Markers + reference

Edgeworthia

3 species · Thymelaeaceae · Malvales

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Species 3
Genome length 172–174 kb
Candidate markers 289
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 289 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1184 0.0121 1.00 54.1 yes View details
rps16-trnQ-UUG LSC 1260 0.0152 0.87 53.6 yes View details
rps4-trnT-UGU LSC 486 0.0279 0.98 66.8 yes View details
accD-psaI LSC 770 0.0254 0.99 62.2 yes View details
petA-psbJ LSC 788 0.0186 1.00 70.6 yes View details
rpl20 LSC 351 0.0171 1.00 49.9 yes View details
rpl36-rps8 LSC 505 0.0212 1.00 57.8 yes View details
trnL-UAG-ndhF SSC 2509 0.0362 0.99 66.3 yes View details
ndhF SSC 606 0.0446 1.00 72.5 yes View details
ndhF-rpl32 SSC 339 0.1460 1.00 74.3 yes View details
psbI-trnS-GCU LSC 82 0.0470 0.95 81.2 yes View details
ndhK-ndhC LSC 71 0.0798 1.00 73.4 yes View details
ycf3-trnS-GGA LSC 926 0.0137 1.00 70.9 yes View details
trnL-UAA-trnF-GAA LSC 380 0.0161 0.98 68.5 yes View details
trnK-UUU-rps16 LSC 675 0.0173 1.00 67.0 yes View details
psbT-psbN LSC 82 0.0325 1.00 66.3 yes View details
psbN-psbH LSC 107 0.0249 1.00 65.8 yes View details
psbA-trnK-UUU LSC 284 0.0122 0.96 64.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AACACACCAAACCATCCGAT CGGTTTGGGGAGGGATTTTT 475–485 1.000 78.8
psbA-trnK-UUU_p2 psbA-trnK-UUU AACACACCAAACCATCCGAT AAAATGCAAGCACGGTTTGG 487–497 1.000 78.3
psbA-trnK-UUU_p3 psbA-trnK-UUU ACACACCAAACCATCCGATG CGGTTTGGGGAGGGATTTTT 474–484 1.000 77.4
psbA-trnK-UUU_p4 psbA-trnK-UUU CACACCAAACCATCCGATGT CGGTTTGGGGAGGGATTTTT 473–483 1.000 77.4
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACACCAAACCATCCGAT TGAAAAATGCAAGCACGGTT 490–500 1.000 76.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTAAAGAAGGCGGGGGTTT 807–828 1.000 77.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTTAAAGAAGGCGGGGGTT 808–829 1.000 77.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTTAAAGAAGGCGGGGGTTT 806–827 1.000 77.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTTTAAAGAAGGCGGGGGTT 807–828 1.000 77.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC CGGGGGTTTACGGAACTAAA 795–816 1.000 77.3
rps16_p1 rps16 GTTGAGTTAGCAACCCCCAA ACTGCGTACTAAATGAACCGA 1973–1990 0.667 55.3
rps16_p2 rps16 TGAGTCATCCACACCCTCTT ACTGCGTACTAAATGAACCGA 1346–1350 0.667 55.0
rps16_p3 rps16 GCATTCGTTCAGATCCGCTA ACTGCGTACTAAATGAACCGA 1839–1856 0.667 54.1
rps16_p4 rps16 AAAGCCGAGTACTCTACCGT ACTGCGTACTAAATGAACCGA 1991–2008 0.667 54.0
rps16_p5 rps16 AAGCCGAGTACTCTACCGTT ACTGCGTACTAAATGAACCGA 1990–2007 0.667 54.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAGGTTCGAATCCTTCCGTC 668–1333 1.000 81.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AAGGTTCGAATCCTTCCGTC 679–1344 1.000 80.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA AAGGTTCGAATCCTTCCGTC 680–1345 1.000 76.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG AAGGTTCGAATCCTTCCGTC 660–1325 1.000 76.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 665–1330 1.000 75.9
psbI-trnS-GCU_p1 psbI-trnS-GCU TTTCGCTCTTCATCTTCGGA TGGACTAAAGCGTCGGATTG 213–220 1.000 76.2
psbI-trnS-GCU_p2 psbI-trnS-GCU TTTCGCTCTTCATCTTCGGA GTGGACTAAAGCGTCGGATT 214–221 1.000 76.1
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTCGCTCTTCATCTTCGG TGGACTAAAGCGTCGGATTG 214–221 1.000 75.8
psbI-trnS-GCU_p4 psbI-trnS-GCU TCGCTCTTCATCTTCGGATTC TGGACTAAAGCGTCGGATTG 211–218 1.000 75.8
psbI-trnS-GCU_p5 psbI-trnS-GCU GTTTCGCTCTTCATCTTCGG GTGGACTAAAGCGTCGGATT 215–222 1.000 75.7
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TGAATTAGGTGAAGGTGCGG 1049–1052 1.000 74.4
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTGAA 983–986 1.000 74.0
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTAGGTGAAGGTGCGGAAAG 1045–1048 1.000 73.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA GTGCGGAAAGAGAGGGATTC 1035–1038 1.000 72.6
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA GAATTAGGTGAAGGTGCGGA 1048–1051 1.000 72.1

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
Edgeworthia albiflora NC_058012.1 173621 View on NCBI ↗
Edgeworthia chrysantha NC_050847.1 172446 View on NCBI ↗
Edgeworthia gardneri NC_058013.1 173309 View on NCBI ↗