Markers + reference

Albizia

3 species · Fabaceae · Fabales

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Species 3
Genome length 176–176 kb
Candidate markers 284
Primer pairs 90

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 284 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1148 0.0552 0.96 81.1 yes View details
rps16-trnQ-UUG LSC 680 0.0465 0.89 82.9 yes View details
trnQ-UUG-psbK LSC 670 0.0462 0.95 80.0 yes View details
trnS-GCU-trnG-UCC LSC 1296 0.0325 0.74 65.3 yes View details
trnR-UCU-atpA LSC 515 0.0474 0.94 76.5 yes View details
trnC-GCA-petN LSC 1128 0.0369 0.99 68.4 yes View details
petA-psbJ LSC 1596 0.0235 0.95 77.8 yes View details
ndhF-rpl32 SSC 984 0.0601 0.97 85.1 yes View details
rpl32-trnL-UAG SSC 475 0.0681 0.96 81.5 yes View details
ccsA-ndhD IRa 569 0.0686 0.91 90.3 yes View details
rps3-rps19 LSC 508 0.0443 0.87 81.8 yes View details
psbI-trnS-GCU LSC 355 0.0446 0.99 78.9 yes View details
ndhC-trnV-UAC LSC 670 0.0258 0.97 72.8 yes View details
rbcL-accD LSC 907 0.0235 1.00 72.2 yes View details
rpl16-rps3 LSC 153 0.0389 0.90 68.4 yes View details
rps19-trnH-GUG LSC 14 0.2222 0.64 68.0 no View details
trnG-UCC-trnR-UCU LSC 363 0.0349 1.00 67.9 yes View details
trnF-GAA-ndhJ LSC 753 0.0109 0.97 67.1 yes View details
atpF-atpH LSC 764 0.0283 0.96 66.5 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 90 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 AAAAAGGCGCTCAACCTACA 1380–1623 1.000 87.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1518–1761 1.000 87.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1519–1762 1.000 87.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TGAGGTTGCGAATACGAGTG 1724–1968 1.000 86.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAGCTAACGGATCGTGGAAC 1926–2172 1.000 86.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 694–760 1.000 88.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 696–762 1.000 86.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 682–748 1.000 86.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 697–763 1.000 86.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATAAAAATGGGGCGTGGC 751–817 1.000 85.1
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAGACCAAACTAAAGATATTAAGCA 712–737 1.000 48.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAAATACAGACCAAACTAAAGA 718–743 1.000 48.7
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG ACAGACCAAACTAAAGATATTAAGCA 754–779 1.000 48.5
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG ACAAATACAGACCAAACTAAAGA 760–785 1.000 48.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AATGGATATGCTCTGGGACG ACAGACCAAACTAAAGATATTAAGCA 758–783 1.000 48.4
psbI-trnS-GCU_p1 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TGGACTAAAGCGTCGGATTG 471–510 1.000 71.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GTGGACTAAAGCGTCGGATT 472–511 1.000 71.1
psbI-trnS-GCU_p3 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TTTTTCGTACCGAGGGTTCG 434–473 1.000 69.9
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GACTAAAGCGTCGGATTGCT 469–508 1.000 68.3
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTATCTAACGATCCAGGACG CTGAGTGGACTAAAGCGTCG 476–515 1.000 68.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 1064–1376 1.000 78.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 1063–1375 1.000 78.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATCCATAGAACGAATCGCA 1118–1430 1.000 77.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 1053–1365 1.000 77.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 1052–1364 1.000 77.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 443–459 1.000 66.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 446–462 1.000 66.5
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 449–465 1.000 66.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 452–468 1.000 65.8
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 513–529 1.000 64.4

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
Albizia bracteata NC_047354.1 176054 View on NCBI ↗
Albizia julibrissin NC_058305.1 175922 View on NCBI ↗
Albizia kalkora NC_072259.1 176402 View on NCBI ↗