Markers + reference

Fagopyrum

6 species · Polygonaceae · Caryophyllales

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Species 6
Genome length 159–160 kb
Candidate markers 266
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 811 0.0998 0.98 83.8 yes View details
atpH-atpI LSC 659 0.0811 0.95 77.8 yes View details
rpoB-trnC-GCA LSC 1279 0.0792 0.93 84.1 yes View details
trnE-UUC-trnT-GGU LSC 544 0.0934 0.98 83.1 yes View details
trnT-GGU-psbD LSC 1259 0.0669 0.98 82.6 yes View details
ycf3-trnS-GGA LSC 836 0.0714 0.94 80.4 yes View details
rps4-trnT-UGU LSC 572 0.0903 0.87 84.9 yes View details
ndhC-trnV-UAC LSC 967 0.0732 0.96 86.0 yes View details
accD LSC 1389 0.0403 1.00 71.7 yes View details
trnP-UGG-psaJ LSC 303 0.0948 0.99 69.4 yes View details
ndhF-rpl32 SSC 945 0.0898 0.94 83.4 yes View details
rpl32-trnL-UAG SSC 757 0.0933 0.72 69.6 yes View details
psbM-trnD-GUC LSC 876 0.0649 0.97 87.9 yes View details
psbE-petL LSC 920 0.0559 0.96 86.9 yes View details
petA-psbJ LSC 697 0.0646 0.97 84.3 yes View details
trnK-UUU-rps16 LSC 750 0.0619 0.92 83.6 yes View details
rbcL-accD LSC 507 0.0592 0.95 83.2 yes View details
accD-psaI LSC 619 0.0536 0.93 82.8 yes View details
ycf4-cemA LSC 806 0.0660 0.92 82.6 yes View details
rpl16 LSC 1360 0.0492 0.93 82.1 yes View details
trnD-GUC-trnY-GUA LSC 430 0.0693 0.89 81.0 yes View details
atpB-rbcL LSC 617 0.0458 0.96 80.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAACCTTTCCCGCATCAGT TTTTCTTGAGCCGTACGAGG 1428–1464 0.833 83.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAACCTTTCCCGCATCAGT GCCGTACGAGGAGAAAACTT 1419–1455 0.833 83.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TAAAGAACTTCGCCCGACTG 907–916 0.500 62.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTTGAGCCGTACGAGG 1172–1181 0.500 61.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAACCTTTCCCGCATCAGT TAAAGAACTTCGCCCGACTG 1183 0.333 52.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TTTCCGTGAAAGACCCTGTG TTCATCGGGAGGGAAAGGAT 1429–1584 0.500 64.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC TTTCCGTGAAAGACCCTGTG TCATCGGGAGGGAAAGGATT 1428–1583 0.500 64.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CCCTGTGAGGTTTTCCACAA TCATCGGGAGGGAAAGGATT 1415–1570 0.500 63.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GTTTGGCAAGCTGCTGTAAG TTCATCGGGAGGGAAAGGAT 1569–1724 0.500 63.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GTTTGGCAAGCTGCTGTAAG TCATCGGGAGGGAAAGGATT 1568–1723 0.500 63.5
atpH-atpI_p1 atpH-atpI TTCTGGCTGTCTCGCAATAC CCCTTGGGTTCCCTTTATCG 1252–1261 1.000 88.3
atpH-atpI_p2 atpH-atpI TTCTGGCTGTCTCGCAATAC CCTTGGGTTCCCTTTATCGG 1251–1260 1.000 88.2
atpH-atpI_p3 atpH-atpI TTCTGGCTGTCTCGCAATAC CTTGGGTTCCCTTTATCGGG 1250–1259 1.000 88.2
atpH-atpI_p4 atpH-atpI TTCTGGCTGTCTCGCAATAC CCACAAACCATTCCGACTGA 1347–1356 1.000 87.4
atpH-atpI_p5 atpH-atpI TTCTGGCTGTCTCGCAATAC CTTATTAAGCTCAGCCGCCA 1381–1389 0.833 81.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CTTACCGCTCGGCCATGT 1247–1327 1.000 56.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG TTACCGCTCGGCCATGTC 1246–1326 1.000 56.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CTTACCGCTCGGCCATGTC 1247–1327 1.000 55.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC CTTACCGCTCGGCCATGT 1249–1329 1.000 52.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC TTACCGCTCGGCCATGTC 1248–1328 1.000 52.0
psbM-trnD-GUC_p1 psbM-trnD-GUC CGTTTTGGCTGACCGTTTTT TTCAATTGGTCAGAGCACCG 1040–1153 1.000 85.0
psbM-trnD-GUC_p2 psbM-trnD-GUC CGTTTTGGCTGACCGTTTTT GTTCAATTGGTCAGAGCACC 1041–1154 1.000 80.9
psbM-trnD-GUC_p3 psbM-trnD-GUC CGTTTTGGCTGACCGTTTTT TCAATTGGTCAGAGCACCG 1039–1152 1.000 79.0
psbM-trnD-GUC_p4 psbM-trnD-GUC TCGTTTTGGCTGACCGTTTT TTCAATTGGTCAGAGCACCG 1041–1154 1.000 78.5
psbM-trnD-GUC_p5 psbM-trnD-GUC CGTTTTGGCTGACCGTTTTTA TTCAATTGGTCAGAGCACCG 1040–1153 1.000 77.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CTGGTTCAAATCCAGCTCGG 445–490 1.000 80.9
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TCTACGCTGGTTCAAATCCA 451–496 1.000 79.1
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGTTCAAATCCAGCTCGG 444–489 1.000 78.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GTCTACGCTGGTTCAAATCCA 452–497 1.000 77.7
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGTCTACGCTGGTTCAAATCC 453–498 1.000 77.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Fagopyrum dibotrys NC_037705.1 159320 View on NCBI ↗
Fagopyrum esculentum NC_064334.1 159576 View on NCBI ↗
Fagopyrum leptopodum var. leptopodum MW752361.1 159323 View on NCBI ↗
Fagopyrum longistylum OK054489.1 159325 View on NCBI ↗
Fagopyrum luojishanense NC_037706.1 159265 View on NCBI ↗
Fagopyrum tataricum NC_027161.1 159272 View on NCBI ↗