Markers + reference

Kaempferia

4 species · Zingiberaceae · Zingiberales

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Species 4
Genome length 163–164 kb
Candidate markers 270
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1453 0.0160 0.90 64.3 yes View details
trnQ-UUG-psbK LSC 343 0.0136 0.99 57.5 yes View details
trnS-GCU-trnR-UCU LSC 1640 0.0158 0.98 64.9 yes View details
atpH-atpI LSC 1204 0.0143 0.97 58.6 yes View details
petN-psbM LSC 1280 0.0145 0.99 59.9 yes View details
trnT-UGU-trnL-UAA LSC 1116 0.0231 0.94 63.4 yes View details
ndhC-trnV-UAC LSC 1525 0.0129 0.99 59.3 yes View details
ndhF SSC 2229 0.0055 0.99 47.0 yes View details
ndhF-rpl32 SSC 779 0.0283 0.88 64.2 yes View details
psaC-ndhE SSC 717 0.0449 0.96 81.1 yes View details
trnH-GUG-rpl2 IRb 46 0.0543 1.00 79.8 yes View details
rpl2-trnH-GUG IRa 46 0.0543 1.00 79.8 yes View details
psbT-psbN LSC 64 0.0833 1.00 78.1 yes View details
psbC-trnS-UGA LSC 149 0.0302 0.99 73.2 yes View details
ycf1-ndhF SSC 19 0.3684 1.00 72.6 yes View details
trnfM-CAU-rps14 LSC 157 0.0372 1.00 69.5 yes View details
trnE-UUC-trnT-GGU LSC 840 0.0117 1.00 65.8 yes View details
rpl22-rps19 IRb 250 0.0290 0.98 63.6 yes View details
matK-trnK-UUU LSC 827 0.0073 0.99 61.0 yes View details
trnD-GUC-trnY-GUA LSC 436 0.0149 1.00 61.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA TGAAGGGTTGGGTTGCTAAC 929–951 0.750 69.1
matK-trnK-UUU_p2 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA TTTTGAAGGGTTGGGTTGCT 932–954 0.750 68.2
matK-trnK-UUU_p3 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA AACGGTAGAGTACTCGGCTT 907–929 0.750 67.9
matK-trnK-UUU_p4 matK-trnK-UUU AGAAACTGTTGTTGCCGAGA ACGGTAGAGTACTCGGCTTT 906–928 0.750 67.9
matK-trnK-UUU_p5 matK-trnK-UUU AACTGTTGTTGCCGAGATCT TGAAGGGTTGGGTTGCTAAC 926–948 0.750 67.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 839–1545 1.000 85.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 837–1543 1.000 85.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 845–1551 1.000 85.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 821–1527 1.000 84.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 843–1549 1.000 84.5
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG ACTGTTCGAATAAAGGACAGA 458–467 1.000 48.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG AACTGTTCGAATAAAGGACAGA 459–468 1.000 46.7
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG ACTGTTCGAATAAAGGACAGAA 458–467 1.000 46.7
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA ACTGTTCGAATAAAGGACAGA 456–465 1.000 46.5
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AAGGATTCGAACCTCCGAGT ACTGTTCGAATAAAGGACAGA 457–466 1.000 46.4
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1693–1795 1.000 68.3
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1692–1794 1.000 68.3
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU AGTATCAAGCGGGTCGAGTA AGAAGACCTCTGTCCTATCCA 1777–1879 1.000 67.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1699–1801 1.000 67.6
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1698–1800 1.000 67.6
atpH-atpI_p1 atpH-atpI CTTCCGGTTGTCTCGCAATA TCACGTCCGTCGCATATTTT 1654–2075 1.000 85.4
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TCACGTCCGTCGCATATTTT 1553–1974 1.000 85.2
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT TCACGTCCGTCGCATATTTT 1636–2057 1.000 85.0
atpH-atpI_p4 atpH-atpI CTTCCGGTTGTCTCGCAATA ACATTCAACCAACCCCCATC 1591–2012 1.000 84.9
atpH-atpI_p5 atpH-atpI AAGTGCTAATGCCACAACCA TCACGTCCGTCGCATATTTT 1743–2164 0.750 74.7
petN-psbM_p1 petN-psbM TATCCAGACTCACGAGGGTC AGGGAAGACGATAGGGTTGG 2117–2185 1.000 81.1
petN-psbM_p2 petN-psbM AGACTCACGAGGGTCTTTGA AGGGAAGACGATAGGGTTGG 2112–2180 0.750 70.2
petN-psbM_p3 petN-psbM CAGACTCACGAGGGTCTTTG AGGGAAGACGATAGGGTTGG 2113–2181 0.750 69.7
petN-psbM_p4 petN-psbM AGACTCACGAGGGTCTTTGA CCAGTTCCAGTCCCAATTGA 2351–2419 0.750 69.5
petN-psbM_p5 petN-psbM AGACTCACGAGGGTCTTTGA TCCAGTTCCAGTCCCAATTG 2352–2420 0.750 69.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Kaempferia elegans NC_040852.1 163555 View on NCBI ↗
Kaempferia galanga NC_040851.1 163811 View on NCBI ↗
Kaempferia parviflora NC_085808.1 163075 View on NCBI ↗
Kaempferia rotunda MT473710.1 162630 View on NCBI ↗