Markers + reference

Acacia

3 species · Fabaceae · Fabales

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Species 3
Genome length 174–176 kb
Candidate markers 283
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1177 0.0827 0.99 87.3 yes View details
trnT-UGU-trnL-UAA LSC 1490 0.0398 0.96 78.9 yes View details
accD LSC 1581 0.0614 1.00 81.0 yes View details
accD-psaI LSC 575 0.0646 0.97 81.5 yes View details
clpP LSC 2207 0.1132 0.98 81.9 yes View details
clpP-psbB LSC 508 0.0687 0.96 78.0 yes View details
rps3-rps19 LSC 730 0.0549 0.92 77.2 yes View details
rpl23 IRb 300 0.0111 1.00 45.0 no View details
rpl23 IRa 300 0.2297 0.25 61.1 yes View details
trnS-GCU-trnG-UCC LSC 1077 0.0481 0.91 85.2 yes View details
rpl33-rps18 LSC 245 0.0747 0.95 84.3 yes View details
ndhC-trnV-UAC LSC 1054 0.0432 0.95 82.8 yes View details
psbZ-trnG-GCC LSC 713 0.0419 0.93 81.3 yes View details
trnR-UCU-atpA LSC 502 0.0434 0.99 80.6 yes View details
psbI-trnS-GCU LSC 439 0.0630 0.94 80.2 yes View details
trnI-CAU-ycf2 IRb 88 0.0833 1.00 77.9 yes View details
ndhF-rpl32 SSC 965 0.0469 0.97 77.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAGGCGGGTGTTTTTATGGA 1285–1488 1.000 85.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGGCGGGTGTTTTTATGGAA 1284–1487 1.000 85.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA AAGGCGGGTGTTTTTATGGA 1286–1489 1.000 85.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA AGGCGGGTGTTTTTATGGAA 1285–1488 1.000 85.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGCGGGTGTTTTTATGGAAC 1283–1486 1.000 84.6
psbI-trnS-GCU_p1 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TGGACTAAAGCGTCGGATTG 495–566 1.000 74.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GTGGACTAAAGCGTCGGATT 496–567 1.000 74.6
psbI-trnS-GCU_p3 psbI-trnS-GCU CCTATCTAACGATCCAGGACG AAGGGCCCTTTTCAATTGGT 540–611 1.000 73.3
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCTAACGATCCAGGACG AGGGCCCTTTTCAATTGGTT 539–610 1.000 73.3
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TTTTTCGTACCGAGGGTTCG 458–529 1.000 73.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 1090–1189 1.000 82.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 1089–1188 1.000 82.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGGATCCC 1144–1243 1.000 81.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 1058–1157 1.000 80.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 1057–1156 1.000 80.4
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACTCGGGAAGCAGAA 556–662 1.000 73.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACTCGGGAAGC 560–666 1.000 73.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 546–652 1.000 71.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTCACTCGGGAAGCAGAAG 555–661 1.000 71.5
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTCACTCGGGAAGCAGAA 591–697 1.000 70.8
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG GCGTCTTCTCTTTGGCAAAG 789–868 1.000 85.0
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG ATACATAAATAGGGGGCGCG 833–912 1.000 84.2
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GCGTCTTCTCTTTGGCAAAG 792–871 1.000 83.5
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TCCTGATGGTTGGTCGAGTA GCGTCTTCTCTTTGGCAAAG 785–864 1.000 83.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC GCGTCTTCTCTTTGGCAAAG 790–869 1.000 83.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1348–1572 1.000 86.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1356–1580 1.000 85.7
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AAATGCGACGCTCTAACCTC ACCAATTTCGCCATATCCCC 1320–1544 1.000 85.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA AAATGCGACGCTCTAACCTC TAGCGTCTACCAATTTCGCC 1328–1552 1.000 84.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT AGTCCGTAGCGTCTACCAAT 1362–1586 1.000 84.3

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
Acacia crassicarpa NC_067032.1 176493 View on NCBI ↗
Acacia ligulata NC_026134.2 174233 View on NCBI ↗
Acacia podalyriifolia NC_047330.1 175589 View on NCBI ↗