Markers + reference

Libertia

13 species · Iridaceae · Asparagales

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Species 13
Genome length 153–154 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

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Ser-tRNA-Gly LSC 961 0.0092 0.99 60.4 yes View details
rpoB-tRNA-Cys LSC 1225 0.0166 0.99 76.9 yes View details
tRNA-Asp-tRNA-Tyr LSC 376 0.0094 1.00 43.8 yes View details
tRNA-Thr-tRNA-Leu LSC 866 0.0063 0.99 58.8 yes View details
petA-psbJ LSC 868 0.0157 1.00 68.9 yes View details
clpP LSC 2049 0.0031 1.00 50.2 yes View details
clpP-psbB LSC 437 0.0320 1.00 76.8 yes View details
ycf1 SSC 5388 0.0056 1.00 46.1 yes View details
ycf1-rps15 SSC 431 0.0175 0.96 63.1 yes View details
tRNA-Leu-rpl32 SSC 616 0.0115 0.99 61.1 yes View details
rpl32-ndhF SSC 962 0.0106 0.98 56.8 yes View details
ycf1 IRa 1044 0.0010 1.00 49.8 no View details
rps16-tRNA-Gln LSC 1229 0.0086 1.00 70.5 yes View details
tRNA-Glu-tRNA-Thr LSC 488 0.0108 1.00 68.0 yes View details
petN-psbM LSC 886 0.0054 1.00 65.3 yes View details
matK-tRNA-Lys LSC 797 0.0064 1.00 61.3 yes View details
tRNA-Thr-psbD LSC 1024 0.0048 0.99 60.5 yes View details
tRNA-Phe-ndhJ LSC 704 0.0054 1.00 60.5 yes View details
ndhC-tRNA-Val LSC 629 0.0078 1.00 59.2 yes View details
ndhA SSC 2176 0.0047 1.00 59.1 yes View details
psbE-petL LSC 953 0.0056 0.99 57.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-tRNA-Lys_p1 matK-tRNA-Lys ACGATCATGAGCAAGTGCAT AACGGTAGAGTACTCGGCTT 921–947 1.000 81.6
matK-tRNA-Lys_p2 matK-tRNA-Lys ACGATCATGAGCAAGTGCAT ACGGTAGAGTACTCGGCTTT 920–946 1.000 81.6
matK-tRNA-Lys_p3 matK-tRNA-Lys ACGATCATGAGCAAGTGCAT TTGGGGTTGCTAACTCAACG 937–963 1.000 79.7
matK-tRNA-Lys_p4 matK-tRNA-Lys ACCACGATCATGAGCAAGTG AACGGTAGAGTACTCGGCTT 924–950 0.923 76.4
matK-tRNA-Lys_p5 matK-tRNA-Lys ACCACGATCATGAGCAAGTG ACGGTAGAGTACTCGGCTTT 923–949 0.923 76.4
rps16-tRNA-Gln_p1 rps16-tRNA-Gln AAGTCGCACGTTGCTTTCTA CAAGTGGTAAGGCAATGGGT 1292–1350 1.000 85.1
rps16-tRNA-Gln_p2 rps16-tRNA-Gln TCATGTCCTTCAAGTCGCAC CAAGTGGTAAGGCAATGGGT 1303–1361 1.000 84.6
rps16-tRNA-Gln_p3 rps16-tRNA-Gln AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGTTACTC 1276–1334 1.000 82.0
rps16-tRNA-Gln_p4 rps16-tRNA-Gln TCATGTCCTTCAAGTCGCAC GGGTTTTGGTCCCGTTACTC 1287–1345 1.000 81.5
rps16-tRNA-Gln_p5 rps16-tRNA-Gln AAGTCGCACGTTGCTTTCTA TAAATCGAAATGGGGCGTGG 1313–1371 1.000 80.8
tRNA-Ser-tRNA-Gly_p1 tRNA-Ser-tRNA-Gly GAAGTGATCAGAAGGAGCGG AACCGAAAGACCCCTTAACT 1132–1169 1.000 71.3
tRNA-Ser-tRNA-Gly_p2 tRNA-Ser-tRNA-Gly AATCTGCCGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 1061–1098 1.000 70.1
tRNA-Ser-tRNA-Gly_p3 tRNA-Ser-tRNA-Gly CAATCTGCCGCTTTAGTCCA AACCGAAAGACCCCTTAACT 1062–1099 1.000 70.1
tRNA-Ser-tRNA-Gly_p4 tRNA-Ser-tRNA-Gly GAAGTGATCAGAAGGAGCGG AAACCGAAAGACCCCTTAACT 1133–1170 1.000 69.4
tRNA-Ser-tRNA-Gly_p5 tRNA-Ser-tRNA-Gly ATCAGAAGGAGCGGAGAGAG AACCGAAAGACCCCTTAACT 1126–1163 1.000 69.4
rpoB-tRNA-Cys_p1 rpoB-tRNA-Cys CGCCAAGCCCCTATTAATGA CCGGGGATAAAGGATTTGCA 1249–1386 1.000 86.0
rpoB-tRNA-Cys_p2 rpoB-tRNA-Cys CGCCAAGCCCCTATTAATGA ACCGGGGATAAAGGATTTGC 1250–1387 1.000 86.0
rpoB-tRNA-Cys_p3 rpoB-tRNA-Cys CGCCAAGCCCCTATTAATGA TAAAGGATTTGCAGTCCCCC 1242–1379 1.000 82.4
rpoB-tRNA-Cys_p4 rpoB-tRNA-Cys CGCCAAGCCCCTATTAATGA CCTTACCACTTGGCCATGTC 1221–1358 1.000 82.3
rpoB-tRNA-Cys_p5 rpoB-tRNA-Cys CCGCCAAGCCCCTATTAATG CCGGGGATAAAGGATTTGCA 1250–1387 1.000 82.1
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC ACGTAAAAACAGTCAGCCAA 925–960 1.000 65.9
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT ACGTAAAAACAGTCAGCCAA 924–959 1.000 65.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGCCAA 983–1018 1.000 65.5
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC ACGTAAAAACAGTCAGCCAA 923–958 1.000 65.5
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG ACGTAAAAACAGTCAGCCAA 920–955 1.000 65.2
tRNA-Asp-tRNA-Tyr_p1 tRNA-Asp-tRNA-Tyr GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 555–570 1.000 81.5
tRNA-Asp-tRNA-Tyr_p2 tRNA-Asp-tRNA-Tyr GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 522–537 1.000 79.2
tRNA-Asp-tRNA-Tyr_p3 tRNA-Asp-tRNA-Tyr GGATCCTAGTTCGGGACTGA GGGACGGACTGTAAATTCGT 521–536 1.000 79.0
tRNA-Asp-tRNA-Tyr_p4 tRNA-Asp-tRNA-Tyr CGGTGCTCTGACCAATTGAA AATTCTTCCTGGGTCGATGC 500–515 1.000 78.5
tRNA-Asp-tRNA-Tyr_p5 tRNA-Asp-tRNA-Tyr GGATCCTAGTTCGGGACTGA GGACTGTAAATTCGTTGGCG 516–531 1.000 77.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Libertia chilensis PV221543.1 153686 View on NCBI ↗
Libertia colombiana PV221540.1 153409 View on NCBI ↗
Libertia cranwelliae PV221548.1 153921 View on NCBI ↗
Libertia edgariae PV221550.1 153877 View on NCBI ↗
Libertia flaccidifolia PV221547.1 153897 View on NCBI ↗
Libertia grandiflora PV221546.1 153778 View on NCBI ↗
Libertia ixioides PV221551.1 153946 View on NCBI ↗
Libertia micrantha PV221552.1 153698 View on NCBI ↗
Libertia mooreae PV221539.1 153692 View on NCBI ↗
Libertia paniculata PV221545.1 153858 View on NCBI ↗
Libertia peregrinans PV221549.1 153890 View on NCBI ↗
Libertia sessiliflora PV221542.1 153614 View on NCBI ↗
Libertia tricocca PV221541.1 153768 View on NCBI ↗