Markers + reference

Khaya

5 species · Meliaceae · Sapindales

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Species 5
Genome length 160–161 kb
Candidate markers 260
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 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 867 0.0037 1.00 54.2 yes View details
trnS-trnG LSC 769 0.0047 1.00 50.1 yes View details
rpoC1 LSC 2806 0.0031 1.00 53.0 yes View details
psbZ-trnG LSC 581 0.0072 1.00 69.5 yes View details
ycf3 LSC 2043 0.0035 1.00 46.0 yes View details
ndhC-trnV LSC 903 0.0040 1.00 54.3 yes View details
petA-psbJ LSC 1061 0.0041 1.00 55.1 yes View details
rpl22 LSC 474 0.0127 1.00 46.1 yes View details
ndhF-rpl32 SSC 1007 0.0016 1.00 61.4 yes View details
rpl32-trnL SSC 1095 0.0031 1.00 39.5 yes View details
rpl16 LSC 1328 0.0012 1.00 65.6 yes View details
ycf4-cemA LSC 915 0.0015 1.00 63.6 yes View details
psbE-petL LSC 1273 0.0020 1.00 60.5 yes View details
petN-psbM LSC 1116 0.0029 1.00 59.2 yes View details
clpP1 LSC 2112 0.0014 1.00 59.1 yes View details
rpoC2 LSC 4194 0.0008 1.00 54.4 yes View details
trnE-trnT LSC 808 0.0025 1.00 53.1 yes View details
trnT-psbD LSC 1280 0.0020 1.00 52.8 yes View details
rps3 LSC 660 0.0021 1.00 52.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 AGCCGTACTTAAAAGCCGAG AGGTAGGGGTTTTTACAGAACT 943–964 1.000 55.5
trnK-rps16_p2 trnK-rps16 AAAGCCGAGTACTCTACCGT AGGTAGGGGTTTTTACAGAACT 932–953 1.000 54.3
trnK-rps16_p3 trnK-rps16 AAGCCGAGTACTCTACCGTT AGGTAGGGGTTTTTACAGAACT 931–952 1.000 54.3
trnK-rps16_p4 trnK-rps16 GCCGTACTTAAAAGCCGAGT AGGTAGGGGTTTTTACAGAACT 942–963 1.000 53.3
trnK-rps16_p5 trnK-rps16 AGCCGTACTTAAAAGCCGAG AGGTAGGGGTTTTTACAGAACTT 943–964 1.000 53.1
trnS-trnG_p1 trnS-trnG TAAGCCACTCAGCCATCTCT AACTGAAGGACCCCTTAACT 657–863 1.000 65.0
trnS-trnG_p2 trnS-trnG ACGGAAAGAGAGGGATTCGA AACTGAAGGACCCCTTAACT 724–930 1.000 64.8
trnS-trnG_p3 trnS-trnG AAGATACCAAGCCATCGACG AACTGAAGGACCCCTTAACT 747–953 1.000 64.2
trnS-trnG_p4 trnS-trnG TAAGCCACTCAGCCATCTCT AAACTGAAGGACCCCTTAACT 658–864 1.000 63.5
trnS-trnG_p5 trnS-trnG ACGGAAAGAGAGGGATTCGA AAACTGAAGGACCCCTTAACT 725–931 1.000 63.2
rpoC2_p1 rpoC2 TACTTTTGGAAGACCCTGCG TCTTGGGCAGCTTATTTGTGA 244 1.000 70.3
rpoC2_p2 rpoC2 TTTTGGAAGACCCTGCGTTA TCTTGGGCAGCTTATTTGTGA 241 1.000 66.6
rpoC2_p3 rpoC2 CTTTTGGAAGACCCTGCGTT TCTTGGGCAGCTTATTTGTGA 242 1.000 66.3
rpoC2_p4 rpoC2 TACTTTTGGAAGACCCTGCG CTTGGGCAGCTTATTTGTGA 243 1.000 66.0
rpoC2_p5 rpoC2 TACTTTTGGAAGACCCTGCG TCTTGGGCAGCTTATTTGTG 244 1.000 66.0
rpoC1_p1 rpoC1 CTTGAACCGGAAAGACCCAA TTGCTCGTTCGAGAACTACG 2942–2995 1.000 81.4
rpoC1_p2 rpoC1 TTGAACCGGAAAGACCCAAA TTGCTCGTTCGAGAACTACG 2941–2994 1.000 78.1
rpoC1_p3 rpoC1 CTTGAACCGGAAAGACCCAA GCTCGTTCGAGAACTACGAT 2940–2993 1.000 78.1
rpoC1_p4 rpoC1 ACCCAAATTCACACCACACC TTGCTCGTTCGAGAACTACG 2928–2981 1.000 76.9
rpoC1_p5 rpoC1 ACCGGAAAGACCCAAATTCA TTGCTCGTTCGAGAACTACG 2937–2990 1.000 76.3
petN-psbM_p1 petN-psbM GCCGCCTTAATGGTAGTCTT TGCTACTGCACTGTTCATTCT 1207–1270 1.000 70.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1163–1226 1.000 70.5
petN-psbM_p3 petN-psbM GCCGCCTTAATGGTAGTCTT ACGGTCAGTCAAAGTGATTCA 1149–1212 1.000 70.2
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT ACGGTCAGTCAAAGTGATTCA 1105–1168 1.000 70.0
petN-psbM_p5 petN-psbM GCCGCCTTAATGGTAGTCTT TGCTACTGCACTGTTCATTC 1207–1270 1.000 66.5
trnE-trnT_p1 trnE-trnT TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 949 1.000 79.1
trnE-trnT_p2 trnE-trnT TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 928 1.000 78.6
trnE-trnT_p3 trnE-trnT TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 925 1.000 78.5
trnE-trnT_p4 trnE-trnT GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 911 1.000 78.3
trnE-trnT_p5 trnE-trnT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 890 1.000 78.1

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
Khaya anthotheca MZ274122.1 159841 View on NCBI ↗
Khaya grandifoliola MZ274123.1 159794 View on NCBI ↗
Khaya ivorensis MZ274124.1 159750 View on NCBI ↗
Khaya madagascariensis NC_043863.1 160843 View on NCBI ↗
Khaya senegalensis NC_037362.1 159787 View on NCBI ↗