Markers + reference

Linaria

5 species · Plantaginaceae · Lamiales

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Species 5
Genome length 151–151 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 693 0.0084 1.00 59.5 yes View details
rpoC2 LSC 4158 0.0016 1.00 40.0 yes View details
rpoB-trnC-GCA LSC 1178 0.0056 1.00 46.3 yes View details
ndhC-trnV-UAC LSC 1070 0.0065 1.00 49.5 yes View details
psbE-petL LSC 837 0.0058 1.00 43.4 yes View details
ycf1 IRb 1056 0.0004 1.00 38.3 no View details
ndhF SSC 2229 0.0034 1.00 37.9 yes View details
ndhF-rpl32 SSC 573 0.0049 1.00 33.9 yes View details
rpl32-trnL-UAG SSC 652 0.0093 1.00 47.2 yes View details
ndhG-ndhI SSC 339 0.0183 1.00 54.4 yes View details
ycf1 SSC 5460 0.0038 1.00 44.3 yes View details
psbF-psbE LSC 14 0.0429 1.00 62.0 yes View details
ndhH SSC 1182 0.0032 1.00 60.8 yes View details
atpB LSC 1497 0.0025 1.00 60.6 yes View details
trnT-GGU-psbD LSC 1209 0.0018 0.99 59.1 yes View details
psbM-trnD-GUC LSC 697 0.0040 1.00 56.8 yes View details
rpoA LSC 1011 0.0042 1.00 54.1 yes View details
cemA LSC 690 0.0035 1.00 53.7 yes View details
trnS-GCU-trnG-UCC LSC 667 0.0051 1.00 52.9 yes View details
psbZ-trnG-GCC LSC 245 0.0057 0.98 52.4 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 815–829 1.000 66.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 814–828 1.000 66.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC GTGCTCAACCCACAGGAAC 900–914 1.000 66.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT GTGCTCAACCCACAGGAAC 899–913 1.000 66.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 829–843 1.000 66.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGGAATAAAACCGAAAGACCCT 780–782 1.000 59.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGGAATAAAACCGAAAGACCCT 779–781 1.000 59.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGGAATAAAACCGAAAGACCCT 834–836 1.000 58.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGGAATAAAACCGAAAGACCCTT 780–782 1.000 56.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AGGAATAAAACCGAAAGACCCT 782–784 1.000 56.7
rpoC2_p1 rpoC2 AGGAGATTTTGCCAAGTCAA GATCTGTTGCAGGAATGGGA 243 1.000 54.4
rpoC2_p2 rpoC2 AGGAGATTTTGCCAAGTCAA AGATCTGTTGCAGGAATGGG 244 1.000 54.3
rpoC2_p3 rpoC2 AGGAGATTTTGCCAAGTCAA CCCAGATCTGTTGCAGGAAT 247 1.000 54.3
rpoC2_p4 rpoC2 AGGAGATTTTGCCAAGTCAA TTTAGCAACGCCTTTCTCCC 265 1.000 54.0
rpoC2_p5 rpoC2 AGGAGATTTTGCCAAGTCAA TTTCTCCCCAGATCTGTTGC 253 1.000 53.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TGCTTCATTTGCATCTCCCA CCGGATTTGAACTGGGGAAA 1264–1268 1.000 78.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCATTTGCATCTCCCAGCA CCGGATTTGAACTGGGGAAA 1261–1265 1.000 78.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTGCATCTCCCAGCAT CCGGATTTGAACTGGGGAAA 1260–1264 1.000 76.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGCTTCATTTGCATCTCCCA AAAAGGATTTGCAGTCCCCC 1246–1250 1.000 76.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCATTTGCATCTCCCAGCA AAAAGGATTTGCAGTCCCCC 1243–1247 1.000 76.3
psbM-trnD-GUC_p1 psbM-trnD-GUC TGGCTGGCTGTTTTTACGTA TTCAATTGGTCAGAGCACCG 855–858 1.000 75.1
psbM-trnD-GUC_p2 psbM-trnD-GUC TTTGGCTGGCTGTTTTTACG TTCAATTGGTCAGAGCACCG 857–860 1.000 73.1
psbM-trnD-GUC_p3 psbM-trnD-GUC TTGGCTGGCTGTTTTTACGT TTCAATTGGTCAGAGCACCG 856–859 1.000 72.3
psbM-trnD-GUC_p4 psbM-trnD-GUC TGGCTGGCTGTTTTTACGTA GTTCAATTGGTCAGAGCACC 856–859 1.000 70.9
psbM-trnD-GUC_p5 psbM-trnD-GUC TGGCTGGCTGTTTTTACGTA TCAATTGGTCAGAGCACCG 854–857 1.000 69.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1358–1370 1.000 79.6
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1361–1373 1.000 79.4
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1348–1360 1.000 78.5
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1351–1363 1.000 78.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCTTCGTAACCAGTCATCC 1332–1344 1.000 78.0

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
Linaria angustissima PP336775.1 150621 View on NCBI ↗
Linaria buriatica NC_072593.1 150665 View on NCBI ↗
Linaria japonica NC_085416.1 150660 View on NCBI ↗
Linaria vulgaris NC_068047.1 150708 View on NCBI ↗
Linaria vulgaris subsp. vulgaris PP336776.1 150628 View on NCBI ↗