Markers + reference

Lancea

2 species · Phrymaceae · Lamiales

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Species 2
Genome length 154–154 kb
Candidate markers 240
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 240 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCT-trnR-TCT LSC 1717 0.0093 1.00 56.3 yes View details
rps4-trnF-GAA LSC 1900 0.0304 0.99 74.1 yes View details
rpl20-rps12 LSC 806 0.0211 1.00 71.1 yes View details
petB LSC 1370 0.0212 1.00 70.9 yes View details
rpl2 IRb 1493 0.0081 0.99 52.0 yes View details
rps12-trnV-GAC IRb 1653 0.0087 0.98 65.7 yes View details
trnV-GAC-rps7 IRa 2500 0.0057 0.98 61.5 yes View details
rpl2 IRa 1493 0.0081 0.99 52.0 no View details
rps2-rpoC2 LSC 232 0.0390 1.00 75.3 yes View details
matK-rps16 LSC 1021 0.0127 1.00 66.2 yes View details
rpl36-infA LSC 95 0.0211 1.00 64.6 yes View details
ycf4-cemA LSC 907 0.0034 0.97 64.0 yes View details
petD LSC 1228 0.0000 0.95 63.6 yes View details
rpl16 LSC 1304 0.0054 0.99 62.7 yes View details
psbI-trnS-GCT LSC 118 0.0169 1.00 62.2 yes View details
psbA-matK LSC 531 0.0000 0.95 61.9 yes View details
ycf3 LSC 1955 0.0026 0.98 61.3 yes View details
psbZ-trnG-GCC LSC 303 0.0133 0.99 60.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-matK_p1 psbA-matK AAGACGGTTTTCGGTGCTAG CCCAAAAGCCTCTTCCACTT 683–718 1.000 82.3
psbA-matK_p2 psbA-matK AAGACGGTTTTCGGTGCTAG TTCCCAAAAGCCTCTTCCAC 685–720 1.000 82.3
psbA-matK_p3 psbA-matK AAGACGGTTTTCGGTGCTAG TTGACCTTCCCAAAAGCCTC 691–726 1.000 82.3
psbA-matK_p4 psbA-matK AAAGACGGTTTTCGGTGCTA CCCAAAAGCCTCTTCCACTT 684–719 1.000 82.0
psbA-matK_p5 psbA-matK TAAAGACGGTTTTCGGTGCT CCCAAAAGCCTCTTCCACTT 685–720 1.000 82.0
matK-rps16_p1 matK-rps16 CCACGATCATGAGCAAATGC GTGCTCAACCCACAGGAAC 1216–1217 1.000 66.6
matK-rps16_p2 matK-rps16 ACAACCACGATCATGAGCAA GTGCTCAACCCACAGGAAC 1220–1221 1.000 66.1
matK-rps16_p3 matK-rps16 CCACGATCATGAGCAAATGC TGCTCAACCCACAGGAACT 1215–1216 1.000 65.8
matK-rps16_p4 matK-rps16 ACAACCACGATCATGAGCAA TGCTCAACCCACAGGAACT 1219–1220 1.000 65.3
matK-rps16_p5 matK-rps16 CCACGATCATGAGCAAATGC TCCTTGAAAAAGGTGCTCAAC 1228–1229 1.000 63.4
psbI-trnS-GCT_p1 psbI-trnS-GCT ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 231 1.000 80.1
psbI-trnS-GCT_p2 psbI-trnS-GCT TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 232 1.000 80.1
psbI-trnS-GCT_p3 psbI-trnS-GCT ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 232 1.000 80.1
psbI-trnS-GCT_p4 psbI-trnS-GCT TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 233 1.000 80.1
psbI-trnS-GCT_p5 psbI-trnS-GCT ATCTAATGATCCGGGGCGTA ATTGGGAGAGATGGCTGAGT 250 1.000 79.2
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1788–1789 1.000 64.3
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1787–1788 1.000 64.3
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1794–1795 1.000 63.6
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1793–1794 1.000 63.6
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1842–1843 1.000 63.1
rps2-rpoC2_p1 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TTCGATGGGGAAATGAGAGA 394–395 1.000 62.9
rps2-rpoC2_p2 rps2-rpoC2 AAATGAACTCCTGCCTCCAG TTCGATGGGGAAATGAGAGA 407–408 1.000 61.4
rps2-rpoC2_p3 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TCGATGGGGAAATGAGAGAT 393–394 1.000 61.0
rps2-rpoC2_p4 rps2-rpoC2 CCATGGCCAAAATGAACTCC TTCGATGGGGAAATGAGAGA 416–417 1.000 60.0
rps2-rpoC2_p5 rps2-rpoC2 GCCAAAATGAACTCCTGCCT TTCGATGGGGAAATGAGAGA 411–412 1.000 59.5
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CCGGTACATCGTTGTGGATT AATCGAACCCGCATCTTCTC 426–430 1.000 80.5
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CCGGTACATCGTTGTGGATT GAATCGAACCCGCATCTTCT 427–431 1.000 80.5
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTTCCGGTACATCGTTGTGG AATCGAACCCGCATCTTCTC 429–433 1.000 79.0
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTTCCGGTACATCGTTGTGG GAATCGAACCCGCATCTTCT 430–434 1.000 79.0
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG AATCGAACCCGCATCTTCTC 471–475 1.000 78.9

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
Lancea hirsuta NC_037506.1 154045 View on NCBI ↗
Lancea tibetica NC_037693.1 153665 View on NCBI ↗