Markers + reference

Kielmeyera

2 species · Calophyllaceae · Malpighiales

Back to catalogue

Species 2
Genome length 159–159 kb
Candidate markers 275
Primer pairs 75

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 6 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-CGA-trnR-UCU LSC 691 0.0263 0.99 74.8 yes View details
psbC-trnS-UGA LSC 224 0.0446 1.00 78.2 yes View details
trnS-UGA-psbZ LSC 371 0.0027 1.00 49.1 yes View details
psbZ-trnG-GCC LSC 858 0.0117 0.99 66.2 yes View details
petA-psbJ LSC 697 0.3522 0.96 82.5 yes View details
psbJ-psbL LSC 143 0.4965 0.99 73.9 yes View details
psbE LSC 252 0.5274 0.94 77.3 yes View details
psbE-petL LSC 1211 0.2402 0.93 83.1 yes View details
ycf1 IRb 1083 0.0000 1.00 27.4 no View details
ycf1 SSC 5733 0.0040 1.00 45.4 yes View details
psbF-psbE LSC 9 0.5000 0.89 75.7 yes View details
psbJ LSC 123 0.5152 0.80 73.3 yes View details
psbL LSC 117 0.4957 1.00 72.6 yes View details
psbL-psbF LSC 26 0.4615 1.00 72.5 yes View details
psbF LSC 120 0.4416 0.64 68.7 yes View details
rpl32-trnL-UAG SSC 794 0.0065 0.96 66.1 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTTTGTCCTATCCA 772–784 1.000 55.8
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTTTGTCCT 778–790 1.000 55.6
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTTTGTCCTATCCA 775–787 1.000 55.6
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTTTGTCCT 781–793 1.000 55.3
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTTTGTCCTATCCA 776–788 1.000 53.4
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 328 1.000 80.7
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCCTGTTCTTTCCATGACC GGTTGATAGCTCCGGTCTTG 330 1.000 80.3
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GATGGCCGAGTGGTTGATAG 339 1.000 80.0
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCCTGTTCTTTCCATGACC GATGGCCGAGTGGTTGATAG 341 1.000 79.7
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCAGGATTCGAAAAAGG GGTTGATAGCTCCGGTCTTG 367 1.000 79.6
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC GTTGACCAACCATCAGGAGA 511–536 1.000 73.0
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC AGTTGACCAACCATCAGGAG 512–537 1.000 72.9
trnS-UGA-psbZ_p3 trnS-UGA-psbZ CTATCAACCACTCGGCCATC GTTGACCAACCATCAGGAGA 500–525 1.000 72.4
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CTATCAACCACTCGGCCATC AGTTGACCAACCATCAGGAG 501–526 1.000 72.3
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC TGCAAAAACAGCCAATTGGA 440–465 1.000 71.9
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TCTCCTGATGGTTGGTCAAC CGTCTTCTCCTTGGCAAAGA 1010–1044 1.000 73.0
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CTCCTGATGGTTGGTCAACT CGTCTTCTCCTTGGCAAAGA 1009–1043 1.000 73.0
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTCTCCTGATGGTTGGTCAAC CGTCTTCTCCTTGGCAAAGA 1011–1045 1.000 70.8
psbZ-trnG-GCC_p4 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCA CGTCTTCTCCTTGGCAAAGA 1012–1046 1.000 70.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TCTTCTCCTGATGGTTGGTCA CGTCTTCTCCTTGGCAAAGA 1013–1047 1.000 68.8
petA-psbJ_p1 petA-psbJ TATGATACCTCCAGGGCCAG AACTGGCCGTTTTGATCCTT 1534 0.500 59.7
petA-psbJ_p2 petA-psbJ TATGATACCTCCAGGGCCAG ACTGGCCGTTTTGATCCTTT 1533 0.500 59.7
petA-psbJ_p3 petA-psbJ GAGGGCGAATCCATCAAACT AACTGGCCGTTTTGATCCTT 1500 0.500 59.6
petA-psbJ_p4 petA-psbJ GAGGGCGAATCCATCAAACT ACTGGCCGTTTTGATCCTTT 1499 0.500 59.6
petA-psbJ_p5 petA-psbJ TATGATACCTCCAGGGCCAG GAGAACCGACAAGGGATTCC 1560 0.500 59.6
psbJ_p1 psbJ GTGGGACCCCCTTTTCTCTA AACTGGCCGTTTTGATCCTT 677 0.500 57.3
psbJ_p2 psbJ GTGGGACCCCCTTTTCTCTA ACTGGCCGTTTTGATCCTTT 676 0.500 57.3
psbJ_p3 psbJ TAAGAACTCAGTGGGACCCC AACTGGCCGTTTTGATCCTT 687 0.500 57.2
psbJ_p4 psbJ TAAGAACTCAGTGGGACCCC ACTGGCCGTTTTGATCCTTT 686 0.500 57.2
psbJ_p5 psbJ GTGGGACCCCCTTTTCTCTA GAGAACCGACAAGGGATTCC 703 0.500 57.1

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
Kielmeyera appariciana MW853788.1 158986 View on NCBI ↗
Kielmeyera coriacea MW853789.1 159470 View on NCBI ↗