Markers + reference

Araucaria

2 species · Araucariaceae · Araucariales

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Species 2
Genome length 146–146 kb
Candidate markers 252
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn23-trnA-UGC Genome 930 0.0178 0.97 61.6 yes View details
trnI-GAU-rrn16 Genome 849 0.0212 1.00 70.5 yes View details
rrn16-trnV-GAC Genome 1060 0.0280 0.98 68.7 yes View details
rps7-ndhB Genome 940 0.0196 0.98 63.0 yes View details
ndhB-trnL-CAA Genome 598 0.0225 0.97 62.9 yes View details
ycf2-trnI-CAU Genome 829 0.0218 0.83 60.3 yes View details
psbK-psbI Genome 796 0.0201 1.00 64.1 yes View details
rpoC2 Genome 3606 0.0050 1.00 55.1 yes View details
psbM-trnD-GUC Genome 2206 0.0200 1.00 69.1 yes View details
trnL-UAA-trnF-GAA Genome 459 0.0211 0.93 59.0 yes View details
psbT-psbN Genome 71 0.0563 1.00 82.0 yes View details
psbI-trnS-GCU Genome 91 0.0440 1.00 71.4 yes View details
rpoA-rps11 Genome 63 0.0317 1.00 70.8 yes View details
trnW-CCA-petG Genome 118 0.0424 1.00 70.4 yes View details
psaM-trnG-UCC Genome 569 0.0160 0.99 68.5 yes View details
trnM-CAU-atpB Genome 269 0.0336 1.00 67.7 yes View details
clpP-rrn5 Genome 410 0.0220 1.00 67.4 yes View details
rrn5-rrn4.5 Genome 437 0.0206 1.00 67.2 yes View details
trnI-CAU-trnD Genome 711 0.0113 1.00 65.2 yes View details
trnN-GUU-trnR-ACG Genome 711 0.0183 0.92 64.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rrn5-rrn4.5_p1 rrn5-rrn4.5 GCATCGAGCTATTTTTCCGC GTCAAGTGGAAGTGCAGTGA 613–614 1.000 80.6
rrn5-rrn4.5_p2 rrn5-rrn4.5 GCATCGAGCTATTTTTCCGC CAGCTGAGGCATCCTAACAG 587–588 1.000 80.6
rrn5-rrn4.5_p3 rrn5-rrn4.5 GCATCGAGCTATTTTTCCGC GCTGAGGCATCCTAACAGAC 585–586 1.000 80.6
rrn5-rrn4.5_p4 rrn5-rrn4.5 AGTATCGTCACCGCAGTAGA GTCAAGTGGAAGTGCAGTGA 579–580 1.000 80.6
rrn5-rrn4.5_p5 rrn5-rrn4.5 TATCGTCACCGCAGTAGAGT GTCAAGTGGAAGTGCAGTGA 577–578 1.000 80.6
rrn23-trnA-UGC_p1 rrn23-trnA-UGC ATTCGGGAATCTCCGGATCT GACAGTGGTTTACCCTGTGG 1062–1084 1.000 82.4
rrn23-trnA-UGC_p2 rrn23-trnA-UGC ATTCGGGAATCTCCGGATCT GGTTCGAGTCCGCTTATCTC 1031–1053 1.000 82.4
rrn23-trnA-UGC_p3 rrn23-trnA-UGC ATTCGGGAATCTCCGGATCT GTTCGAGTCCGCTTATCTCC 1030–1052 1.000 82.4
rrn23-trnA-UGC_p4 rrn23-trnA-UGC GTCTCTGGGTGCCTAGGTAT GACAGTGGTTTACCCTGTGG 990–1012 1.000 82.1
rrn23-trnA-UGC_p5 rrn23-trnA-UGC GTCTCTGGGTGCCTAGGTAT GTTCGAGTCCGCTTATCTCC 958–980 1.000 82.1
trnI-GAU-rrn16_p1 trnI-GAU-rrn16 CGCTGATGAGCACATTGAAC CAAGGTAGCCGTACTGGAAG 992–994 1.000 77.8
trnI-GAU-rrn16_p2 trnI-GAU-rrn16 CGCTGATGAGCACATTGAAC AGTGACTGGAGTGAAGTCGT 1014–1016 1.000 77.7
trnI-GAU-rrn16_p3 trnI-GAU-rrn16 GGCACAACGACGCAATTATC CAAGGTAGCCGTACTGGAAG 941–943 1.000 77.7
trnI-GAU-rrn16_p4 trnI-GAU-rrn16 GGCACAACGACGCAATTATC AGTGACTGGAGTGAAGTCGT 963–965 1.000 77.6
trnI-GAU-rrn16_p5 trnI-GAU-rrn16 CGCTGATGAGCACATTGAAC AAGTCGTAACAAGGTAGCCG 1001–1003 1.000 77.3
rrn16-trnV-GAC_p1 rrn16-trnV-GAC TCCGACTTGCATGTGTTAGG TTGACGTGGTGATGGTCATC 1160–1169 1.000 82.1
rrn16-trnV-GAC_p2 rrn16-trnV-GAC TCCGACTTGCATGTGTTAGG CTTGACGTGGTGATGGTCAT 1161–1170 1.000 82.0
rrn16-trnV-GAC_p3 rrn16-trnV-GAC TCCGACTTGCATGTGTTAGG GATGGTCATCGGTTCGAGTC 1150–1159 1.000 81.6
rrn16-trnV-GAC_p4 rrn16-trnV-GAC GCAGGTTCTTACGCGTTACT TTGACGTGGTGATGGTCATC 1212–1221 1.000 80.3
rrn16-trnV-GAC_p5 rrn16-trnV-GAC GCAGGTTCTTACGCGTTACT CTTGACGTGGTGATGGTCAT 1213–1222 1.000 80.3
rps7-ndhB_p1 rps7-ndhB GCAGAGGCCAATAGAGCTTT TCCATTGAAGAGAAGCAAATGA 988–1009 1.000 50.7
rps7-ndhB_p2 rps7-ndhB TTAATGGACGCTGCCAGAAA TCCATTGAAGAGAAGCAAATGA 1051–1072 1.000 49.4
rps7-ndhB_p3 rps7-ndhB GCAAGAAGGAGGAAACCCAT TCCATTGAAGAGAAGCAAATGA 1014–1035 1.000 49.3
rps7-ndhB_p4 rps7-ndhB GCTTTTGCGCATTACCGTTA TCCATTGAAGAGAAGCAAATGA 973–994 1.000 49.2
rps7-ndhB_p5 rps7-ndhB TAATGGACGCTGCCAGAAAG TCCATTGAAGAGAAGCAAATGA 1050–1071 1.000 48.9
ndhB-trnL-CAA_p1 ndhB-trnL-CAA TGCAATTGCTCAAGAGACCT GTCTCGCGTGTCTACCATTT 639–658 1.000 79.4
ndhB-trnL-CAA_p2 ndhB-trnL-CAA TGCAATTGCTCAAGAGACCT CTCGCGTGTCTACCATTTCA 637–656 1.000 79.4
ndhB-trnL-CAA_p3 ndhB-trnL-CAA TGCAATTGCTCAAGAGACCT GCGTGTCTACCATTTCACCA 634–653 1.000 77.9
ndhB-trnL-CAA_p4 ndhB-trnL-CAA TGCAATTGCTCAAGAGACCT TCTCGCGTGTCTACCATTTC 638–657 1.000 77.3
ndhB-trnL-CAA_p5 ndhB-trnL-CAA TGCAATTGCTCAAGAGACCT TCGCGTGTCTACCATTTCAC 636–655 1.000 77.1

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
Araucaria araucana NC_045394.1 146005 View on NCBI ↗
Araucaria bidwillii NC_045395.1 146042 View on NCBI ↗