Markers + reference

Agapanthus

3 species · Amaryllidaceae · Asparagales

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Species 3
Genome length 157–157 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 698 0.0029 1.00 52.9 yes View details
psbK-psbI LSC 427 0.0031 1.00 56.5 yes View details
psbM-trnD-GUC LSC 1065 0.0019 1.00 60.3 yes View details
trnE-UUC-trnT-GGU LSC 477 0.0042 1.00 58.9 yes View details
rbcL LSC 1443 0.0025 1.00 60.3 yes View details
ndhF-rpl32 SSC 908 0.0029 1.00 60.6 yes View details
ndhA SSC 2076 0.0013 1.00 58.4 yes View details
rps15-ycf1 SSC 393 0.0052 0.99 58.9 yes View details
psaA-ycf3 LSC 598 0.0022 1.00 60.1 yes View details
rps16-trnQ-UUG LSC 1479 0.0009 1.00 59.9 yes View details
rps16 LSC 1121 0.0012 1.00 59.7 yes View details
trnT-GGU-psbD LSC 1088 0.0012 1.00 59.6 yes View details
trnC-GCA-petN LSC 689 0.0010 1.00 59.5 yes View details
rpl16 LSC 1353 0.0010 1.00 59.5 yes View details
atpF LSC 1382 0.0010 1.00 59.4 yes View details
ndhC-trnV-UAC LSC 1544 0.0009 1.00 59.4 yes View details
rpl33-rps18 LSC 167 0.0081 0.99 58.7 yes View details
psaA LSC 2253 0.0006 1.00 57.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGACCAAATCTAAACGCACCA ACGTAGTTGTACAGTGCAAT 2810 1.000 47.3
trnK-UUU_p2 trnK-UUU TGACCAAATCTAAACGCACCA CGTAGTTGTACAGTGCAATTCA 2809 1.000 47.1
trnK-UUU_p3 trnK-UUU TGACCAAATCTAAACGCACCA ACGTAGTTGTACAGTGCAATTC 2810 1.000 47.1
trnK-UUU_p4 trnK-UUU ACGCACCAAATCTAAATGCAC ACGTAGTTGTACAGTGCAAT 2797 1.000 46.7
trnK-UUU_p5 trnK-UUU ACGCACCAAATCTAAATGCAC CGTAGTTGTACAGTGCAATTCA 2796 1.000 46.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 799–800 1.000 77.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 798–799 1.000 77.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTACCAATAGCCTGGACGA GGTGCTCAACCTACAGGAAC 864–865 1.000 75.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 785–786 1.000 75.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 810–811 1.000 74.2
rps16_p1 rps16 GCAAGAAAAGAGCAAATTGTGG ACCGTTGAGCCAATGACTAT 1270–1272 1.000 49.8
rps16_p2 rps16 GCAAGAAAAGAGCAAATTGTGG ATACCGTTGAGCCAATGACT 1272–1274 1.000 49.8
rps16_p3 rps16 AGAAAAGAGCAAATTGTGGGT ACCGTTGAGCCAATGACTAT 1267–1269 1.000 49.5
rps16_p4 rps16 AGAAAAGAGCAAATTGTGGGT ATACCGTTGAGCCAATGACT 1269–1271 1.000 49.5
rps16_p5 rps16 GCAAGAAAAGAGCAAATTGTGG ACCGTTGAGCCAATGACTATT 1270–1272 1.000 47.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1545–1552 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1549–1556 1.000 77.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGCGAATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1562–1569 1.000 77.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGAATCCACAGCGAATCGTG GAGGTTCGAATCCTTCCGTC 1571–1578 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGAATCCACAGCGAATCGT GAGGTTCGAATCCTTCCGTC 1572–1579 1.000 76.8
psbK-psbI_p1 psbK-psbI CTTTGTTTGGCAAGCTGCTA GGCCCGGATCGTTAGATAAG 549 1.000 71.0
psbK-psbI_p2 psbK-psbI CTTTGTTTGGCAAGCTGCTAT GGCCCGGATCGTTAGATAAG 549 1.000 66.9
psbK-psbI_p3 psbK-psbI CTTTGTTTGGCAAGCTGCTA TCCTCACGTCCAGGATTACG 568 1.000 66.7
psbK-psbI_p4 psbK-psbI TGCCTTTTTCAGTCCAATCG GGCCCGGATCGTTAGATAAG 612 1.000 66.4
psbK-psbI_p5 psbK-psbI GCCTTTTTCAGTCCAATCGT GGCCCGGATCGTTAGATAAG 611 1.000 66.3
trnG-GCC_p1 trnG-GCC TTTGTTCGACAAAGGGTCCA GAATGGATGATGCATATAGAATAA 836 1.000 40.1
trnG-GCC_p2 trnG-GCC TTTGTTCGACAAAGGGTCCA GAATGGATGATGCATATAGAATAAA 836 1.000 40.1
trnG-GCC_p3 trnG-GCC TGTTCGACAAAGGGTCCATT GAATGGATGATGCATATAGAATAA 834 1.000 40.1
trnG-GCC_p4 trnG-GCC TTGTTCGACAAAGGGTCCAT GAATGGATGATGCATATAGAATAA 835 1.000 40.1
trnG-GCC_p5 trnG-GCC TGTTCGACAAAGGGTCCATT GAATGGATGATGCATATAGAATAAA 834 1.000 40.1

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
Agapanthus caulescens PP853183.1 157047 View on NCBI ↗
Agapanthus coddii NC_035971.1 157055 View on NCBI ↗
Agapanthus praecox subsp. orientalis PP853184.1 157019 View on NCBI ↗