Markers + reference

Azadirachta

2 species · Meliaceae · Sapindales

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Species 2
Genome length 160–161 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 466 0.0244 0.97 73.0 yes View details
trnK-UUU-rps16 LSC 1000 0.0417 0.96 71.8 yes View details
rps16-trnQ-UUG LSC 1739 0.0182 0.89 62.1 yes View details
trnS-UGA-psbZ LSC 367 0.0140 0.98 55.9 yes View details
ycf4-cemA LSC 941 0.0225 0.99 66.2 yes View details
petA-psbJ LSC 775 0.0181 1.00 62.4 yes View details
petD LSC 525 0.0057 1.00 49.4 yes View details
petD-rpoA LSC 268 0.0532 0.98 71.3 yes View details
ycf1 IRb 1083 0.0018 1.00 48.0 no View details
rpl32-trnL-UAG SSC 1100 0.0173 1.00 57.2 yes View details
ycf1 SSC 5478 0.0077 1.00 49.3 yes View details
ndhI-ndhA SSC 88 0.0341 1.00 71.5 yes View details
psbC-trnS-UGA LSC 246 0.0329 0.99 69.9 yes View details
rpoC2-rpoC1 LSC 178 0.0281 1.00 68.7 yes View details
psbI-trnS-GCU LSC 140 0.0357 1.00 68.2 yes View details
rps19-trnH-GUG IRa 257 0.0000 1.00 68.0 no View details
petG-trnW-CCA LSC 144 0.0347 1.00 65.6 yes View details
matK LSC 1524 0.0118 1.00 65.5 yes View details
clpP LSC 2083 0.0082 0.99 62.9 yes View details
trnE-UUC-trnT-GGU LSC 804 0.0050 0.99 62.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 536–539 1.000 82.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 550–553 1.000 82.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 549–552 1.000 82.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 551–554 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 585–588 1.000 79.8
trnK-UUU_p1 trnK-UUU GATTCAAATTCAGAAGAAATTTGT CCGATTGTATCTACCCATTCGA 2713–2718 1.000 40.7
trnK-UUU_p2 trnK-UUU GATTCAAATTCAGAAGAAATTTGT TCCGATTGTATCTACCCATTCG 2714–2719 1.000 40.7
trnK-UUU_p3 trnK-UUU TGAATGAATGAAGTAAGTAAGAAAACT CCGATTGTATCTACCCATTCGA 2681 0.500 20.0
trnK-UUU_p4 trnK-UUU TGAATGAATGAAGTAAGTAAGAAAACT TCCGATTGTATCTACCCATTCG 2682 0.500 20.0
trnK-UUU_p5 trnK-UUU TGAATGAATGAAGTAAGTAAGAAAAC CCGATTGTATCTACCCATTCGA 2681 0.500 20.0
matK_p1 matK TGTTATCGATTCCCTATTTAGGA TGTTTTCGCTGTATCGCACT 1655 1.000 40.9
matK_p2 matK TGTTATCGATTCCCTATTTAGGAA TGTTTTCGCTGTATCGCACT 1655 1.000 40.9
matK_p3 matK TTGTTATCGATTCCCTATTTAGGA TGTTTTCGCTGTATCGCACT 1656 1.000 40.9
matK_p4 matK ACTCAGTTGATCAACCTTTAT TGTTTTCGCTGTATCGCACT 1720 1.000 40.8
matK_p5 matK ACTCAGTTGATCAACCTTTATT TGTTTTCGCTGTATCGCACT 1720 1.000 40.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CGAGCCGTACGAAGAGAAAA 1313–1342 1.000 84.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TTTTCTCGAGCCGTACGAAG 1319–1348 1.000 84.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGAGCCGTACGAAGAGAAAA 1397–1426 1.000 84.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTCGAGCCGTACGAAG 1403–1432 1.000 84.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG GGTGTGTTGCTGCCATTTTT 1703–1742 1.000 84.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1623–1812 1.000 83.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1634–1823 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1644–1833 1.000 79.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GGGTTTTGGTCCCGGTATTC 1655–1844 1.000 79.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1627–1816 1.000 78.8
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCCGGACGCGAAGAATA TGAGTGGATTAAAGCGTCGG 238–241 1.000 71.6
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA TGAGTGGATTAAAGCGTCGG 237–240 1.000 71.6
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCCGGACGCGAAGAAT TGAGTGGATTAAAGCGTCGG 239–242 1.000 71.6
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCCGGACGCGAAGAATA TAGGAGAGATGGCTGAGTGG 251–254 1.000 70.9
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA TAGGAGAGATGGCTGAGTGG 250–253 1.000 70.9

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
Azadirachta indica NC_023792.1 160737 View on NCBI ↗
Azadirachta indica var. siamensis OK037101.1 160477 View on NCBI ↗