Markers + reference

Swartzia

2 species · Fabaceae · Fabales

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Species 2
Genome length 159–160 kb
Candidate markers 266
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf3 LSC 1953 0.4964 0.86 80.2 yes View details
psaA LSC 2253 0.4834 0.84 79.0 yes View details
psaB LSC 2205 0.4925 0.88 80.3 yes View details
ndhC-trnV-UAC LSC 630 0.0727 0.96 93.7 yes View details
trnG-GCC-trnL-UAA LSC 1299 0.1612 0.90 82.3 yes View details
psbZ-trnT-UGU LSC 726 0.2567 0.88 81.7 yes View details
rpl32-trnL-UAG SSC 823 0.0691 0.91 81.2 yes View details
trnP-UGG-psaJ LSC 528 0.0594 0.83 81.1 yes View details
trnG-UCC-trnR-UCU LSC 315 0.0719 0.93 80.3 yes View details
ycf3-psaA LSC 762 0.4685 0.79 79.4 yes View details
trnK-UUU-rps16 LSC 867 0.0679 0.90 78.4 yes View details
rpoC1-rpoB LSC 26 0.0769 1.00 77.9 yes View details
trnT-UGU-rps4 LSC 394 0.4618 0.90 77.8 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG GGTTGCGAATACGAGGAGTT 1449–1451 1.000 87.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAGACAGGCAAGAAAAGGGG 1546–1553 1.000 87.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCTTTTCCCACATCAAGCA GGTTGCGAATACGAGGAGTT 1708–1711 1.000 86.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCTTTTCCCACATCAAGCA AAGACAGGCAAGAAAAGGGG 1805–1813 1.000 86.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCTTTTCCCACATCAAGCA AAAAGGGGGTAGAGACTGCT 1793–1801 1.000 86.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 395–422 1.000 71.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 398–425 1.000 71.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 401–428 1.000 70.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 404–431 1.000 70.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 399–426 1.000 69.0
rpoC1-rpoB_p1 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTGCTCGTTCGAGAACTACG 192 1.000 80.4
rpoC1-rpoB_p2 rpoC1-rpoB TGGCCCAAGCACTTATTTGT ACGATCTTTGGCTCTGGAAC 175 1.000 80.0
rpoC1-rpoB_p3 rpoC1-rpoB GCTTTGTTACCTCCCCAACT TTGCTCGTTCGAGAACTACG 237 1.000 78.0
rpoC1-rpoB_p4 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTCGATTGCTCGTTCGAGAA 197 1.000 78.0
rpoC1-rpoB_p5 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTTCGATTGCTCGTTCGAGA 198 1.000 78.0
psbZ-trnT-UGU_p1 psbZ-trnT-UGU CTTCTCCTGATGGTTGGTCG AAAATCTGACCGGTTGACCC 1548 0.500 59.1
psbZ-trnT-UGU_p2 psbZ-trnT-UGU CTTCTCCTGATGGTTGGTCG CCGGTTGACCCTTTAGCTTT 1539 0.500 59.1
psbZ-trnT-UGU_p3 psbZ-trnT-UGU CTTCTCCTGATGGTTGGTCG AGCGCGATTGGTTTCTAAGT 1412 0.500 59.1
psbZ-trnT-UGU_p4 psbZ-trnT-UGU CTTCTCCTGATGGTTGGTCG CTGACCGGTTGACCCTTTAG 1543 0.500 59.1
psbZ-trnT-UGU_p5 psbZ-trnT-UGU TCGATCCATGCCTCAAAAGG CCGGTTGACCCTTTAGCTTT 1793 0.500 58.9
trnT-UGU-rps4_p1 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC CGAAGCCATACCCAATCGAA 763 0.500 58.5
trnT-UGU-rps4_p2 trnT-UGU-rps4 AGGGAGGGGTCAAACTTCTT CGAAGCCATACCCAATCGAA 1386 0.500 58.3
trnT-UGU-rps4_p3 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AAAATCTGACCGGTTGACCC 705 0.500 58.2
trnT-UGU-rps4_p4 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC CCGGTTGACCCTTTAGCTTT 696 0.500 58.2
trnT-UGU-rps4_p5 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AGCGCGATTGGTTTCTAAGT 569 0.500 58.2
ycf3_p1 ycf3 GGCCCAGAAATCGAGTGAAT ATCACGTGAGCAGCCATTAG 2567 0.500 59.2
ycf3_p2 ycf3 GGCCCAGAAATCGAGTGAAT ACACATACAAAGAGACCCGC 2937 0.500 58.9
ycf3_p3 ycf3 GGCCCAGAAATCGAGTGAAT TGGGGGACATACCGGTATTT 2541 0.500 58.8
ycf3_p4 ycf3 GGCCCAGAAATCGAGTGAAT CAAAGAGACCCGCCAACATA 2930 0.500 58.8
ycf3_p5 ycf3 GGCCCAGAAATCGAGTGAAT CATACAAAGAGACCCGCCAA 2934 0.500 58.8

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
Swartzia bahiensis MW628941.1 160100 View on NCBI ↗
Swartzia simplex PV870697.1 159162 View on NCBI ↗