Markers + reference

Schoepfia

2 species · Schoepfiaceae · Santalales

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Species 2
Genome length 122–122 kb
Candidate markers 251
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 10 remaining regions by MarkerSeek score (out of 251 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA Genome 1062 0.0047 1.00 47.9 yes View details
trnK-UUU-rps16 Genome 378 0.0219 0.97 55.1 yes View details
trnS-GCU-trnG-UCC Genome 444 0.0180 1.00 56.4 yes View details
atpH-atpI Genome 720 0.0183 0.99 60.9 yes View details
ndhK-ndhC Genome 339 0.0268 0.99 56.5 yes View details
rpl32-trnL-UAG Genome 493 0.0205 0.99 58.5 yes View details
ycf1 Genome 5496 0.0113 1.00 46.0 yes View details
trnV-UAC-trnM-CAU Genome 143 0.0420 1.00 74.8 yes View details
trnF-GAA-ndhJ Genome 695 0.0118 0.98 67.6 yes View details
atpF-atpH Genome 397 0.0207 0.97 66.8 yes View details
psbE-petL Genome 782 0.0065 0.98 64.5 yes View details
ycf1-trnN-GUU Genome 439 0.0117 0.97 64.5 yes View details
psbI-trnS-GCU Genome 101 0.0297 1.00 64.1 yes View details
psbM-trnD-GUC Genome 1051 0.0096 0.99 63.4 yes View details
rpl14-rpl16 Genome 102 0.0294 1.00 63.2 yes View details
atpB-rbcL Genome 732 0.0055 0.99 62.8 yes View details
trnR-ACG-trnN-GUU Genome 434 0.0048 0.95 62.5 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
psbA_p1 psbA AGGACTCGTATACACTAAGACGA CGACTAGTTTCGGGTTCGAG 1331 1.000 55.6
psbA_p2 psbA AGGACTCGTATACACTAAGACGA GTGCTAGAACTTTGGCTCGT 1744–1759 1.000 55.6
psbA_p3 psbA AGGACTCGTATACACTAAGACGA TGAGAATTCTCGTGCTTGGG 1144 1.000 55.5
psbA_p4 psbA AGGACTCGTATACACTAAGACGA AATTCTCGTGCTTGGGAGTC 1140 1.000 55.5
psbA_p5 psbA AGGACTCGTATACACTAAGACGA GAATTCTCGTGCTTGGGAGT 1141 1.000 55.5
trnK-UUU_p1 trnK-UUU ACGGTTTTCGGTGTTGGTTA AACAGAGTAAGAGGCGGTCT 2817–2832 1.000 80.2
trnK-UUU_p2 trnK-UUU TCAAAACACCAAACCACCCA AACAGAGTAAGAGGCGGTCT 2845–2860 1.000 80.0
trnK-UUU_p3 trnK-UUU CCCAAGCACGAGAATTCTCA AACAGAGTAAGAGGCGGTCT 2702–2717 1.000 79.7
trnK-UUU_p4 trnK-UUU ACTCCCAAGCACGAGAATTC AACAGAGTAAGAGGCGGTCT 2705–2720 1.000 79.7
trnK-UUU_p5 trnK-UUU GACTCCCAAGCACGAGAATT AACAGAGTAAGAGGCGGTCT 2706–2721 1.000 79.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TCCTGAAACAAGGAAAGCCC 1016–1019 1.000 82.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCTGAAACAAGGAAAGCCC 1015–1018 1.000 82.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACCCAACCGCTCTTTTGATT AAAAAGGCGCTCAACCTACA 907–916 1.000 82.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AACCCAACCGCTCTTTTGAT TCCTGAAACAAGGAAAGCCC 1360–1363 1.000 81.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACCCAACCGCTCTTTTGATT TCCTGAAACAAGGAAAGCCC 1359–1362 1.000 81.7
psbI-trnS-GCU_p1 psbI-trnS-GCU TCCTGTCTAACGATCCAGGG TGGACTAAAGCGGTGGATTG 218–226 1.000 78.4
psbI-trnS-GCU_p2 psbI-trnS-GCU TCCTGTCTAACGATCCAGGG GTGGACTAAAGCGGTGGATT 219–227 1.000 78.4
psbI-trnS-GCU_p3 psbI-trnS-GCU TCTAACGATCCAGGGCGTAA TGGACTAAAGCGGTGGATTG 213–221 1.000 78.4
psbI-trnS-GCU_p4 psbI-trnS-GCU TCTAACGATCCAGGGCGTAA GTGGACTAAAGCGGTGGATT 214–222 1.000 78.4
psbI-trnS-GCU_p5 psbI-trnS-GCU TCCTGTCTAACGATCCAGGG ATTGGGAGAGATGGCTGAGT 237–245 1.000 78.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCACCGCTTTAGTCCA GAACGAATCGCGCTTTTACC 518–525 1.000 78.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCACCGCTTTAGTCCAC GAACGAATCGCGCTTTTACC 517–524 1.000 78.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GAACGAATCGCGCTTTTACC 572–579 1.000 78.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCACCGCTTTAGTC GAACGAATCGCGCTTTTACC 520–527 1.000 77.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CACCGCTTTAGTCCACTCAG GAACGAATCGCGCTTTTACC 513–520 1.000 77.3
atpF-atpH_p1 atpF-atpH GGATGGCCAATGACCTAAGG GGAGGGGAAGATACGAGGTA 547–557 1.000 77.1
atpF-atpH_p2 atpF-atpH CGGATGGCCAATGACCTAAG GGAGGGGAAGATACGAGGTA 548–558 1.000 74.0
atpF-atpH_p3 atpF-atpH TATTAAACCCGAAACCCCCG GGAGGGGAAGATACGAGGTA 569–579 1.000 73.8
atpF-atpH_p4 atpF-atpH GGATGGCCAATGACCTAAGG GGAGGGGAAGATACGAGGT 547–557 1.000 70.2
atpF-atpH_p5 atpF-atpH GGATGGCCAATGACCTAAGG CGAAGCGGAGGGGAAGATA 553–563 1.000 69.9

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
Schoepfia arenaria OR712480.1 122210 View on NCBI ↗
Schoepfia schreberi OR712481.1 122120 View on NCBI ↗