Markers + reference

Trifolium

3 species · Fabaceae · Fabales

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Species 3
Genome length 126–128 kb
Candidate markers 76
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 76 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Thr-tRNA-Ser Genome 1153 0.3293 0.93 82.9 yes View details
tRNA-Ser-tRNA-Thr Genome 4065 0.3397 0.87 76.0 yes View details
tRNA-Asp-tRNA-Cys Genome 2161 0.3453 0.86 79.0 yes View details
tRNA-Cys-tRNA-Arg Genome 18464 0.3297 0.82 72.5 yes View details
tRNA-Gln-tRNA-Trp Genome 10128 0.3197 0.87 74.3 yes View details
23S ribosomal RNA Genome 2799 0.3492 0.84 77.0 yes View details
16S ribosomal RNA Genome 1493 0.3423 0.92 82.2 yes View details
tRNA-Leu-tRNA-Met Genome 6292 0.3131 0.91 75.6 yes View details
tRNA-Leu-tRNA-Thr Genome 1263 0.3039 0.93 82.8 yes View details
tRNA-Thr-tRNA-Glu Genome 773 0.3223 0.90 81.5 yes View details
tRNA-Ile-tRNA-Ile Genome 672 0.3101 0.88 81.0 yes View details
tRNA-Gly-tRNA-Ser Genome 696 0.3092 0.87 80.6 yes View details
tRNA-Ser-tRNA-Gln Genome 1497 0.3153 0.87 80.5 yes View details
tRNA-Leu-tRNA-Leu Genome 542 0.3130 0.88 79.8 yes View details
tRNA-Gly-tRNA-Gly Genome 683 0.2999 0.83 79.4 yes View details
tRNA-Lys-tRNA-His Genome 1812 0.3370 0.80 77.7 yes View details
tRNA-Asn-tRNA-Arg Genome 445 0.3017 0.88 77.7 yes View details
tRNA-Val-tRNA-Met Genome 176 0.3355 0.87 77.6 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
tRNA-Val-tRNA-Met_p1 tRNA-Val-tRNA-Met GTGTGTAAACGAGGTGCTCT TCCTGCCGTATGAAAGCAAT 262 0.333 48.8
tRNA-Val-tRNA-Met_p2 tRNA-Val-tRNA-Met CGTGTGTAAACGAGGTGCT TCCTGCCGTATGAAAGCAAT 263 0.333 41.1
tRNA-Val-tRNA-Met_p3 tRNA-Val-tRNA-Met CGTGTGTAAACGAGGTGCTC TCCTGCCGTATGAAAGCAAT 263 0.333 40.2
tRNA-Val-tRNA-Met_p4 tRNA-Val-tRNA-Met GTGTGTAAACGAGGTGCTCT TCCTGCCGTATGAAAGCAATA 262 0.333 39.7
tRNA-Val-tRNA-Met_p5 tRNA-Val-tRNA-Met TGTGTAAACGAGGTGCTCTAC TCCTGCCGTATGAAAGCAAT 261 0.333 39.6
tRNA-Lys-tRNA-His_p1 tRNA-Lys-tRNA-His GGGCATCCCATTAGTAAGCC CAATCCACTGCCTTGATCCA 2451 0.333 51.6
tRNA-Lys-tRNA-His_p2 tRNA-Lys-tRNA-His GGGCATCCCATTAGTAAGCC AATCCACTGCCTTGATCCAC 2450 0.333 51.5
tRNA-Lys-tRNA-His_p3 tRNA-Lys-tRNA-His GGGCATCCCATTAGTAAGCC ACAATCCACTGCCTTGATCC 2452 0.333 51.5
tRNA-Lys-tRNA-His_p4 tRNA-Lys-tRNA-His TGGTACGGAGTCAAATGCTG CAATCCACTGCCTTGATCCA 2576 0.333 51.5
tRNA-Lys-tRNA-His_p5 tRNA-Lys-tRNA-His GTGGTACGGAGTCAAATGCT CAATCCACTGCCTTGATCCA 2577 0.333 51.5
tRNA-Leu-tRNA-Leu_p1 tRNA-Leu-tRNA-Leu TTTGAACTGGTGACACGAGG GGGGATATGGCGAAATTGGT 816–833 1.000 91.5
tRNA-Leu-tRNA-Leu_p2 tRNA-Leu-tRNA-Leu TGAGCTATCCCGACCATTCT GGGGATATGGCGAAATTGGT 771–788 1.000 91.3
tRNA-Leu-tRNA-Leu_p3 tRNA-Leu-tRNA-Leu TACAAACGAATTGCCGGGAA GGGGATATGGCGAAATTGGT 841–858 1.000 91.1
tRNA-Leu-tRNA-Leu_p4 tRNA-Leu-tRNA-Leu TTTGAACTGGTGACACGAGG GGCGAAATTGGTAGACGCTA 808–825 1.000 91.0
tRNA-Leu-tRNA-Leu_p5 tRNA-Leu-tRNA-Leu ATACAAACGAATTGCCGGGA GGGGATATGGCGAAATTGGT 842–859 1.000 91.0
tRNA-Leu-tRNA-Thr_p1 tRNA-Leu-tRNA-Thr ACCAATTTCGCCATATCCCC CAGTTAGTCCGGGTAAAGCC 1692–1739 1.000 91.8
tRNA-Leu-tRNA-Thr_p2 tRNA-Leu-tRNA-Thr ACCAATTTCGCCATATCCCC CCAGTTAGTCCGGGTAAAGC 1693–1740 1.000 91.8
tRNA-Leu-tRNA-Thr_p3 tRNA-Leu-tRNA-Thr ACCAATTTCGCCATATCCCC CGAAGCCATACCCAATCGAA 1922–1978 1.000 91.5
tRNA-Leu-tRNA-Thr_p4 tRNA-Leu-tRNA-Thr ACCAATTTCGCCATATCCCC TTTTCCAGCGATACGAACGT 1838–1894 1.000 91.4
tRNA-Leu-tRNA-Thr_p5 tRNA-Leu-tRNA-Thr ACCAATTTCGCCATATCCCC TTGACCAGTTGACCCTTTGG 1915 0.333 52.8
tRNA-Thr-tRNA-Ser_p1 tRNA-Thr-tRNA-Ser TGTGTTATGAAAGCCCGCTT GAGGCTGCATTAATCGGGAA 1885 0.333 52.3
tRNA-Thr-tRNA-Ser_p2 tRNA-Thr-tRNA-Ser TTGTGTTATGAAAGCCCGCT GAGGCTGCATTAATCGGGAA 1886 0.333 52.3
tRNA-Thr-tRNA-Ser_p3 tRNA-Thr-tRNA-Ser CTCAGAGGTTAGAGCATCGC GAGGCTGCATTAATCGGGAA 1863 0.333 52.0
tRNA-Thr-tRNA-Ser_p4 tRNA-Thr-tRNA-Ser TGTGTTATGAAAGCCCGCTT CGGGAATACACGACAGAAGG 1871 0.333 51.9
tRNA-Thr-tRNA-Ser_p5 tRNA-Thr-tRNA-Ser TTGTGTTATGAAAGCCCGCT CGGGAATACACGACAGAAGG 1872 0.333 51.9
tRNA-Ser-tRNA-Thr_p1 tRNA-Ser-tRNA-Thr CGAGCACCTCCTAGCATTTT TTGCTACTCCTCTCCTCCAC 884 0.333 51.9
tRNA-Ser-tRNA-Thr_p2 tRNA-Ser-tRNA-Thr CGAGCACCTCCTAGCATTTT CTCCGCAAGAATCTGTCGAT 945 0.333 51.4
tRNA-Ser-tRNA-Thr_p3 tRNA-Ser-tRNA-Thr GATGGAACCTTCGAGGCTTT TTGCTACTCCTCTCCTCCAC 860 0.333 51.2
tRNA-Ser-tRNA-Thr_p4 tRNA-Ser-tRNA-Thr CGAGCACCTCCTAGCATTTT CACGCGGAAGGACTTATTCT 867 0.333 50.7
tRNA-Ser-tRNA-Thr_p5 tRNA-Ser-tRNA-Thr GATGGAACCTTCGAGGCTTT CTCCGCAAGAATCTGTCGAT 921 0.333 50.7

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
Trifolium alpinum PP328811.1 127983 View on NCBI ↗
Trifolium aureum subsp. aureum PP328812.1 126973 View on NCBI ↗
Trifolium badium PP328813.1 126247 View on NCBI ↗