Markers + reference

Vachellia

6 species · Fabaceae · Fabales

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Species 6
Genome length 165–166 kb
Candidate markers 266
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1476 0.0329 0.69 63.0 yes View details
psbI-trnS-GCU LSC 571 0.0393 0.93 81.0 yes View details
trnS-GCU-trnG-UCC LSC 2015 0.0314 0.87 74.5 yes View details
trnC-GCA-petN LSC 1516 0.0171 0.95 66.7 yes View details
psbZ-trnG-GCC LSC 683 0.0407 0.86 75.8 yes View details
psaA-ycf3 LSC 910 0.0283 0.90 80.8 yes View details
trnT-UGU-trnL-UAA LSC 1417 0.0303 0.90 73.2 yes View details
accD-psaI LSC 813 0.0458 0.80 74.3 yes View details
petA-psbJ LSC 1371 0.0182 0.99 70.5 yes View details
rps8-rpl14 LSC 558 0.0579 0.62 72.5 yes View details
ndhC-trnV-UAC LSC 992 0.0255 0.87 78.3 yes View details
rpl33-rps18 LSC 400 0.0346 0.94 76.3 yes View details
rps2-rpoC2 LSC 244 0.0371 0.97 75.1 yes View details
trnL-UAG-rpl32 SSC 509 0.0319 0.98 74.6 yes View details
ycf4-cemA LSC 462 0.0114 1.00 69.1 yes View details
trnQ-UUG-psbK LSC 875 0.0183 0.94 68.0 yes View details
rps11-rpl36 LSC 153 0.0277 0.97 65.7 yes View details
trnG-GCC-trnfM-CAU LSC 232 0.0216 1.00 65.2 yes View details
trnR-ACG-trnN-GUU IRb 616 0.0080 0.99 65.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 GGGCCCGATCCAATAACAAT AAAAAGGCGCTCAACCTACA 1378–1872 1.000 88.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 GGGCCCGATCCAATAACAAT TGAGGTTGCGAATACGAGTG 1728–2220 1.000 87.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TGAGGTTGCGAATACGAGTG 1655–2147 1.000 87.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGGCCCGATCCAATAACAAT AAGCTAACGGATCGTGGAAC 1934–2418 1.000 87.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAGCTAACGGATCGTGGAAC 1861–2345 1.000 87.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG AGGCTTCAGGTAATTTCGCG 1043–1187 1.000 78.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG GGCTTCAGGTAATTTCGCGA 1042–1186 1.000 78.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCTTCAGGTAATTTCGCG 1001–1145 1.000 76.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGCTTCAGGTAATTTCGCGA 1000–1144 1.000 76.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AATGGATATGCTCTGGGACG AGGCTTCAGGTAATTTCGCG 1047–1191 1.000 74.8
psbI-trnS-GCU_p1 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TGGACTAAAGCGTCGGATTG 611–691 1.000 74.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GTGGACTAAAGCGTCGGATT 612–692 1.000 74.2
psbI-trnS-GCU_p3 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TTTTTCGTACCGAGGGTTCG 574–654 1.000 72.8
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCTAACGATCCAGGACG CAATTGGGGAGAGATGGCTG 633–713 1.000 71.6
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GACTAAAGCGTCGGATTGCT 609–689 1.000 71.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 1886–2127 1.000 83.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 1885–2126 1.000 83.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGGATCCC 1940–2181 1.000 82.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA TGAATCAAACGAGGGATCCC 1945–2186 1.000 81.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 1854–2095 1.000 80.9
rps2-rpoC2_p1 rps2-rpoC2 CCATGGCCAAAATGAACTCC TCAGAGCAATCATTTCGAGGA 329–348 1.000 68.1
rps2-rpoC2_p2 rps2-rpoC2 GGCCAAAATGAACTCCTGCT TCAGAGCAATCATTTCGAGGA 325–344 1.000 67.7
rps2-rpoC2_p3 rps2-rpoC2 TGGCCAAAATGAACTCCTGC TCAGAGCAATCATTTCGAGGA 326–345 1.000 65.3
rps2-rpoC2_p4 rps2-rpoC2 GCCAAAATGAACTCCTGCTTC TCAGAGCAATCATTTCGAGGA 324–343 1.000 65.2
rps2-rpoC2_p5 rps2-rpoC2 GGTGCCATTCTAGGATTCCA TCAGAGCAATCATTTCGAGGA 359–378 1.000 64.9
trnC-GCA-petN_p1 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 1538–1650 1.000 84.3
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGAGTCCACTTCTTCCCCAT 1599–1711 1.000 82.6
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1504–1616 1.000 82.6
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG TCTTCCCCATACTACGAGGG 1589–1701 1.000 82.4
trnC-GCA-petN_p5 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 1479–1591 1.000 81.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Vachellia farnesiana PV870726.1 165463 View on NCBI ↗
Vachellia flava NC_036734.1 165829 View on NCBI ↗
Vachellia nilotica NC_045514.1 165343 View on NCBI ↗
Vachellia nilotica subsp. tomentosa KY100264.1 165585 View on NCBI ↗
Vachellia pennatula PV870729.1 165925 View on NCBI ↗
Vachellia seyal NC_036735.1 165383 View on NCBI ↗