Markers + reference

Bistorta

9 species · Polygonaceae · Caryophyllales

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Species 9
Genome length 159–161 kb
Candidate markers 266
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 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0079 1.00 43.7 yes View details
trnK-UUU-rps16 LSC 767 0.0266 0.93 68.0 yes View details
rps16-trnQ-UUG LSC 530 0.0509 0.92 79.8 yes View details
trnS-GCU-trnG-UCC LSC 806 0.0515 0.86 77.3 yes View details
psbM-trnD-GUC LSC 1121 0.0220 0.88 63.5 yes View details
trnT-UGU-trnL-UAA LSC 865 0.0395 0.94 69.7 yes View details
psaJ-rpl33 LSC 484 0.0389 0.98 75.7 yes View details
rpl33-rps18 LSC 507 0.0488 0.77 67.9 yes View details
ndhF-rpl32 SSC 875 0.0341 0.93 66.4 yes View details
rpl32-trnL-UAG SSC 810 0.0333 0.95 73.7 yes View details
trnT-GGU-psbD LSC 1292 0.0228 0.98 71.9 yes View details
trnC-GCA-petN LSC 801 0.0260 1.00 68.7 yes View details
trnF-GAA-ndhJ LSC 719 0.0253 1.00 68.7 yes View details
psbA-trnK-UUU LSC 227 0.0481 1.00 68.1 yes View details
psbI-trnS-GCU LSC 100 0.0473 0.88 65.8 yes View details
atpH-atpI LSC 710 0.0232 0.98 63.8 yes View details
rpl16-rps3 LSC 129 0.0334 1.00 63.1 yes View details
psbE-petL LSC 652 0.0162 0.97 63.0 yes View details
ycf4-cemA LSC 909 0.0235 0.98 62.9 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
psbA_p1 psbA AGGAGCAATACCAACCCTCT CGCGGAGTTTTAGGTGTGTA 1540 0.222 48.3
psbA_p2 psbA GAGCAATACCAACCCTCTCG CGCGGAGTTTTAGGTGTGTA 1538 0.222 48.0
psbA_p3 psbA AGGAGCAATACCAACCCTCT CATCTAGGAAAGTCGCGGAG 1553 0.222 47.8
psbA_p4 psbA GAGCAATACCAACCCTCTCG CATCTAGGAAAGTCGCGGAG 1551 0.222 47.6
psbA_p5 psbA AGGAGCAATACCAACCCTCT GGACCTCGAGTTCTACTGGT 1320 0.222 47.5
psbA-trnK-UUU_p1 psbA-trnK-UUU CGTCTCTCTAAAATTGCAGTCA ACTCCATCCGACTAGTTCCG 292–315 1.000 53.7
psbA-trnK-UUU_p2 psbA-trnK-UUU CGTCTCTCTAAAATTGCAGTCA ATCCGACTAGTTCCGGGTTC 287–310 1.000 51.6
psbA-trnK-UUU_p3 psbA-trnK-UUU CGTCTCTCTAAAATTGCAGTCAT ACTCCATCCGACTAGTTCCG 292–315 1.000 49.5
psbA-trnK-UUU_p4 psbA-trnK-UUU CGTCTCTCTAAAATTGCAGTCA CATCCGACTAGTTCCGGGTT 288–311 1.000 49.3
psbA-trnK-UUU_p5 psbA-trnK-UUU CGTCTCTCTAAAATTGCAGTCA TCCATCCGACTAGTTCCGG 290–313 1.000 49.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1601–1651 1.000 86.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAAAGGGTATGTTGCTGCCA 1554–1604 1.000 86.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAAAGGGTATGTTGCTGCCA 1555–1605 1.000 86.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAAAGGGTATGTTGCTGCCA 1557–1607 1.000 86.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAGGGTATGTTGCTGCCA 1597–1647 1.000 86.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGAAATCTAAGTGGGGCG 626–660 1.000 85.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 565–599 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA TTCGAAATCTAAGTGGGGCG 629–663 1.000 83.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 568–602 1.000 82.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAAATCTAAGTGGGGCGTGG 623–657 1.000 80.7
psbI-trnS-GCU_p1 psbI-trnS-GCU AAAGGGAGGCTCCTAACACT GTCATTCGTACCGAGGGTTC 389–391 0.222 48.5
psbI-trnS-GCU_p2 psbI-trnS-GCU AAGGGAGGCTCCTAACACTT GTCATTCGTACCGAGGGTTC 388–390 0.222 48.5
psbI-trnS-GCU_p3 psbI-trnS-GCU AAAGGGAGGCTCCTAACACT TAGGGAGAGATGGCTGAGTG 443–445 0.222 48.4
psbI-trnS-GCU_p4 psbI-trnS-GCU AAGGGAGGCTCCTAACACTT TAGGGAGAGATGGCTGAGTG 442–444 0.222 48.4
psbI-trnS-GCU_p5 psbI-trnS-GCU AAGAGAAAAGGGAGGCTCCT TAGGGAGAGATGGCTGAGTG 449–451 0.222 48.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GGAATCAAATCGAAGGATCCCT 771–894 1.000 66.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTCC GGAATCAAATCGAAGGATCCCT 772–895 1.000 63.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GGAATCAAATCGAAGGATCCC 771–894 1.000 62.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTCC GGAATCAAATCGAAGGATCCC 772–895 1.000 59.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TCGAAGGATCCCTTAACTCT 762–885 1.000 58.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Bistorta affinis PZ301186.1 161030 View on NCBI ↗
Bistorta amplexicaulis NC_082238.1 159789 View on NCBI ↗
Bistorta coriacea MW770449.1 158839 View on NCBI ↗
Bistorta emodi NC_066665.1 161117 View on NCBI ↗
Bistorta ochotensis NC_082240.1 159626 View on NCBI ↗
Bistorta officinalis NC_065784.1 159476 View on NCBI ↗
Bistorta paleacea NC_082267.1 158866 View on NCBI ↗
Bistorta sinomontana NC_082241.1 159075 View on NCBI ↗
Bistorta vivipara PP328779.1 158819 View on NCBI ↗