Markers + reference

Linum

5 species · Linaceae · Malpighiales

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Species 5
Genome length 152–158 kb
Candidate markers 269
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
clpP1 LSC 2093 0.2183 0.62 72.8 yes View details
rpl23 IRb 282 0.1113 0.94 68.9 no View details
ycf2 IRb 6855 0.0978 0.94 76.6 yes View details
ndhF-rpl32 SSC 889 0.3620 0.90 78.9 yes View details
rps15-trnN-GUU SSC 6070 0.1541 0.93 78.1 yes View details
ycf2 IRa 6855 0.0522 0.81 72.1 no View details
rpl23 IRa 282 0.2738 0.96 68.3 yes View details
ndhC-trnS-ACU LSC 644 0.0885 0.98 85.0 yes View details
trnD-GUC-trnY-GUA LSC 473 0.1011 1.00 84.9 yes View details
accD LSC 1470 0.0834 0.99 84.3 yes View details
rpl16 LSC 1456 0.0596 0.97 84.2 yes View details
petD LSC 1346 0.0547 0.97 84.0 yes View details
rpl20-rps12 LSC 786 0.0541 1.00 83.8 yes View details
rpoB-trnC-GCA LSC 1122 0.0858 0.98 83.7 yes View details
trnF-GAA-ndhJ LSC 757 0.0862 0.96 83.3 yes View details
trnS-UGA-psbZ LSC 402 0.0682 0.97 83.2 yes View details
atpB-rbcL LSC 768 0.1010 0.93 82.8 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAAATATTGGATCGCCGCCT GGGAAACATTACGCACAAGC 2070 0.200 47.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GGGAAACATTACGCACAAGC 1864 0.200 47.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTGATAATAGATGCCGGGGC GGGAAACATTACGCACAAGC 1757 0.200 47.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGTTCTTGCATATCCCTGCC GGGAAACATTACGCACAAGC 1642 0.200 47.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG GGGAAACATTACGCACAAGC 1744 0.200 47.3
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 474–556 1.000 86.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 473–555 1.000 86.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 495–577 1.000 85.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 494–576 1.000 85.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 490–572 1.000 84.0
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC TGCAAAAACAGCCAATTGGA 451–500 1.000 83.6
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CTATCAACCACTCGGCCATC TGCAAAAACAGCCAATTGGA 440–489 1.000 83.0
trnS-UGA-psbZ_p3 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC TGCAAAAACAGCCAATTGGAA 451–500 1.000 81.4
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC AAACAGCCAATTGGAAAGCA 446–495 1.000 81.1
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC AACAGCCAATTGGAAAGCAA 445–494 1.000 81.1
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AATGCCGGAAAGCTGGATAG 879–910 0.800 83.8
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA CGTTCCCAATGTGCCTATGA 1121–1152 0.800 83.7
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA ATCTACGTTCCCAATGTGCC 1126–1157 0.400 62.7
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA GGGTCCATATCCTCCCATGA 1444 0.200 47.6
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AGGGTCCATATCCTCCCATG 1445 0.200 47.6
ndhC-trnS-ACU_p1 ndhC-trnS-ACU TCTCACTAACGAAGGAGCCA AGCCTGACAAAAAGTTCGGT 1876–2389 1.000 88.1
ndhC-trnS-ACU_p2 ndhC-trnS-ACU TCTCACTAACGAAGGAGCCA GCACAAGGGCTATAGCTCAG 2020–2538 1.000 87.5
ndhC-trnS-ACU_p3 ndhC-trnS-ACU TCTCACTAACGAAGGAGCCA ACAAGCACAAGGGCTATAGC 2024–2047 0.400 58.1
ndhC-trnS-ACU_p4 ndhC-trnS-ACU TTTAACCAAGCATCGCCCAT ACAAGCACAAGGGCTATAGC 1506–1527 0.400 58.1
ndhC-trnS-ACU_p5 ndhC-trnS-ACU TTAACCAAGCATCGCCCATT ACAAGCACAAGGGCTATAGC 1505 0.200 46.4
atpB-rbcL_p1 atpB-rbcL TGAATAGGGGATGTTGTGCG CGGTCTCTCCAACGCATAAA 1795–1953 0.600 73.8
atpB-rbcL_p2 atpB-rbcL GCCGACTGGAACACTTAGAG CCTGGAATCCAACACTTGCT 1099–1138 0.400 58.4
atpB-rbcL_p3 atpB-rbcL GCCGACTGGAACACTTAGAG CGGTCTCTCCAACGCATAAA 1706–1745 0.400 58.1
atpB-rbcL_p4 atpB-rbcL AGCTACAGCCCGAACTCTAT CGGTCTCTCCAACGCATAAA 1631 0.200 47.4
atpB-rbcL_p5 atpB-rbcL ATAGCTACAGCCCGAACTCT CGGTCTCTCCAACGCATAAA 1633 0.200 47.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Linum catharticum PP484609.1 152123 View on NCBI ↗
Linum grandiflorum NC_058845.1 158234 View on NCBI ↗
Linum narbonense NC_058855.1 157907 View on NCBI ↗
Linum tenuifolium PP484610.1 153439 View on NCBI ↗
Linum usitatissimum NC_036356.1 156721 View on NCBI ↗