Markers + reference

Nuphar

4 species · Nymphaeaceae · Nymphaeales

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Species 4
Genome length 161–161 kb
Candidate markers 271
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 801 0.0125 1.00 52.4 yes View details
trnE-UUC-trnT-GGU LSC 795 0.0100 0.91 59.8 yes View details
trnT-GGU-psbD LSC 1554 0.0038 0.99 56.8 yes View details
accD-psaI LSC 797 0.0106 0.99 54.1 yes View details
petA-psbJ LSC 1226 0.0109 0.99 57.8 yes View details
psbE-petL LSC 1284 0.0070 1.00 58.5 yes View details
petD-rpoA LSC 399 0.0343 0.98 72.1 yes View details
rps19 LSC 279 0.0036 1.00 30.6 yes View details
rps19-trnH-GUG IRb 188 0.0641 0.28 60.7 yes View details
ycf1 IRb 442 0.0000 1.00 36.7 no View details
ndhF-rpl32 SSC 1111 0.0116 0.98 59.6 yes View details
ycf1 SSC 5607 0.0047 1.00 55.7 yes View details
rpl14-rpl16 LSC 139 0.0180 1.00 65.9 yes View details
atpH-atpI LSC 1341 0.0035 0.98 63.5 yes View details
rps16-trnQ-UUG LSC 2177 0.0054 0.99 62.2 yes View details
rbcL-accD LSC 777 0.0032 0.99 61.5 yes View details
ycf3-trnS-GGA LSC 892 0.0028 1.00 60.7 yes View details
atpF LSC 1319 0.0025 1.00 60.5 yes View details
psbM-trnD-GUC LSC 780 0.0028 1.00 60.1 yes View details
rps12-trnV-GAC IRb 1803 0.0025 1.00 59.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG CAAAAGGTATGTTGCTGCCG 1614–1647 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CAAAAGGTATGTTGCTGCCG 1613–1646 1.000 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GGATCCGTTTGCTATCGGTT 1274–1307 1.000 81.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GGATCCGTTTGCTATCGGTT 1273–1306 1.000 81.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTTTCAGGATCAGTCGT CAAAAGGTATGTTGCTGCCG 1615–1648 1.000 81.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 2251–2276 1.000 80.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 2234–2259 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACGTTGCCTTCTACCACATC GAGGTTCGAATCCTTCCGTC 2220–2245 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTTGCCTTCTACCACATCGT GAGGTTCGAATCCTTCCGTC 2218–2243 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CATGTCATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 2237–2262 1.000 79.9
atpF_p1 atpF TTTCTTCGGCTCGAATGGTT TCGGGAATCTAAATAAGGAGTGA 1507–1512 1.000 43.2
atpF_p2 atpF TTTCTTCGGCTCGAATGGTT TCCATAAGATAAGAGGAGAGCA 1430 1.000 43.0
atpF_p3 atpF TTTCTTCGGCTCGAATGGTT AAGTGTCTTATCGGGAATCT 1517–1522 1.000 42.5
atpF_p4 atpF TCTTCGGCTCGAATGGTTAC TCGGGAATCTAAATAAGGAGTGA 1505–1510 1.000 42.3
atpF_p5 atpF TCTTCGGCTCGAATGGTTAC TCCATAAGATAAGAGGAGAGCA 1428 1.000 42.1
atpH-atpI_p1 atpH-atpI GATACCTTCTACGGCTTGGC ATTTTTGCAACCTTAGCCGC 1492–1518 1.000 80.5
atpH-atpI_p2 atpH-atpI CGATACCTTCTACGGCTTGG ATTTTTGCAACCTTAGCCGC 1493–1519 1.000 80.5
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC ATTTTTGCAACCTTAGCCGC 1422–1448 1.000 80.0
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG ATTTTTGCAACCTTAGCCGC 1417–1443 1.000 79.6
atpH-atpI_p5 atpH-atpI GATACCTTCTACGGCTTGGC TACCTGTGATGTTCCTCGGA 1539–1565 1.000 79.3
psbM-trnD-GUC_p1 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT TTCAATTGGTCAGAGCACCG 886–888 1.000 74.7
psbM-trnD-GUC_p2 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA TTCAATTGGTCAGAGCACCG 885–887 1.000 73.7
psbM-trnD-GUC_p3 psbM-trnD-GUC AATGAACAGCGCAGTAGCAA TTCAATTGGTCAGAGCACCG 887–889 1.000 72.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGCGCAGTAGC TTCAATTGGTCAGAGCACCG 889–891 1.000 71.6
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAGAATGAACAGCGCAGT TTCAATTGGTCAGAGCACCG 892–894 1.000 70.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA ACCTTTGCAGCTTCATGGAA 834–920 1.000 83.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA ACCTTTGCAGCTTCATGGAA 832–918 1.000 83.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 796–882 1.000 83.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 794–880 1.000 83.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC ACCTTTGCAGCTTCATGGAA 831–917 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Nuphar advena NC_008788.1 160866 View on NCBI ↗
Nuphar japonica NC_045072.1 160761 View on NCBI ↗
Nuphar lutea MH161175.1 160623 View on NCBI ↗
Nuphar shimadae NC_037845.1 160645 View on NCBI ↗