Markers + reference

Pilea

16 species · Urticaceae · Rosales

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Species 16
Genome length 150–152 kb
Candidate markers 275
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 698 0.1121 0.97 82.1 yes View details
ycf1 IRb 927 0.0241 1.00 67.8 no View details
ndhF-rpl32 SSC 1032 0.0921 0.99 80.8 yes View details
ycf1 SSC 5274 0.0924 0.99 78.0 yes View details
trnE-UUC-trnT-GGU LSC 581 0.0704 0.98 88.4 yes View details
trnT-UGU-trnL-UAA LSC 570 0.0839 0.99 86.0 yes View details
rbcL-accD LSC 753 0.0517 1.00 84.2 yes View details
trnK-UUU-rps16 LSC 700 0.0748 0.99 83.8 yes View details
atpH-atpI LSC 673 0.0605 1.00 83.1 yes View details
matK-trnK-UUU LSC 762 0.0528 0.99 82.8 yes View details
psbM-trnD-GUC LSC 495 0.0677 0.97 82.1 yes View details
ycf3-trnS-GCU LSC 622 0.0553 0.95 82.0 yes View details
rps16 LSC 1178 0.0508 0.99 81.7 yes View details
rpl16 LSC 1476 0.0444 0.97 81.7 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU GGCATTTCCACAATGACTGC CTTTGATTTGATTGCGCCGT 1203–1210 0.188 48.2
matK-trnK-UUU_p2 matK-trnK-UUU TGAGAAGATTCGTTGCGGAG CTTTGATTTGATTGCGCCGT 1581–1588 0.188 48.1
matK-trnK-UUU_p3 matK-trnK-UUU GTCGTAGGGAACATGGCATT CTTTGATTTGATTGCGCCGT 1217–1224 0.188 47.9
matK-trnK-UUU_p4 matK-trnK-UUU GGCATTTCCACAATGACTGC CGCTTCGATATGTAGTGCCA 1540–1556 0.188 47.7
matK-trnK-UUU_p5 matK-trnK-UUU TCTCTGCCCGTTAAGGAAGA CTTTGATTTGATTGCGCCGT 1242–1249 0.188 47.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG ATTTCAAAGAAGGCGGGTGT 821–998 0.750 81.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG AAAAGGGTATGTTGCTGCCA 1490–1690 0.750 81.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAGGCGGGTGT 783–961 0.750 81.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAGGCGGGTGT 782–960 0.750 81.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG AAAGGGTATGTTGCTGCCAA 1590–1613 0.188 48.8
rps16_p1 rps16 ACGGCGCAATCAAATCAAAG GAGGTTCGAATCCTTCCGTC 2198–2536 0.188 52.7
rps16_p2 rps16 TGGCACTACATATCGAAGCG GAGGTTCGAATCCTTCCGTC 1853–2199 0.188 51.8
rps16_p3 rps16 ACGGCGCAATCAAATCAAAG GCGACTTCGTCAGAAACTCT 1948–1971 0.188 48.7
rps16_p4 rps16 TGGCACTACATATCGAAGCG GCGACTTCGTCAGAAACTCT 1611–1625 0.188 47.6
rps16_p5 rps16 ACGGCGCAATCAAATCAAAG TTCCGTCCCAGAGCATATCT 2523 0.062 41.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 423–877 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 444–898 1.000 86.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 427–881 1.000 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 453–907 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 415–869 1.000 85.1
atpH-atpI_p1 atpH-atpI AGCAGAAATCAGCGGATTCA TTTTTGCAACTTTAGCCGCG 723–782 1.000 84.6
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 732–791 0.938 84.5
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTTGCAACTTTAGCCGCG 744–803 0.938 83.3
atpH-atpI_p4 atpH-atpI AATCCAGCAGCAATAACGGA TTTTTGCAACTTTAGCCGCG 746–805 0.938 82.0
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TTTTTGCAACTTTAGCCGCG 745–804 0.938 82.0
psbM-trnD-GUC_p1 psbM-trnD-GUC ACCTACCCCCTTTTAGTCCT TAGTATGATGGCGGTTGTGC 1801–1814 0.188 40.0
psbM-trnD-GUC_p2 psbM-trnD-GUC ACCTACCCCCTTTTAGTCCT AAGTATGCCCCCATCGTCTA 1781–1794 0.188 39.6
psbM-trnD-GUC_p3 psbM-trnD-GUC ACCTACCCCCTTTTAGTCCT TAGCGGTTCAGGACATCTCT 1763–1776 0.188 39.3
psbM-trnD-GUC_p4 psbM-trnD-GUC ACCTACCCCCTTTTAGTCCT TCTAGCGGTTCAGGACATCT 1765–1778 0.188 39.3
psbM-trnD-GUC_p5 psbM-trnD-GUC ACCTACCCCCTTTTAGTCCT GTCTAGCGGTTCAGGACATC 1766–1779 0.188 38.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (16)

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

Species Accession Length (bp) Link
Pilea cadierei NC_054343.1 152245 View on NCBI ↗
Pilea cavaleriei NC_057226.1 151557 View on NCBI ↗
Pilea cavernicola NC_072531.1 152343 View on NCBI ↗
Pilea danxiaensis ON496932.1 151857 View on NCBI ↗
Pilea glauca (nom. nud.) NC_054338.1 151210 View on NCBI ↗
Pilea menghaiensis PP504911.1 152079 View on NCBI ↗
Pilea microphylla NC_054344.1 150019 View on NCBI ↗
Pilea mollis NC_054341.1 150587 View on NCBI ↗
Pilea monilifera NC_057227.1 150938 View on NCBI ↗
Pilea peperomioides NC_054339.1 152327 View on NCBI ↗
Pilea peploides NC_056133.1 150924 View on NCBI ↗
Pilea plataniflora NC_056134.1 152143 View on NCBI ↗
Pilea pumila NC_054345.1 152036 View on NCBI ↗
Pilea sinocrassifolia NC_069841.1 151462 View on NCBI ↗
Pilea thymifolia NC_054340.1 150398 View on NCBI ↗
Pilea verrucosa NC_054346.1 150969 View on NCBI ↗