Markers + reference

Pratia

2 species · Campanulaceae · Asterales

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Species 2
Genome length 165–165 kb
Candidate markers 283
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 6 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ORF192 LSC 579 0.0725 1.00 75.0 yes View details
rpoB-ORF238 LSC 378 0.0989 0.99 75.0 yes View details
ORF238 LSC 717 0.2472 0.99 80.0 yes View details
ORF238-trnC (GCA) LSC 854 0.1451 0.61 72.6 yes View details
trnC (GCA)-petN LSC 267 0.0498 0.98 73.1 yes View details
ndhC-ORF224 LSC 307 0.0903 0.97 74.5 yes View details
ORF224 LSC 675 0.0711 1.00 75.2 yes View details
trnL (UAG)-rpl32 SSC 693 0.0893 0.99 79.6 yes View details
rpl32-ndhF SSC 1120 0.0510 1.00 75.0 yes View details
psbA-rbcL LSC 1042 0.0358 0.99 80.1 yes View details
trnT (UGU)-trnL (UAA) LSC 679 0.0433 0.99 77.3 yes View details
rpoA-rps11 LSC 80 0.0500 1.00 76.3 yes View details
trnS (GCU)-trnG (UCC) LSC 739 0.0430 0.98 74.3 yes View details
psaC-ndhD SSC 112 0.0804 1.00 73.2 yes View details
trnI (CAU)-ycf2 IRb 122 0.0331 0.99 72.3 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-rbcL_p1 psbA-rbcL TACAGAAGCGACCCCATAGG ATTTGAGTTTGCCGCAATGG 1128–1129 1.000 77.9
psbA-rbcL_p2 psbA-rbcL TACAGAAGCGACCCCATAGG TGAGTTTGCCGCAATGGATA 1125–1126 1.000 77.6
psbA-rbcL_p3 psbA-rbcL TACAGAAGCGACCCCATAGG GCTGCTTGTGAGGTATGGAA 1157–1158 1.000 77.5
psbA-rbcL_p4 psbA-rbcL TACAGAAGCGACCCCATAGG AGTTTGCCGCAATGGATACT 1123–1124 1.000 77.5
psbA-rbcL_p5 psbA-rbcL ATCCAGTTACAGAAGCGACC ATTTGAGTTTGCCGCAATGG 1135–1136 1.000 77.2
ORF192_p1 ORF192 AGCGAACATCAATTGCAACG GTCCCGGTAATCGAAGGTTC 1064–1134 1.000 89.3
ORF192_p2 ORF192 GCGAACATCAATTGCAACGA GTCCCGGTAATCGAAGGTTC 1063–1133 1.000 89.3
ORF192_p3 ORF192 AGCGAACATCAATTGCAACG AAGGATTTGGGCAGGTCTTG 1256–1266 1.000 88.7
ORF192_p4 ORF192 AGCGAACATCAATTGCAACG GCAGGTCTTGACACCAAAGA 1246 0.500 59.5
ORF192_p5 ORF192 GCGAACATCAATTGCAACGA GCAGGTCTTGACACCAAAGA 1245 0.500 59.4
trnS (GCU)-trnG (UCC)_p1 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA AGGAGGTTCATAGAACGAATCAC 860–876 1.000 59.2
trnS (GCU)-trnG (UCC)_p2 trnS (GCU)-trnG (UCC) ACGAAAACGGAAAGAGAGGG AGGAGGTTCATAGAACGAATCAC 866–882 1.000 59.1
trnS (GCU)-trnG (UCC)_p3 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA GGAGGTTCATAGAACGAATCACA 859–875 1.000 57.4
trnS (GCU)-trnG (UCC)_p4 trnS (GCU)-trnG (UCC) ACGAAAACGGAAAGAGAGGG GGAGGTTCATAGAACGAATCACA 865–881 1.000 57.2
trnS (GCU)-trnG (UCC)_p5 trnS (GCU)-trnG (UCC) AGTCATCGACGAAAACGGAA AGGAGGTTCATAGAACGAATCAC 874–890 1.000 56.9
rpoB-ORF238_p1 rpoB-ORF238 AGTCCCGCGGATACATAGAA CGCGGAAATGTTTTCAGACC 855 0.500 59.6
rpoB-ORF238_p2 rpoB-ORF238 ATTGGATCCCCACCTACACA CGCGGAAATGTTTTCAGACC 1311 0.500 59.5
rpoB-ORF238_p3 rpoB-ORF238 AGTCCCGCGGATACATAGAA ACACCAGAACCTGACAAACC 1169 0.500 59.5
rpoB-ORF238_p4 rpoB-ORF238 AGTCCCGCGGATACATAGAA CTACAGGAGGGACACCAGAA 1180 0.500 59.4
rpoB-ORF238_p5 rpoB-ORF238 ATTGGATCCCCACCTACACA ACACCAGAACCTGACAAACC 1625 0.500 59.4
ORF238_p1 ORF238 AGTCCCGCGGATACATAGAA GAAGCCTGTTGAGGAACCAA 2202–2447 1.000 91.8
ORF238_p2 ORF238 AGTCCCGCGGATACATAGAA GGTGCAGAGTCAAAAAGGGA 2230–2475 1.000 91.8
ORF238_p3 ORF238 ATTGGATCCCCACCTACACA GAAGCCTGTTGAGGAACCAA 2658–2903 1.000 91.7
ORF238_p4 ORF238 ATTGGATCCCCACCTACACA GGTGCAGAGTCAAAAAGGGA 2686–2931 1.000 91.7
ORF238_p5 ORF238 AGAACCCCACCACATACTCA GAAGCCTGTTGAGGAACCAA 2022 0.500 59.5
ORF238-trnC (GCA)_p1 ORF238-trnC (GCA) GGTCTGAAAACATTTCCGCG GAAGCCTGTTGAGGAACCAA 1612 0.500 59.6
ORF238-trnC (GCA)_p2 ORF238-trnC (GCA) GGTCTGAAAACATTTCCGCG GGTGCAGAGTCAAAAAGGGA 1640 0.500 59.6
ORF238-trnC (GCA)_p3 ORF238-trnC (GCA) GGTTTGTCAGGTTCTGGTGT GAAGCCTGTTGAGGAACCAA 1298 0.500 59.4
ORF238-trnC (GCA)_p4 ORF238-trnC (GCA) GGTTTGTCAGGTTCTGGTGT GGTGCAGAGTCAAAAAGGGA 1326 0.500 59.4
ORF238-trnC (GCA)_p5 ORF238-trnC (GCA) TTCTGGTGTCCCTCCTGTAG GAAGCCTGTTGAGGAACCAA 1287 0.500 59.4

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
Pratia angulata NC_035367.1 164856 View on NCBI ↗
Pratia nummularia NC_035381.1 165428 View on NCBI ↗