Markers + reference

Afzelia

5 species · Fabaceae · Fabales

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Species 5
Genome length 156–160 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 298 0.0880 0.93 79.3 yes View details
atpH-atpI LSC 1405 0.0185 0.98 70.3 yes View details
rpoC2 LSC 4041 0.0039 1.00 42.6 yes View details
psbZ-trnG-UCC LSC 745 0.0150 0.93 59.7 yes View details
trnT-UGU-trnL-UAA LSC 950 0.0243 0.93 78.6 yes View details
rrn16S IRb 1492 0.0000 1.00 28.3 no View details
rpl32-trnL-UAG SSC 1367 0.0114 0.99 63.7 yes View details
ccsA SSC 972 0.0019 1.00 46.9 yes View details
ccsA-ndhD SSC 265 0.0531 0.99 69.9 yes View details
ndhA SSC 2307 0.0048 1.00 61.4 yes View details
rrn16S IRa 1492 0.0070 1.00 39.6 yes View details
trnR-ACG-trnN-GUU IRb 686 0.0118 0.98 71.8 yes View details
ndhC-trnV-UAC LSC 560 0.0109 0.99 70.4 yes View details
trnK-UUU-rps16 LSC 885 0.0056 1.00 68.2 yes View details
trnN-GUU-trnR-ACG IRa 686 0.0076 0.99 67.6 yes View details
atpB-rbcL LSC 781 0.0045 1.00 66.4 yes View details
trnG-GCC-trnR-UCU LSC 286 0.0124 0.98 65.2 yes View details
petA-psbJ LSC 838 0.0021 1.00 64.3 yes View details
trnC-GCA-petN LSC 1029 0.0030 0.98 63.7 yes View details
rbcL-accD LSC 888 0.0078 0.97 63.1 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCCAT 238–398 1.000 90.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCCAT 252–412 1.000 90.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCCAT 251–411 1.000 90.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCCAT 253–413 1.000 90.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GCTATGTTATGGGCGAACGA CCTCTAGACCTAGCTGCCAT 302–462 1.000 90.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CAAAAAGGGCGGGTGTTTTT 878–1030 1.000 80.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA CAAAAAGGGCGGGTGTTTTT 879–1031 1.000 80.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGAGTCGCACTTAAAAGCC CAAAAAGGGCGGGTGTTTTT 881–1033 1.000 80.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA CAAAAAGGGCGGGTGTTTTT 876–1028 1.000 78.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC CAAAAAGGGCGGGTGTTTTT 875–1027 1.000 78.4
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 322–372 1.000 68.9
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 328–378 1.000 68.9
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 328–378 1.000 68.3
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTCTGTCCT 334–384 1.000 68.2
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 392–442 1.000 66.9
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1308–1735 1.000 85.1
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1274–1701 1.000 85.1
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TCCCTGTCATGTTCCTTGGA 1357–1784 1.000 84.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1323–1750 1.000 84.0
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1275–1702 1.000 83.9
rpoC2_p1 rpoC2 TTCTCCCGTTTTCGTCCATT CGCGTCTACTCAACAATGGA 240–243 1.000 85.4
rpoC2_p2 rpoC2 AATTCTCCCGTTTTCGTCCA CGCGTCTACTCAACAATGGA 242–245 1.000 85.3
rpoC2_p3 rpoC2 TGTTACTGCATAGATCGGGC CGCGTCTACTCAACAATGGA 267–270 1.000 84.6
rpoC2_p4 rpoC2 ATTCTCCCGTTTTCGTCCAT CGCGTCTACTCAACAATGGA 241–244 1.000 83.5
rpoC2_p5 rpoC2 TGTTACTGCATAGATCGGGC ACGCGTCTACTCAACAATGG 268–271 1.000 82.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1072–1102 1.000 80.7
trnC-GCA-petN_p2 trnC-GCA-petN TTTATCGTTTTGGCGGCATG AGCCCAAGCGAGACTTACTA 1125–1155 1.000 79.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 1123–1153 1.000 78.8
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1090–1120 1.000 78.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTATCGTTTTGGCGGCATG TCTTCCCCATACTACGAGGG 1176–1206 1.000 77.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Afzelia africana MZ274094.1 159730 View on NCBI ↗
Afzelia bella MZ274095.1 159884 View on NCBI ↗
Afzelia bipindensis MN540450.1 156066 View on NCBI ↗
Afzelia quanzensis NC_047329.1 159275 View on NCBI ↗
Afzelia xylocarpa NC_057262.1 159155 View on NCBI ↗