Markers + reference

Senegalia

3 species · Fabaceae · Fabales

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Species 3
Genome length 163–173 kb
Candidate markers 262
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1540 0.0668 0.95 78.1 yes View details
rps16-trnQ-UUG LSC 789 0.0696 0.91 84.4 yes View details
trnQ-UUG-psbK LSC 676 0.0719 0.99 85.0 yes View details
trnS-GCU-trnG-UCC LSC 1139 0.0534 0.74 72.8 yes View details
atpH-atpI LSC 1442 0.0711 0.96 77.0 yes View details
trnC-GCA-petN LSC 1156 0.0384 0.98 77.8 yes View details
trnT-UGU-trnL-UAA LSC 1312 0.0534 0.90 73.4 yes View details
ndhC-trnM-CAU LSC 1799 0.0326 0.98 67.9 yes View details
rps3-rps19 LSC 787 0.0757 0.92 81.1 yes View details
ndhF SSC 2232 0.0112 1.00 50.1 yes View details
atpF-atpH LSC 687 0.0451 1.00 92.3 yes View details
psbZ-trnG-GCC LSC 562 0.0444 0.99 83.5 yes View details
ccsA-ndhD SSC 566 0.0561 1.00 81.7 yes View details
accD-psaI LSC 556 0.0583 0.99 80.1 yes View details
rpl33-rps18 LSC 377 0.0457 0.97 78.3 yes View details
psbI-trnS-GCU LSC 391 0.0549 0.92 75.6 yes View details
psbF-psbE LSC 9 0.0741 1.00 75.0 yes View details
ycf4-cemA LSC 434 0.0236 0.98 73.0 yes View details
ycf1-ndhF SSC 111 0.2042 1.00 72.7 yes View details
psbA-trnK-UUU LSC 289 0.0346 1.00 72.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTCCATCCGACTAGTTCCG 392–404 1.000 79.1
psbA-trnK-UUU_p2 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTAGTTCCGGGTTCGAGTC 382–394 1.000 77.4
psbA-trnK-UUU_p3 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC GACTAGTTCCGGGTTCGAGT 383–395 1.000 77.4
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 412–424 1.000 77.1
psbA-trnK-UUU_p5 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ATCCGACTAGTTCCGGGTTC 387–399 1.000 76.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGAACTTAATCCTAATCAACAAACGA 837–1667 1.000 50.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA GGAACTTAATCCTAATCAACAAACGA 838–1668 1.000 50.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCCTAATCAACAAACGAAATTCA 828–1658 1.000 50.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA TCCTAATCAACAAACGAAATTCA 829–1659 1.000 50.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGGAACTTAATCCTAATCAACAAACG 838–1668 1.000 50.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 715–869 1.000 90.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 717–871 1.000 89.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 703–857 1.000 89.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 718–872 1.000 89.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 716–870 1.000 88.0
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG AGCAGCTTGCCAAACAAAAG 927–1006 1.000 85.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG CTTACAGCAGCTTGCCAAAC 932–1011 1.000 85.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGCAGCTTGCCAAACAAAAG 885–964 1.000 83.9
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA CTTACAGCAGCTTGCCAAAC 890–969 1.000 83.9
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG GCACAAGCAAGGAAAACACA 1279–1359 1.000 81.7
psbI-trnS-GCU_p1 psbI-trnS-GCU TCTAACGATCCAGGACGTAA TTCGAATCCCTCTCTTTCCG 381–455 1.000 60.9
psbI-trnS-GCU_p2 psbI-trnS-GCU TCTAACGATCCAGGACGTAA GGGTTCGAATCCCTCTCTTT 384–458 1.000 59.9
psbI-trnS-GCU_p3 psbI-trnS-GCU TCTAACGATCCAGGACGTAA GGGTTCGAATCCCTCTCTTTC 384–458 1.000 59.9
psbI-trnS-GCU_p4 psbI-trnS-GCU TCTAACGATCCAGGACGTAA GGTTCGAATCCCTCTCTTTCC 383–457 1.000 59.9
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAACGATCCAGGACGTA TTCGAATCCCTCTCTTTCCG 382–456 1.000 59.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 700–1220 1.000 80.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 699–1219 1.000 80.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 689–1209 1.000 78.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 688–1208 1.000 78.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 689–1209 1.000 78.3

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
Senegalia burkei PX394258.1 163218 View on NCBI ↗
Senegalia catechu NC_047594.1 173228 View on NCBI ↗
Senegalia pennata NC_086866.1 162859 View on NCBI ↗