Markers + reference

Monotropa

3 species · Ericaceae · Ericales

Back to catalogue

Species 3
Genome length 34–43 kb
Candidate markers 97
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 97 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
A3228_gt05-A3228_gp09 Genome 564 0.3511 1.00 78.8 yes View details
A3228_gt06-A3228_gr04 Genome 858 0.3337 1.00 79.9 yes View details
A3228_gt18-A3228_gt19 Genome 364 0.2963 0.07 56.6 yes View details
A3228_gp07-A3228_gp06 Genome 1278 0.2261 0.99 84.5 yes View details
A3228_gp12-A3228_gp11 Genome 761 0.1592 0.99 84.0 yes View details
A3228_gp07 Genome 876 0.2246 0.98 83.0 yes View details
A3228_gp24 Genome 1507 0.1429 0.99 82.4 yes View details
A3228_gp06 Genome 1905 0.2031 0.97 82.4 yes View details
A3228_gp21-A3228_gp20 Genome 1171 0.1528 0.98 81.5 yes View details
A3228_gp09-A3228_gp08 Genome 447 0.2384 1.00 80.9 yes View details
A3228_gp09 Genome 612 0.2533 1.00 80.4 yes View details
A3228_gp05 Genome 753 0.1598 1.00 79.4 yes View details
A3228_gr04 Genome 1474 0.0927 1.00 79.2 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
A3228_gp24_p1 A3228_gp24 GCCAAGTGGATTAAGGCAGT TTTCTGGATAAGAACGCCCG 2562–2713 0.667 72.4
A3228_gp24_p2 A3228_gp24 GCCAAGTGGATTAAGGCAGT CGTAGGCGAAAATTCTCCCA 2485 0.333 51.9
A3228_gp24_p3 A3228_gp24 GCCAAGTGGATTAAGGCAGT ACGTAGGCGAAAATTCTCCC 2486 0.333 51.9
A3228_gp24_p4 A3228_gp24 GCCAAGTGGATTAAGGCAGT ATAATGGTAGATGCCCGGGA 2376 0.333 51.7
A3228_gp24_p5 A3228_gp24 CAGTGCATCATGGATGGGAT CGTAGGCGAAAATTCTCCCA 2250 0.333 50.9
A3228_gp21-A3228_gp20_p1 A3228_gp21-A3228_gp20 CGAATGGATCAGAAAGGGCA TCGTCGATTGCTAGCTCCTA 1903 0.333 52.7
A3228_gp21-A3228_gp20_p2 A3228_gp21-A3228_gp20 GGTTTGCACACCCAAAAGAC TCGTCGATTGCTAGCTCCTA 2381 0.333 52.5
A3228_gp21-A3228_gp20_p3 A3228_gp21-A3228_gp20 CGAATGGATCAGAAAGGGCA AACCCATGCGTGCTTCTTTA 1563 0.333 52.2
A3228_gp21-A3228_gp20_p4 A3228_gp21-A3228_gp20 CGAATGGATCAGAAAGGGCA GGTTTAACAACGGCTACCCA 1606 0.333 52.2
A3228_gp21-A3228_gp20_p5 A3228_gp21-A3228_gp20 CGAATGGATCAGAAAGGGCA TGGTTTAACAACGGCTACCC 1607 0.333 52.2
A3228_gp12-A3228_gp11_p1 A3228_gp12-A3228_gp11 CGTATCCCCGGCTAATTCTG TGGACGCAACCCCAAATTAA 1006–1012 0.667 71.2
A3228_gp12-A3228_gp11_p2 A3228_gp12-A3228_gp11 CGTATCCCCGGCTAATTCTG TTTATGGACGCAACCCCAAA 1010–1016 0.667 71.2
A3228_gp12-A3228_gp11_p3 A3228_gp12-A3228_gp11 TGCGAGTGATCCATAAACGG TGGACGCAACCCCAAATTAA 1168–1174 0.667 70.9
A3228_gp12-A3228_gp11_p4 A3228_gp12-A3228_gp11 TGCGAGTGATCCATAAACGG TTTATGGACGCAACCCCAAA 1172–1178 0.667 70.9
A3228_gp12-A3228_gp11_p5 A3228_gp12-A3228_gp11 TGCGAGTGATCCATAAACGG AAGGTTATGAGCCTTGCGAG 1374 0.333 52.6
A3228_gt05-A3228_gp09_p1 A3228_gt05-A3228_gp09 GTAGCTCGCAAGGCTCATAA AGGCTTTTGTCCATCCCTTG 1645 0.333 51.0
A3228_gt05-A3228_gp09_p2 A3228_gt05-A3228_gp09 TAGCTCGCAAGGCTCATAAC AGGCTTTTGTCCATCCCTTG 1644 0.333 51.0
A3228_gt05-A3228_gp09_p3 A3228_gt05-A3228_gp09 GTAGCTCGCAAGGCTCATAA TGAAACGGGGCCCTCTATAA 1241 0.333 50.6
A3228_gt05-A3228_gp09_p4 A3228_gt05-A3228_gp09 TAGCTCGCAAGGCTCATAAC TGAAACGGGGCCCTCTATAA 1240 0.333 50.6
A3228_gt05-A3228_gp09_p5 A3228_gt05-A3228_gp09 TAGCTCGCAAGGCTCATAAC TTGAAACGGGGCCCTCTATA 1241 0.333 50.6
A3228_gp09_p1 A3228_gp09 GGCTCAGGATTGCCCTTTTA AATCCAGCTTTTCCTTGCCA 1396 0.333 52.1
A3228_gp09_p2 A3228_gp09 GGCTCAGGATTGCCCTTTTA ACTAGATCCGGTTACCCCTG 1672 0.333 51.5
A3228_gp09_p3 A3228_gp09 GGCTCAGGATTGCCCTTTTA ATTCCTCGGTGGGGATTGTA 1534 0.333 51.3
A3228_gp09_p4 A3228_gp09 GGCTCAGGATTGCCCTTTTA TATTCCTCGGTGGGGATTGT 1535 0.333 51.3
A3228_gp09_p5 A3228_gp09 GGCTCAGGATTGCCCTTTTA TAGCTCTCGCTCTTCCAGTT 1589 0.333 50.9
A3228_gp09-A3228_gp08_p1 A3228_gp09-A3228_gp08 CAAGGGATGGACAAAAGCCT TCCCTCTCTCTCCCCTTACT 1000–1033 0.667 69.3
A3228_gp09-A3228_gp08_p2 A3228_gp09-A3228_gp08 CAAGGGATGGACAAAAGCCT AATCCAGCTTTTCCTTGCCA 668–700 0.667 69.1
A3228_gp09-A3228_gp08_p3 A3228_gp09-A3228_gp08 CAAGGGATGGACAAAAGCCT GAGAGATGGCTGAGTGGTTG 1073–1106 0.667 69.1
A3228_gp09-A3228_gp08_p4 A3228_gp09-A3228_gp08 CAAGGGATGGACAAAAGCCT CCTCTCTCTCCCCTTACTCG 998–1031 0.667 69.1
A3228_gp09-A3228_gp08_p5 A3228_gp09-A3228_gp08 TATAGAGGGCCCCGTTTCAA TCCCTCTCTCTCCCCTTACT 1403–1436 0.667 68.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Monotropa hypopitys NC_029704.1 35336 View on NCBI ↗
Monotropa hypopitys var. americana MF120264.1 33557 View on NCBI ↗
Monotropa uniflora NC_035582.1 43351 View on NCBI ↗