Markers + reference

Chamaenerion

4 species · Onagraceae · Myrtales

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Species 4
Genome length 159–161 kb
Candidate markers 261
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 Genome 744 0.0188 1.00 58.7 yes View details
atpH-atpI Genome 911 0.0210 0.97 61.4 yes View details
rpoB-trnC Genome 1276 0.0377 0.91 75.7 yes View details
psbM-trnD Genome 1100 0.0105 0.97 64.9 yes View details
trnT-trnL Genome 1183 0.0320 0.88 77.4 yes View details
trnL-trnF Genome 298 0.0561 0.96 85.4 yes View details
ndhF-rpl32 Genome 872 0.0199 0.98 62.7 yes View details
ccsA-ndhD Genome 438 0.0426 1.00 77.6 yes View details
ndhE Genome 306 0.0000 1.00 20.8 yes View details
ndhE-ndhG Genome 216 0.1762 0.60 82.5 yes View details
psbC-trnS Genome 214 0.0210 0.97 66.8 yes View details
ndhD-psaC Genome 240 0.0250 1.00 65.2 yes View details
psbE-petL Genome 1399 0.0068 0.82 62.0 yes View details
rps16-trnQ Genome 1440 0.0127 0.99 61.7 yes View details
atpB-rbcL Genome 745 0.0043 1.00 61.7 yes View details
trnS-GCU-trnG Genome 826 0.0114 0.96 61.0 yes View details
ndhC-trnA-UAC Genome 1360 0.0064 0.99 60.8 yes View details
trnT-GGU-psbD Genome 1439 0.0042 0.94 59.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 CAGTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1168–1189 1.000 81.5
trnK-rps16_p2 trnK-rps16 GTTCAGGATCAGTCGTGGTC GCCGTACGAGGAGAAAACTT 1166–1187 1.000 81.5
trnK-rps16_p3 trnK-rps16 TGCTTTTTCCAGGCATTCCT GCCGTACGAGGAGAAAACTT 1190–1211 1.000 81.4
trnK-rps16_p4 trnK-rps16 ATGCAAAAACCCTTCTCCGT GCCGTACGAGGAGAAAACTT 1416–1443 1.000 81.2
trnK-rps16_p5 trnK-rps16 CGACATGCTGCTTTTTCCAG GCCGTACGAGGAGAAAACTT 1198–1219 1.000 81.2
rps16-trnQ_p1 rps16-trnQ CGCGTTGCTTTTTACCACAT GAGGTTCGAATCCTTCCGTC 1495–1518 1.000 82.0
rps16-trnQ_p2 rps16-trnQ GAATAGAAAGTGGCGGGTGT GAGGTTCGAATCCTTCCGTC 1551–1574 1.000 81.4
rps16-trnQ_p3 rps16-trnQ GAAAGTGGCGGGTGTAAGAA GAGGTTCGAATCCTTCCGTC 1546–1569 1.000 81.4
rps16-trnQ_p4 rps16-trnQ ATCATGTCTGTCAAGTCGCG GAGGTTCGAATCCTTCCGTC 1513–1536 1.000 79.4
rps16-trnQ_p5 rps16-trnQ AAAGTGGCGGGTGTAAGAAC GAGGTTCGAATCCTTCCGTC 1545–1568 1.000 79.1
trnS-GCU-trnG_p1 trnS-GCU-trnG CAATCCGACGCTTTAGTCCA GGGATTAAGCAAACGAATCACA 868–907 1.000 64.0
trnS-GCU-trnG_p2 trnS-GCU-trnG AATCCGACGCTTTAGTCCAC GGGATTAAGCAAACGAATCACA 867–906 1.000 64.0
trnS-GCU-trnG_p3 trnS-GCU-trnG ACTCAACGGAAAGAGAGGGA GGGATTAAGCAAACGAATCACA 927–966 1.000 63.9
trnS-GCU-trnG_p4 trnS-GCU-trnG CAATCCGACGCTTTAGTCCA ACAAGGGATTAAGCAAACGA 872–911 1.000 63.7
trnS-GCU-trnG_p5 trnS-GCU-trnG AATCCGACGCTTTAGTCCAC ACAAGGGATTAAGCAAACGA 871–910 1.000 63.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATGGAGGGTCATCATTGA 937–985 1.000 44.7
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG ATGGAGGGTCATCATTGA 971–1019 1.000 44.5
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATGGAGGGTCATCATTGA 993–1041 1.000 44.4
atpH-atpI_p4 atpH-atpI TACCCTCTACAGCTTGTCCC ATGGAGGGTCATCATTGA 1020–1068 1.000 44.3
atpH-atpI_p5 atpH-atpI GCGATACCCTCTACAGCTTG ATGGAGGGTCATCATTGA 1024–1072 1.000 44.3
rpoB-trnC_p1 rpoB-trnC ACATTCCCCCATTTCCATCC CCGGATTTGAACTGGGGAAA 1257–1366 1.000 82.9
rpoB-trnC_p2 rpoB-trnC GTTCTTCCGTTAAGCCCTGA CCGGATTTGAACTGGGGAAA 1332–1441 1.000 82.8
rpoB-trnC_p3 rpoB-trnC AGTTCTTCCGTTAAGCCCTG CCGGATTTGAACTGGGGAAA 1333–1442 1.000 82.7
rpoB-trnC_p4 rpoB-trnC CATTCCCCCATTTCCATCCG CCGGATTTGAACTGGGGAAA 1256–1365 1.000 81.4
rpoB-trnC_p5 rpoB-trnC CTTCCGTTAAGCCCTGATCA CCGGATTTGAACTGGGGAAA 1329–1438 1.000 81.0
psbM-trnD_p1 psbM-trnD AAAACGCAGTCGGAACTAGA TTCAATTGGTCAGAGCACCG 1185–1228 1.000 74.2
psbM-trnD_p2 psbM-trnD AAACGCAGTCGGAACTAGAA TTCAATTGGTCAGAGCACCG 1184–1227 1.000 74.2
psbM-trnD_p3 psbM-trnD AACGCAGTCGGAACTAGAAT TTCAATTGGTCAGAGCACCG 1183–1226 1.000 72.4
psbM-trnD_p4 psbM-trnD AAAAACGCAGTCGGAACTAGA TTCAATTGGTCAGAGCACCG 1186–1229 1.000 71.8
psbM-trnD_p5 psbM-trnD AAAACGCAGTCGGAACTAGAA TTCAATTGGTCAGAGCACCG 1185–1228 1.000 71.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Chamaenerion angustifolium NC_052848.1 161182 View on NCBI ↗
Chamaenerion angustifolium subsp. angustifolium NC_061021.1 160235 View on NCBI ↗
Chamaenerion angustifolium subsp. circumvagum NC_061014.1 160416 View on NCBI ↗
Chamaenerion conspersum NC_061020.1 159496 View on NCBI ↗