Markers + reference

Kotschya

2 species · Fabaceae · Fabales

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Species 2
Genome length 157–157 kb
Candidate markers 265
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 572 0.0190 0.92 60.0 yes View details
trnF-GAA-trnL-UAA LSC 552 0.0173 0.94 61.7 yes View details
trnG-GCC-psbZ LSC 839 0.0159 0.98 61.9 yes View details
psbM-petN LSC 995 0.0154 0.98 69.7 yes View details
trnG-UCC-trnS-GCU LSC 580 0.0261 0.99 74.1 yes View details
psbK-trnQ-UUG LSC 399 0.0150 1.00 54.1 yes View details
rps11-rpl36 LSC 447 0.0248 0.99 57.4 yes View details
ycf1 IRb 475 0.0021 1.00 43.6 no View details
rpl32-trnL-UAG SSC 976 0.0219 0.98 62.1 yes View details
ndhG SSC 531 0.0075 1.00 48.7 yes View details
ycf1 SSC 5286 0.0112 1.00 47.1 yes View details
rpoB-rpoC1 LSC 26 0.0385 1.00 74.6 yes View details
rps8-rpl14 LSC 434 0.0211 0.98 68.9 yes View details
trnP-UGG-psaJ LSC 756 0.0112 0.95 68.1 yes View details
petA-psbJ LSC 892 0.0125 0.99 67.1 yes View details
atpH-atpF LSC 488 0.0166 0.99 66.9 yes View details
trnH-GUG-psbA LSC 229 0.0349 1.00 66.4 yes View details
rpl33-rps18 LSC 258 0.0233 1.00 65.9 yes View details
ndhG-ndhI SSC 517 0.0135 1.00 64.8 yes View details
ndhD-psaC SSC 133 0.0301 1.00 64.0 yes View details
matK-trnK-UUU LSC 813 0.0086 1.00 63.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTCGAGGCTCCTTCTCTA 279 1.000 80.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAGTCGAGGCTCCTTCTCTA 293 1.000 80.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAGTCGAGGCTCCTTCTCTA 292 1.000 80.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAGTCGAGGCTCCTTCTCTA 294 1.000 80.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCAGT 295 1.000 80.6
psbA-trnK-UUU_p1 psbA-trnK-UUU TCGCGTCTCTCTAAAATTGCA CACGGTTTGGGGAGAGATTT 656–701 1.000 75.2
psbA-trnK-UUU_p2 psbA-trnK-UUU TCGCGTCTCTCTAAAATTGCA AAAATGCAAGCACGGTTTGG 666–711 1.000 73.4
psbA-trnK-UUU_p3 psbA-trnK-UUU CGCGTCTCTCTAAAATTGCAG CACGGTTTGGGGAGAGATTT 655–700 1.000 73.2
psbA-trnK-UUU_p4 psbA-trnK-UUU TCGCGTCTCTCTAAAATTGCA TGAAAAATGCAAGCACGGTT 669–714 1.000 72.0
psbA-trnK-UUU_p5 psbA-trnK-UUU CGCGTCTCTCTAAAATTGCA CACGGTTTGGGGAGAGATTT 655–700 1.000 72.0
matK-trnK-UUU_p1 matK-trnK-UUU GGAAGTTCTGTTGGCGAGAA CGGGACAAAGGGATGTTCAT 980–988 1.000 78.6
matK-trnK-UUU_p2 matK-trnK-UUU GGAAGTTCTGTTGGCGAGAA GGGGTTGCTAACTCAATGGT 906–914 1.000 77.9
matK-trnK-UUU_p3 matK-trnK-UUU ATGACCATAGGCGAGTCCAT CGGGACAAAGGGATGTTCAT 1030–1038 1.000 77.3
matK-trnK-UUU_p4 matK-trnK-UUU ATGACCATAGGCGAGTCCAT GGGGTTGCTAACTCAATGGT 956–964 1.000 76.6
matK-trnK-UUU_p5 matK-trnK-UUU TGACCATAGGCGAGTCCATA CGGGACAAAGGGATGTTCAT 1029–1037 1.000 76.5
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TCTACCAGCTGAGCTATCCC AATCGTGAGGGTTCAAGTCC 576–606 1.000 81.4
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TTTGAACTGGTGACACGAGG AATCGTGAGGGTTCAAGTCC 612–642 1.000 80.9
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA GTGCCAGGAACCAGATTTGA AATCGTGAGGGTTCAAGTCC 627–657 1.000 80.5
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA TCAGTCCTCTGCTCTACCAG AATCGTGAGGGTTCAAGTCC 588–618 1.000 80.3
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA CATGTGCCAGGAACCAGATT AATCGTGAGGGTTCAAGTCC 630–660 1.000 79.9
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGATGGTTGGTCG 993–1043 1.000 81.0
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGCTTCTCCTGATGGTTGG 996–1046 1.000 79.5
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCCTGATGGTTGGTCGAGTA 989–1039 1.000 79.4
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GCTTCTCCTGATGGTTGGTC 994–1044 1.000 79.1
trnG-GCC-psbZ_p5 trnG-GCC-psbZ AAGGGAGGAGGAATACAGGC CTTCTCCTGATGGTTGGTCG 1034–1084 1.000 78.4
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TCTTGCTTGGGCTGCTTTAA 1129–1150 1.000 71.3
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT AGTAAGTCTTGCTTGGGCTG 1135–1156 1.000 69.8
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTC TCTTGCTTGGGCTGCTTTAA 1129–1150 1.000 67.1
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC AGTAAGTCTTGCTTGGGCTG 1135–1156 1.000 65.6
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT TTGCTTGGGCTGCTTTAATG 1127–1148 1.000 65.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Kotschya aeschynomenoides NC_057459.1 157360 View on NCBI ↗
Kotschya parvifolia PV870808.1 156626 View on NCBI ↗