Markers + reference

Onobrychis

4 species · Fabaceae · Fabales

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Species 4
Genome length 122–123 kb
Candidate markers 76
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 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-Phe-tRNA-Val Genome 2791 0.2852 0.88 78.6 yes View details
tRNA-Val-tRNA-Val Genome 580 0.3055 0.89 81.5 yes View details
tRNA-Met-tRNA-Lys Genome 4721 0.2900 0.90 76.3 yes View details
tRNA-Lys-tRNA-His Genome 1507 0.2930 0.90 72.7 yes View details
tRNA-His-tRNA-Leu Genome 3818 0.2825 0.90 77.5 yes View details
tRNA-Leu-tRNA-Asn Genome 16056 0.2640 0.83 73.7 yes View details
23S ribosomal RNA Genome 2809 0.2603 0.76 66.1 yes View details
16S ribosomal RNA Genome 1492 0.3255 0.90 73.2 yes View details
tRNA-Val-tRNA-Met Genome 5843 0.2831 0.88 75.3 yes View details
tRNA-Leu-tRNA-Pro Genome 19210 0.2479 0.75 71.7 yes View details
tRNA-Glu-tRNA-Thr Genome 464 0.3486 0.39 68.3 yes View details
tRNA-Met-tRNA-Ser Genome 8239 0.2850 0.71 68.9 no View details
tRNA-Ser-tRNA-Thr Genome 1102 0.2996 0.93 82.9 yes View details
tRNA-Thr-tRNA-Leu Genome 1180 0.2696 0.88 81.6 yes View details
tRNA-Ser-tRNA-Gly Genome 709 0.2526 0.81 81.1 yes View details
tRNA-Gln-tRNA-Ser Genome 1305 0.2728 0.86 81.0 yes View details
tRNA-Lys-tRNA-Lys Genome 2468 0.2697 0.84 78.6 yes View details
tRNA-Met-tRNA-Leu Genome 6530 0.2332 1.00 77.2 yes View details
tRNA-Asp-tRNA-Tyr Genome 427 0.3028 0.44 73.3 yes View details
tRNA-Ala-tRNA-Ala Genome 803 0.2912 0.87 72.0 yes View details
tRNA-Ile-tRNA-Ile Genome 960 0.2965 0.87 71.9 yes View details
tRNA-Trp-tRNA-Gln Genome 8659 0.2462 0.76 71.9 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-Ser-tRNA-Thr_p1 tRNA-Ser-tRNA-Thr TTGAATTGATTGTGTGCGCC CTCAGAGGTTAGAGCATCGC 1332 0.500 58.6
tRNA-Ser-tRNA-Thr_p2 tRNA-Ser-tRNA-Thr TTGAATTGATTGTGTGCGCC GATGGTCATCGGTTCGACTC 1301 0.500 58.3
tRNA-Ser-tRNA-Thr_p3 tRNA-Ser-tRNA-Thr ATGAGGCTGCATTAATCGGG CTCAGAGGTTAGAGCATCGC 1809 0.500 58.3
tRNA-Ser-tRNA-Thr_p4 tRNA-Ser-tRNA-Thr CACTCGGTTTCTGGGCATAA CTCAGAGGTTAGAGCATCGC 1285 0.500 58.2
tRNA-Ser-tRNA-Thr_p5 tRNA-Ser-tRNA-Thr ATGAGGCTGCATTAATCGGG GATGGTCATCGGTTCGACTC 1778 0.500 58.1
tRNA-Thr-tRNA-Leu_p1 tRNA-Thr-tRNA-Leu CGAAGCCATACCCAATCGAA TCTACCTGCTGAGCTATCCC 2573–2598 0.500 59.6
tRNA-Thr-tRNA-Leu_p2 tRNA-Thr-tRNA-Leu CGAAGCCATACCCAATCGAA ACCAATTTCGCCATATCCCC 1878–1883 0.500 59.6
tRNA-Thr-tRNA-Leu_p3 tRNA-Thr-tRNA-Leu TTGACCCTTTCGCTTTTCCA TCTACCTGCTGAGCTATCCC 2502–2527 0.500 59.5
tRNA-Thr-tRNA-Leu_p4 tRNA-Thr-tRNA-Leu TTGACCCTTTCGCTTTTCCA ACCAATTTCGCCATATCCCC 1807–1812 0.500 59.5
tRNA-Thr-tRNA-Leu_p5 tRNA-Thr-tRNA-Leu AGCGCGATTGGTTTCTAAGT TCTACCTGCTGAGCTATCCC 2379–2404 0.500 59.3
tRNA-Phe-tRNA-Val_p1 tRNA-Phe-tRNA-Val GGGATAGCTCAGCAGGTAGA AGAAGGTCTACGGTTCGAGT 2890–2894 0.500 58.6
tRNA-Phe-tRNA-Val_p2 tRNA-Phe-tRNA-Val AGAATGGTCGGGATAGCTCA AGAAGGTCTACGGTTCGAGT 2899–2903 0.500 57.9
tRNA-Phe-tRNA-Val_p3 tRNA-Phe-tRNA-Val AGGACTGAAAATCCTCGTGC AGAAGGTCTACGGTTCGAGT 2866–2870 0.500 57.8
tRNA-Phe-tRNA-Val_p4 tRNA-Phe-tRNA-Val CAGGTAGAGCAGAGGACTGA AGAAGGTCTACGGTTCGAGT 2878–2882 0.500 57.5
tRNA-Phe-tRNA-Val_p5 tRNA-Phe-tRNA-Val GACTGAAAATCCTCGTGCCA AGAAGGTCTACGGTTCGAGT 2864–2868 0.500 57.1
tRNA-Val-tRNA-Val_p1 tRNA-Val-tRNA-Val GAAATTGTAACCACGCACCG TGCAGAGAAGGGTAGTGACA 1762–1767 0.500 59.8
tRNA-Val-tRNA-Val_p2 tRNA-Val-tRNA-Val GAAATTGTAACCACGCACCG CGAGCTAGGACACGAGTAGA 1641–1646 0.500 59.4
tRNA-Val-tRNA-Val_p3 tRNA-Val-tRNA-Val GCCCATAGGTTCGATTCCTG TGCAGAGAAGGGTAGTGACA 1743–1748 0.500 59.2
tRNA-Val-tRNA-Val_p4 tRNA-Val-tRNA-Val GAAATTGTAACCACGCACCG GCTTTCAGACGAGCTAGGAC 1650–1655 0.500 59.2
tRNA-Val-tRNA-Val_p5 tRNA-Val-tRNA-Val GAAATTGTAACCACGCACCG TTGAACCAATGACTCCTGCC 1478–1483 0.500 59.2
tRNA-Met-tRNA-Lys_p1 tRNA-Met-tRNA-Lys TGTCACTACCCTTCTCTGCA TCGCCAGGGAAATATGTTGG 437 0.500 59.5
tRNA-Met-tRNA-Lys_p2 tRNA-Met-tRNA-Lys TGTCACTACCCTTCTCTGCA GGTTCGCCAGGGAAATATGT 440 0.500 59.5
tRNA-Met-tRNA-Lys_p3 tRNA-Met-tRNA-Lys CATCGTTACCCATTGGTCGT TCGCCAGGGAAATATGTTGG 358 0.500 59.4
tRNA-Met-tRNA-Lys_p4 tRNA-Met-tRNA-Lys CATCGTTACCCATTGGTCGT GGTTCGCCAGGGAAATATGT 361 0.500 59.4
tRNA-Met-tRNA-Lys_p5 tRNA-Met-tRNA-Lys TGTCACTACCCTTCTCTGCA GAGGGTTAGCTGCAAAAGGT 706 0.500 59.2
tRNA-Lys-tRNA-Lys_p1 tRNA-Lys-tRNA-Lys TCAATGGTAGAGTACTCGGCT ACTCCCAAGCACAGGAATTC 2773–2774 0.500 50.3
tRNA-Lys-tRNA-Lys_p2 tRNA-Lys-tRNA-Lys TCAATGGTAGAGTACTCGGCT GACTCCCAAGCACAGGAATT 2774–2775 0.500 50.3
tRNA-Lys-tRNA-Lys_p3 tRNA-Lys-tRNA-Lys TCAATGGTAGAGTACTCGGCT ATATCTACTGGAGGGGCAGC 2989–2990 0.500 49.1
tRNA-Lys-tRNA-Lys_p4 tRNA-Lys-tRNA-Lys AGGGTTGCTAACTCAATGGT ACTCCCAAGCACAGGAATTC 2785–2786 0.500 48.2
tRNA-Lys-tRNA-Lys_p5 tRNA-Lys-tRNA-Lys AGGGTTGCTAACTCAATGGT GACTCCCAAGCACAGGAATT 2786–2787 0.500 48.2

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
Onobrychis arenaria PP328807.1 122095 View on NCBI ↗
Onobrychis gaubae LC647182.1 122688 View on NCBI ↗
Onobrychis montana subsp. montana PP328805.1 122461 View on NCBI ↗
Onobrychis viciifolia NC_053934.1 121932 View on NCBI ↗