Markers + reference

Salvinia

2 species · Salviniaceae · Salviniales

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Species 2
Genome length 150–151 kb
Candidate markers 91
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 91 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Cys-tRNA-Gly LSC 355 0.1590 0.92 79.8 yes View details
tRNA-Ser-tRNA-Thr LSC 4596 0.0689 0.91 72.6 yes View details
tRNA-Asn-tRNA-Pro SSC 4334 0.1091 0.99 80.4 yes View details
tRNA-Leu-tRNA-Asn SSC 20523 0.1053 0.97 80.8 yes View details
tRNA-Arg-tRNA-Gln LSC 8703 0.0854 0.98 74.7 no View details
tRNA-Glu-tRNA-Cys LSC 1562 0.1237 0.93 86.2 yes View details
tRNA-Ile-tRNA-Arg IRb 786 0.0687 0.93 84.1 yes View details
tRNA-Pro-tRNA-Leu SSC 217 0.1561 0.94 83.1 yes View details
tRNA-Gly-tRNA-Gly LSC 839 0.0846 0.97 82.9 yes View details
tRNA-Ser-tRNA-Gly LSC 824 0.0783 0.98 81.0 yes View details
tRNA-Asp-tRNA-Tyr LSC 116 0.1961 0.88 81.0 yes View details
tRNA-Ser-tRNA-Leu LSC 1753 0.0906 0.98 79.7 yes View details
tRNA-Gly-tRNA-Arg LSC 144 0.2000 0.87 78.9 yes View details
tRNA-Phe-tRNA-Val LSC 2371 0.0655 0.96 78.4 yes View details
tRNA-Leu-tRNA-Phe LSC 348 0.1579 0.93 78.2 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-Ser-tRNA-Gly_p1 tRNA-Ser-tRNA-Gly ATTAGCAATCCGACGCGTTA TACCACTAAACCATACCCGC 869–884 1.000 77.9
tRNA-Ser-tRNA-Gly_p2 tRNA-Ser-tRNA-Gly TTAGACCTCTCGGCCATCTC TACCACTAAACCATACCCGC 852–867 1.000 77.3
tRNA-Ser-tRNA-Gly_p3 tRNA-Ser-tRNA-Gly TTAGCAATCCGACGCGTTAG TACCACTAAACCATACCCGC 868–883 1.000 76.0
tRNA-Ser-tRNA-Gly_p4 tRNA-Ser-tRNA-Gly ATTAGCAATCCGACGCGTTA TTACCACTAAACCATACCCGC 870–885 1.000 75.7
tRNA-Ser-tRNA-Gly_p5 tRNA-Ser-tRNA-Gly TTAGACCTCTCGGCCATCTC TTACCACTAAACCATACCCGC 853–868 1.000 75.1
tRNA-Gly-tRNA-Gly_p1 tRNA-Gly-tRNA-Gly TTACTTTGTGGCGGGTATGG CCCGCATCATTAGCTTGGAA 900–924 1.000 84.6
tRNA-Gly-tRNA-Gly_p2 tRNA-Gly-tRNA-Gly TTGTGGCGGGTATGGTTTAG CCCGCATCATTAGCTTGGAA 895–919 1.000 84.6
tRNA-Gly-tRNA-Gly_p3 tRNA-Gly-tRNA-Gly TTACTTTGTGGCGGGTATGG ATCGAACCCGCATCATTAGC 906–930 1.000 83.2
tRNA-Gly-tRNA-Gly_p4 tRNA-Gly-tRNA-Gly TTGTGGCGGGTATGGTTTAG ATCGAACCCGCATCATTAGC 901–925 1.000 83.2
tRNA-Gly-tRNA-Gly_p5 tRNA-Gly-tRNA-Gly TTGTGGCGGGTATGGTTTAG AACCCGCATCATTAGCTTGG 897–921 1.000 82.3
tRNA-Gly-tRNA-Arg_p1 tRNA-Gly-tRNA-Arg ACCCTTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 230–233 1.000 75.3
tRNA-Gly-tRNA-Arg_p2 tRNA-Gly-tRNA-Arg ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTCTGTCCT 236–239 1.000 74.7
tRNA-Gly-tRNA-Arg_p3 tRNA-Gly-tRNA-Arg TTCCAAGCTAATGATGCGGG AGAAGACCTCTGTCCTATCCA 220–223 1.000 73.0
tRNA-Gly-tRNA-Arg_p4 tRNA-Gly-tRNA-Arg TTCCAAGCTAATGATGCGGG AGGTTTAGAAGACCTCTGTCCT 226–229 1.000 72.4
tRNA-Gly-tRNA-Arg_p5 tRNA-Gly-tRNA-Arg GCTAATGATGCGGGTTCGAT AGAAGACCTCTGTCCTATCCA 214–217 1.000 71.7
tRNA-Asp-tRNA-Tyr_p1 tRNA-Asp-tRNA-Tyr TCAATTGGTTAGAGCACCGC CTCGAGTGGTTAATGGGGAC 238–252 1.000 83.6
tRNA-Asp-tRNA-Tyr_p2 tRNA-Asp-tRNA-Tyr TCAATTGGTTAGAGCACCGC ATGCTCGAGTGGTTAATGGG 241–255 1.000 83.4
tRNA-Asp-tRNA-Tyr_p3 tRNA-Asp-tRNA-Tyr GGTTCGAGACCCGTCAATC CTCGAGTGGTTAATGGGGAC 197–211 1.000 81.0
tRNA-Asp-tRNA-Tyr_p4 tRNA-Asp-tRNA-Tyr GTTCGAGACCCGTCAATCC CTCGAGTGGTTAATGGGGAC 196–210 1.000 81.0
tRNA-Asp-tRNA-Tyr_p5 tRNA-Asp-tRNA-Tyr GTTCGAGACCCGTCAATCC ATGCTCGAGTGGTTAATGGG 199–213 1.000 80.7
tRNA-Glu-tRNA-Cys_p1 tRNA-Glu-tRNA-Cys TTGTCCTAGGCCTCTAGACG CATCCCCCAGTTCGAATCTG 1541–1620 1.000 91.2
tRNA-Glu-tRNA-Cys_p2 tRNA-Glu-tRNA-Cys TTGTCCTAGGCCTCTAGACG TCATCCCCCAGTTCGAATCT 1542–1621 1.000 90.6
tRNA-Glu-tRNA-Cys_p3 tRNA-Glu-tRNA-Cys TTGTCCTAGGCCTCTAGACG TTGCAAATCCTTCATCCCCC 1553–1632 1.000 90.5
tRNA-Glu-tRNA-Cys_p4 tRNA-Glu-tRNA-Cys AGAGAGTTGTCCTAGGCCTC CATCCCCCAGTTCGAATCTG 1547–1626 1.000 90.4
tRNA-Glu-tRNA-Cys_p5 tRNA-Glu-tRNA-Cys GAGAGTTGTCCTAGGCCTCT CATCCCCCAGTTCGAATCTG 1546–1625 1.000 90.4
tRNA-Cys-tRNA-Gly_p1 tRNA-Cys-tRNA-Gly CAGATTCGAACTGGGGGATG GTTCGATTCCCGCTATCCG 430–438 1.000 82.2
tRNA-Cys-tRNA-Gly_p2 tRNA-Cys-tRNA-Gly CAGATTCGAACTGGGGGATG GGGTTCGATTCCCGCTATC 432–440 1.000 82.0
tRNA-Cys-tRNA-Gly_p3 tRNA-Cys-tRNA-Gly CAGATTCGAACTGGGGGATG GGTTCGATTCCCGCTATCC 431–439 1.000 82.0
tRNA-Cys-tRNA-Gly_p4 tRNA-Cys-tRNA-Gly AGATTCGAACTGGGGGATGA GTTCGATTCCCGCTATCCG 429–437 1.000 81.5
tRNA-Cys-tRNA-Gly_p5 tRNA-Cys-tRNA-Gly GGGGGATGAAGGATTTGCAA GTTCGATTCCCGCTATCCG 418–426 1.000 81.4

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
Salvinia cucullata MF177095.1 150958 View on NCBI ↗
Salvinia molesta PQ616050.1 149624 View on NCBI ↗