT-GGU-petD_p1 trnT-GGU-petD TGGCGTTACTCTACCACTGA TGGCGCAACATTACCAATTG 2999 0.500 56.4
trnT-GGU-petD_p2 trnT-GGU-petD TGGCGTTACTCTACCACTGA GGCGCAACATTACCAATTGA 2998 0.500 54.1
trnT-GGU-petD_p3 trnT-GGU-petD GGCGTTACTCTACCACTGAG TGGCGCAACATTACCAATTG 2998 0.500 52.6
trnT-GGU-petD_p4 trnT-GGU-petD TGGCGTTACTCTACCACTGA TTGGCGCAACATTACCAATT 3000 0.500 50.4
trnT-GGU-petD_p5 trnT-GGU-petD GGCGTTACTCTACCACTGAG GGCGCAACATTACCAATTGA 2997 0.500 50.3
psbB-psbJ_p1 psbB-psbJ GGCGGTTGTGGATGAAAATG AAGCGCCAGACAAAGGATAG 984–1023 1.000 84.6
psbB-psbJ_p2 psbB-psbJ GGCGGTTGTGGATGAAAATG TGTTCCAACCACCGTGTAAG 1001–1040 1.000 84.5
psbB-psbJ_p3 psbB-psbJ AGGCGGTTGTGGATGAAAAT AAGCGCCAGACAAAGGATAG 985–1024 1.000 84.0
psbB-psbJ_p4 psbB-psbJ AGGCGGTTGTGGATGAAAAT TGTTCCAACCACCGTGTAAG 1002–1041 1.000 83.9
psbB-psbJ_p5 psbB-psbJ CTAAGGCGGTTGTGGATGAA AAGCGCCAGACAAAGGATAG 988–1027 1.000 83.8

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
Gaultheria fragrantissima NC_059849.1 176196 View on NCBI ↗
Gaultheria nummularioides NC_062667.1 176207 View on NCBI ↗