Markers + reference

Parathesis

2 species · Primulaceae · Ericales

Back to catalogue

Species 2
Genome length 156–157 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 610 0.0033 1.00 60.6 yes View details
rpoB-trnC-GCA LSC 1134 0.0018 1.00 59.8 yes View details
trnP-UGG-psaJ LSC 430 0.0047 0.99 58.6 yes View details
rps18-rpl20 LSC 308 0.0032 1.00 49.2 yes View details
rpl16 LSC 1392 0.0014 1.00 59.6 yes View details
rpl32-trnL-UAG SSC 810 0.0074 1.00 63.0 yes View details
rps15-ycf1 SSC 407 0.0025 1.00 48.7 yes View details
rps2 LSC 711 0.0014 1.00 59.6 yes View details
trnT-UGU-trnL-UAA LSC 811 0.0012 1.00 59.5 yes View details
trnF-GAA-ndhJ LSC 733 0.0014 1.00 59.5 yes View details
atpB-rbcL LSC 759 0.0013 1.00 59.5 yes View details
matK LSC 1527 0.0013 1.00 59.4 yes View details
ndhF-rpl32 SSC 878 0.0011 1.00 59.4 yes View details
trnS-GCU-trnS-GCA LSC 753 0.0000 0.99 59.3 yes View details
psbD LSC 1062 0.0009 1.00 59.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CCCGTGTCAACCAACATCTA TGGTTCGTTTTTACGTTCCG 2816–2817 1.000 68.2
trnK-UUU_p2 trnK-UUU ATATGCCCGTGTCAACCAAC TGGTTCGTTTTTACGTTCCG 2821–2822 1.000 67.6
trnK-UUU_p3 trnK-UUU CCCGTGTCAACCAACATCTA GGTTCGTTTTTACGTTCCGA 2815–2816 1.000 66.0
trnK-UUU_p4 trnK-UUU CCCGTGTCAACCAACATCTA TTGGTTCGTTTTTACGTTCCG 2817–2818 1.000 65.8
trnK-UUU_p5 trnK-UUU ATATGCCCGTGTCAACCAAC GGTTCGTTTTTACGTTCCGA 2820–2821 1.000 65.4
matK_p1 matK TTCTCATTTACACGGTCTGA GGCCTCTTTTCTTACTCGCA 1659 1.000 47.7
matK_p2 matK AGCCTTAACTAGATGCTACATGA GGCCTCTTTTCTTACTCGCA 1747 1.000 46.3
matK_p3 matK TCTCATTTACACGGTCTGAT GGCCTCTTTTCTTACTCGCA 1658 1.000 45.8
matK_p4 matK TTCTCATTTACACGGTCTGA AGGCCTCTTTTCTTACTCGC 1660 1.000 45.4
matK_p5 matK TCTCATTTACACGGTCTGATAACA GGCCTCTTTTCTTACTCGCA 1658 1.000 45.1
trnS-GCU-trnS-GCA_p1 trnS-GCU-trnS-GCA GATTCGAACCCTCGGTACAA AGACCGAAAGACCCCTTAAC 899–903 1.000 65.9
trnS-GCU-trnS-GCA_p2 trnS-GCU-trnS-GCA GATTCGAACCCTCGGTACAA GACCGAAAGACCCCTTAACT 898–902 1.000 65.9
trnS-GCU-trnS-GCA_p3 trnS-GCU-trnS-GCA AACAAAGTCATCGAGGGAGG AGACCGAAAGACCCCTTAAC 931–935 1.000 65.0
trnS-GCU-trnS-GCA_p4 trnS-GCU-trnS-GCA AACAAAGTCATCGAGGGAGG GACCGAAAGACCCCTTAACT 930–934 1.000 65.0
trnS-GCU-trnS-GCA_p5 trnS-GCU-trnS-GCA GATTCGAACCCTCGGTACAA AGACCGAAAGACCCCTTAACT 899–903 1.000 64.0
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTGCAACTTTAGCCGCTG 695 1.000 78.3
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCTG 753 1.000 78.3
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTGCAACTTTAGCCGCTG 705 1.000 77.8
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TTTTGCAACTTTAGCCGCTG 757 1.000 77.6
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCT TTTTGCAACTTTAGCCGCTG 735 1.000 75.7
rps2_p1 rps2 GAGGTTCCCAAGTTGTAACCA TTTTTGAAAAGGGGAGGGGG 811 1.000 69.5
rps2_p2 rps2 TGAGGTTCCCAAGTTGTAACC TTTTTGAAAAGGGGAGGGGG 812 1.000 69.5
rps2_p3 rps2 AGGTTCCCAAGTTGTAACCA TTTTTGAAAAGGGGAGGGGG 810 1.000 67.7
rps2_p4 rps2 GAGGTTCCCAAGTTGTAACCA ATTTTTCAGGACACCTCGCC 836 1.000 66.6
rps2_p5 rps2 TGAGGTTCCCAAGTTGTAACC ATTTTTCAGGACACCTCGCC 837 1.000 66.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AGCAGAACCGAATAGGGGAT 1340 1.000 78.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA TTATTGATCAGGCGACACCC 1310 1.000 77.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AAAAGGATTTGCAGTCCCCC 1274 1.000 77.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGAAAGCTCTTCCGTCAAGC AGCAGAACCGAATAGGGGAT 1352 1.000 77.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA GCGACACCCAGATTTGAACT 1299 1.000 76.1

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
Parathesis chiapensis NC_045115.1 156666 View on NCBI ↗
Parathesis donnell-smithii NC_045114.1 156344 View on NCBI ↗