Markers + reference

Jubula

2 species · Jubulaceae · Porellales

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Species 2
Genome length 118–118 kb
Candidate markers 270
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps7 Genome 468 0.0064 1.00 48.2 yes View details
rpoC1 Genome 2653 0.0094 1.00 55.7 yes View details
psaM-trnS-GCU Genome 288 0.0347 1.00 72.5 yes View details
psbl-psbK Genome 292 0.0412 1.00 76.5 yes View details
chlB-trnK Genome 451 0.0222 1.00 55.9 yes View details
trnH-GUG-ycf2 Genome 602 0.0200 1.00 66.5 yes View details
ycf2 Genome 6132 0.0096 1.00 43.6 yes View details
ycf3 Genome 1868 0.0086 0.99 50.7 yes View details
trnR-ACG-trnN-GUU Genome 601 0.0207 0.97 67.4 yes View details
rps15-ycf1 Genome 1608 0.0112 1.00 58.7 yes View details
trnN-GUU-trnR-ACG Genome 601 0.0207 0.97 67.4 yes View details
atpA-trnR-UCU Genome 64 0.0781 1.00 75.2 yes View details
rrn5-trnR-ACG Genome 140 0.0299 0.96 69.8 yes View details
trnR-ACG-5S Genome 140 0.0299 0.96 69.8 yes View details
ndhE-ndhG Genome 102 0.0297 0.99 69.7 yes View details
trnT-UGU-trnL-UAA Genome 219 0.0229 1.00 66.0 yes View details
ccsA-ndhD Genome 148 0.0338 1.00 66.0 yes View details
trnG-UCC Genome 70 0.0429 1.00 65.4 yes View details
trnE-UGA-trnT-GGU Genome 370 0.0227 0.95 64.2 yes View details
ndhH-rps15 Genome 44 0.0455 1.00 64.2 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
rps7_p1 rps7 AATCAAGGGCGTTCTAGTGC AGGCATTCCTGTGCATTCAA 1504 1.000 78.1
rps7_p2 rps7 GCAATCAAGGGCGTTCTAGT AGGCATTCCTGTGCATTCAA 1506 1.000 78.1
rps7_p3 rps7 AATCAAGGGCGTTCTAGTGC ACCAGGAAAAACCATACGCA 1730 1.000 76.3
rps7_p4 rps7 GCAATCAAGGGCGTTCTAGT ACCAGGAAAAACCATACGCA 1732 1.000 76.3
rps7_p5 rps7 AAACCCAATTCCGCCTTACG AGGCATTCCTGTGCATTCAA 1705 1.000 73.4
rpoC1_p1 rpoC1 ACTTGTTCGAGAATTACGATCT ACAAACATACATCAACAATGAGT 2864 1.000 40.8
rpoC1_p2 rpoC1 TGTTCGAGAATTACGATCTTTAGC ACAAACATACATCAACAATGAGT 2861 1.000 40.8
rpoC1_p3 rpoC1 ACTTGTTCGAGAATTACGATCT ACAAACATACATCAACAATGAGTT 2864 1.000 40.8
rpoC1_p4 rpoC1 ACTTGTTCGAGAATTACGATCTT ACAAACATACATCAACAATGAGT 2864 1.000 40.8
rpoC1_p5 rpoC1 GTTCGAGAATTACGATCTTTAGCT ACAAACATACATCAACAATGAGT 2860 1.000 40.8
atpA-trnR-UCU_p1 atpA-trnR-UCU TCGTTCCACTAAAGTTTTTACAGA GTTCGAATCCTATTGGGCGT 182 1.000 42.2
atpA-trnR-UCU_p2 atpA-trnR-UCU CGTTCCACTAAAGTTTTTACAGA GTTCGAATCCTATTGGGCGT 181 1.000 42.2
atpA-trnR-UCU_p3 atpA-trnR-UCU TCGTTCCACTAAAGTTTTTACAG GTTCGAATCCTATTGGGCGT 182 1.000 42.2
atpA-trnR-UCU_p4 atpA-trnR-UCU TCGTTCCACTAAAGTTTTTACAGAA GTTCGAATCCTATTGGGCGT 182 1.000 42.2
atpA-trnR-UCU_p5 atpA-trnR-UCU TTCGTTCCACTAAAGTTTTTACAGA GTTCGAATCCTATTGGGCGT 183 1.000 42.2
psaM-trnS-GCU_p1 psaM-trnS-GCU ACAATGGTCCCAATTTCGGA CGGAGAGAGAGGGATTCGAA 478 1.000 74.4
psaM-trnS-GCU_p2 psaM-trnS-GCU ACAATGGTCCCAATTTCGGA AACGGAGAGAGAGGGATTCG 480 1.000 72.1
psaM-trnS-GCU_p3 psaM-trnS-GCU ACAATGGTCCCAATTTCGGA GATTCGAACCCTCGGTACAA 466 1.000 71.7
psaM-trnS-GCU_p4 psaM-trnS-GCU ACAATGGTCCCAATTTCGGAT CGGAGAGAGAGGGATTCGAA 478 1.000 70.3
psaM-trnS-GCU_p5 psaM-trnS-GCU AACAATGGTCCCAATTTCGGA CGGAGAGAGAGGGATTCGAA 479 1.000 70.2
psbl-psbK_p1 psbl-psbK TCTTTACGGCCAGGATTTCG GCTTTTGTTTGGCAAGCTTC 435–448 1.000 74.0
psbl-psbK_p2 psbl-psbK CTTTACGGCCAGGATTTCGT GCTTTTGTTTGGCAAGCTTC 434–447 1.000 72.0
psbl-psbK_p3 psbl-psbK TTTACGGCCAGGATTTCGTC GCTTTTGTTTGGCAAGCTTC 433–446 1.000 72.0
psbl-psbK_p4 psbl-psbK TCTTTACGGCCAGGATTTCG TTTGTTTGGCAAGCTTCAGT 432–445 1.000 71.5
psbl-psbK_p5 psbl-psbK CTTTACGGCCAGGATTTCGT TTTGTTTGGCAAGCTTCAGT 431–444 1.000 69.5
chlB-trnK_p1 chlB-trnK AAGCTGCTTGGTTTTCGAGA CAAGTCGCACTTAAAAGCCG 1172–1173 1.000 80.1
chlB-trnK_p2 chlB-trnK CAAGCTGCTTGGTTTTCGAG CAAGTCGCACTTAAAAGCCG 1173–1174 1.000 80.0
chlB-trnK_p3 chlB-trnK CTCAAGCTGCTTGGTTTTCG CAAGTCGCACTTAAAAGCCG 1175–1176 1.000 80.0
chlB-trnK_p4 chlB-trnK TGTAAGTTGTGCAGGCACTT CAAGTCGCACTTAAAAGCCG 1048–1049 1.000 80.0
chlB-trnK_p5 chlB-trnK AAGCTGTAGTTTTCGGCGAT CAAGTCGCACTTAAAAGCCG 1121–1122 1.000 79.6

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
Jubula hutchinsiae NC_043782.1 117817 View on NCBI ↗
Jubula hutchinsiae subsp. javanica MT762133.1 117934 View on NCBI ↗