Markers + reference

Parkinsonia

2 species · Fabaceae · Fabales

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Species 2
Genome length 159–160 kb
Candidate markers 264
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1279 0.0526 0.94 80.5 yes View details
rps16-trnQ-UUG LSC 682 0.0481 0.98 87.2 yes View details
trnQ-UUG-psbK LSC 545 0.0620 0.98 80.9 yes View details
trnS-GCU-trnG-UCC LSC 828 0.0720 0.84 79.8 yes View details
trnC-GCA-petN LSC 1076 0.0359 0.96 75.1 yes View details
psbZ-trnG-GCC LSC 396 0.0661 0.95 83.4 yes View details
trnT-UGU-trnL-UAA LSC 1265 0.0344 0.94 76.8 yes View details
ndhC-trnV-UAC LSC 726 0.0828 0.93 82.0 yes View details
rbcL-accD LSC 1062 0.0619 0.93 85.8 yes View details
accD-psaI LSC 472 0.0670 0.98 75.1 yes View details
ndhF SSC 2235 0.0094 1.00 48.2 yes View details
ndhA SSC 2438 0.0192 0.98 69.7 yes View details
ndhG-ndhI SSC 394 0.0705 0.94 89.7 yes View details
trnH-GUG-psbA LSC 389 0.0656 0.94 82.9 yes View details
psbC-trnS-UGA LSC 237 0.0638 0.99 78.0 yes View details
ndhD-psaC SSC 106 0.1226 1.00 76.8 yes View details
rps8-rpl14 LSC 385 0.0696 0.90 76.3 yes View details
rps11-rpl36 LSC 351 0.0523 0.93 75.3 yes View details
trnR-ACG-trnN-GUU IRb 613 0.0261 1.00 73.8 yes View details
trnN-GUU-trnR-ACG IRa 613 0.0261 1.00 73.8 yes View details
trnG-UCC-trnR-UCU LSC 340 0.0511 0.81 71.0 yes View details
trnT-GGU-psbD LSC 1503 0.0265 0.98 70.8 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 110 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 435–458 1.000 86.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 449–472 1.000 86.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 448–471 1.000 86.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 450–473 1.000 86.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 484–507 1.000 84.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTGTTTTTATGGAACTTTGTCCT 1401–1421 1.000 53.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGGAACTTTGTCCTAATCAACA 1391–1411 1.000 51.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ACTTTGTCCTAATCAACAAACCA 1387–1407 1.000 51.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTGTTTTTATGGAACTTTGTCC 1401–1421 1.000 51.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGTTTTTATGGAACTTTGTCCT 1352–1372 1.000 49.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 762–856 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 764–858 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 750–844 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 765–859 1.000 82.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 763–857 1.000 81.4
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCTTCAGGTAATTTCGCG 671–714 1.000 74.8
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGCTTCAGGTAATTTCGCGA 670–713 1.000 74.8
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC AGGCTTCAGGTAATTTCGCG 680–723 1.000 73.0
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC GGCTTCAGGTAATTTCGCGA 679–722 1.000 73.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK ATATGCTCTGGGACGGAAGG AGGCTTCAGGTAATTTCGCG 712–755 1.000 72.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 796–908 1.000 80.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 795–907 1.000 80.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATCCATAGAACGAATCGCA 850–962 1.000 79.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 785–897 1.000 78.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 784–896 1.000 78.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 354–420 1.000 70.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 357–423 1.000 70.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 360–426 1.000 69.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 363–429 1.000 69.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 424–490 1.000 68.0

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
Parkinsonia aculeata MW628953.1 159280 View on NCBI ↗
Parkinsonia africana NC_047387.1 159692 View on NCBI ↗