Markers + reference

Casuarina

3 species · Casuarinaceae · Fagales

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Species 3
Genome length 156–156 kb
Candidate markers 270
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 299 0.0089 1.00 36.4 yes View details
rps16-trnQ-UUG LSC 596 0.0050 1.00 54.0 yes View details
rpoC2 LSC 4185 0.0029 1.00 42.1 yes View details
rpoC1 LSC 2932 0.0027 1.00 45.0 yes View details
trnF-GAA-ndhJ LSC 779 0.0043 1.00 49.1 yes View details
rbcL-accD LSC 732 0.0037 0.99 49.3 yes View details
accD LSC 1521 0.0004 1.00 34.6 yes View details
rps3-rps19 LSC 603 0.0055 1.00 40.5 yes View details
ndhF SSC 2259 0.0021 1.00 43.6 yes View details
ndhF-rpl32 SSC 886 0.0090 1.00 58.5 yes View details
rpl32-trnL-UAG SSC 853 0.0032 0.99 47.2 yes View details
trnR-ACG-trnN-GUU IRb 619 0.0032 1.00 61.3 yes View details
trnN-GUU-trnR-ACG IRa 619 0.0032 1.00 61.3 yes View details
psbM-trnD-GUC LSC 1149 0.0029 1.00 58.6 yes View details
rpl2-trnH-GUG IRa 120 0.0056 1.00 56.1 no View details
psbC-trnS-UGA LSC 255 0.0052 1.00 55.8 yes View details
trnP-UGG-psaJ LSC 380 0.0018 1.00 55.6 yes View details
trnV-UAC LSC 35 0.0190 1.00 52.1 yes View details
ycf1 SSC 5709 0.0014 1.00 50.6 yes View details
rps18-rpl20 LSC 42 0.0159 1.00 50.1 yes View details
rps2-rpoC2 LSC 221 0.0060 1.00 49.6 yes View details
ycf1 IRb 1443 0.0000 1.00 26.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 416–418 1.000 79.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 430–432 1.000 79.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 429–431 1.000 79.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 431–433 1.000 79.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC GCGCTAACCTTGGTATGGAA 445–447 1.000 76.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CACAGCCGACCATATCCTTC GAGGTTCGAATCCTTCCGTC 266–689 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 246–669 1.000 82.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTAAGAATCCACAGCCGACC GAGGTTCGAATCCTTCCGTC 275–698 1.000 81.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGTAAGAATCCACAGCCGAC GAGGTTCGAATCCTTCCGTC 276–699 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACAGCCGACCATATCCTTCA GAGGTTCGAATCCTTCCGTC 265–688 1.000 79.8
rps2-rpoC2_p1 rps2-rpoC2 GGTGCCATTCTAGGATTCCA CCCAAACAATCATTGCGAGG 355–356 1.000 70.0
rps2-rpoC2_p2 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC CCCAAACAATCATTGCGAGG 307–308 1.000 69.0
rps2-rpoC2_p3 rps2-rpoC2 GGTGCCATTCTAGGATTCCA ACACCCAAACAATCATTGCG 358–359 1.000 68.7
rps2-rpoC2_p4 rps2-rpoC2 TGACCAAAATGAACTCCTGCT CCCAAACAATCATTGCGAGG 322–323 1.000 68.4
rps2-rpoC2_p5 rps2-rpoC2 ACTCCTGCTTCCATCATCTCT CCCAAACAATCATTGCGAGG 310–311 1.000 68.3
rpoC2_p1 rpoC2 CCTCGCAATGATTGTTTGGG AAACTGCTCGGGTTTTAGCA 277 1.000 78.4
rpoC2_p2 rpoC2 CGCAATGATTGTTTGGGTGT AAACTGCTCGGGTTTTAGCA 274 1.000 77.2
rpoC2_p3 rpoC2 CCTCGCAATGATTGTTTGGG CTCTCCGAGGTCGTATCGAT 250 1.000 77.1
rpoC2_p4 rpoC2 CCTCGCAATGATTGTTTGGG TCTCCGAGGTCGTATCGATT 249 1.000 76.7
rpoC2_p5 rpoC2 CCTCGCAATGATTGTTTGGG GGTTTTAGCAAAAGCCGCTC 267 1.000 76.2
rpoC1_p1 rpoC1 ACCCTAATTCATATCGGTGTCA CGGAATGAATCAGAATTTTTCTTCT 3000 0.333 13.3
rpoC1_p2 rpoC1 ACCCTAATTCATATCGGTGTCA CGGAATGAATCAGAATTTTTCTTC 3000 0.333 13.3
rpoC1_p3 rpoC1 ACCCTAATTCATATCGGTGTCA CGGAATGAATCAGAATTTTTCT 3000 0.333 13.3
rpoC1_p4 rpoC1 ACCCTAATTCATATCGGTGTCA CGGAATGAATCAGAATTTTTCTT 3000 0.333 13.3
rpoC1_p5 rpoC1 TCATATCGGTGTCATAGAATGA AGCTTAATCGGAATGAATCAGA 3000 0.333 13.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTGCAGTAGCCATAAGTGC TTCAATTGGTCAGAGCACCG 1251–1255 1.000 76.3
psbM-trnD-GUC_p2 psbM-trnD-GUC AGTGCAGTAGCCATAAGTGC GTTCAATTGGTCAGAGCACC 1252–1256 1.000 72.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AATGAACAGTGCAGTAGCCA TTCAATTGGTCAGAGCACCG 1258–1262 1.000 72.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGTGCAGTAGCCATAAGTGC TCAATTGGTCAGAGCACCG 1250–1254 1.000 70.3
psbM-trnD-GUC_p5 psbM-trnD-GUC GCAGTAGCCATAAGTGCGAG TTCAATTGGTCAGAGCACCG 1248–1252 1.000 70.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Casuarina cunninghamiana NC_058688.1 156129 View on NCBI ↗
Casuarina equisetifolia MZ032230.1 156128 View on NCBI ↗
Casuarina glauca NC_042681.1 155669 View on NCBI ↗