Markers + reference

Urera

6 species · Urticaceae · Rosales

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Species 6
Genome length 153–154 kb
Candidate markers 266
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 685 0.0457 0.75 65.6 yes View details
rps16-trnQ-UUG LSC 576 0.0702 0.90 71.7 yes View details
trnG-UCC-trnR-UCU LSC 270 0.0608 0.92 68.2 yes View details
trnE-UUC-trnT-GGU LSC 584 0.0307 0.99 61.7 yes View details
trnT-UGU-trnL-UAA LSC 618 0.0337 0.87 74.5 yes View details
ndhF-rpl32 SSC 662 0.0349 0.96 69.4 yes View details
rpl32-trnL-UAG SSC 826 0.0413 0.98 75.2 yes View details
ndhG-ndhI SSC 381 0.0376 1.00 55.1 yes View details
ycf1 SSC 5472 0.0257 0.99 58.7 yes View details
psbE-petL LSC 1149 0.0252 0.94 69.7 yes View details
accD-psaI LSC 567 0.0326 0.98 68.8 yes View details
rpl36-rps8 LSC 550 0.0301 0.90 67.5 yes View details
matK-trnK-UUU LSC 799 0.0221 0.95 64.9 yes View details
ccsA-ndhD SSC 280 0.0430 0.96 64.9 yes View details
ycf4-cemA LSC 800 0.0271 0.94 64.6 yes View details
trnG-GCC-trnfM-CAU LSC 162 0.0417 0.99 64.4 yes View details
rpl22-rps19 LSC 145 0.0629 0.94 64.1 yes View details
rpl33-rps18 LSC 222 0.0309 1.00 64.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU GGGCAAAGGGTATTTCCACA TCAACCGGCGTTTTTCAGTA 1652–1670 0.333 58.3
matK-trnK-UUU_p2 matK-trnK-UUU TTTACCCAATAGCGAAGGGC TCAACCGGCGTTTTTCAGTA 1833–1851 0.333 58.1
matK-trnK-UUU_p3 matK-trnK-UUU TTTACCCAATAGCGAAGGGC CGGAAAGAAGGTGCGGATAA 1997 0.167 46.1
matK-trnK-UUU_p4 matK-trnK-UUU GGGCAAAGGGTATTTCCACA CGGAAAGAAGGTGCGGATAA 1816 0.167 46.0
matK-trnK-UUU_p5 matK-trnK-UUU GCTCTGCCCGTTAAAGAAGA CGGAAAGAAGGTGCGGATAA 1847 0.167 45.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG ATTTCAAAGAAGGCGGGTGT 737–910 1.000 91.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG GAGCCGTACGAGGTGAAAAT 968–1141 1.000 89.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGCCCGATTCCCATAACAAT ATTTCAAAGAAGGCGGGTGT 956 0.167 46.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGCCCGATTCCCATAACAAT GAGCCGTACGAGGTGAAAAT 1188 0.167 46.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGCCCGATTCCCATAACAAT CGTTGCAATTGATGTTCGCT 1107 0.167 46.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 649–702 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGCAGCTTGCCAAACAAAAG 1220–1272 1.000 88.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1225–1277 1.000 88.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACCCTAGATTCTTGCCTCCA AGCAGCTTGCCAAACAAAAG 1420–1478 1.000 87.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACCCTAGATTCTTGCCTCCA CTTACAGCAGCTTGCCAAAC 1425–1483 1.000 87.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGTCCTATCCATTAGACAATG 320–340 1.000 52.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGTCCTATCCATTAGACAATG 323–343 1.000 52.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGTCCTATCCATTAGACAATG 324–344 1.000 52.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGTCCTATCCATTAGACAATG 309–329 1.000 52.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TAACGATGCGGGTTCGATTC TGTCCTATCCATTAGACAATG 308–328 1.000 52.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 671–687 1.000 84.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 669–685 1.000 84.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 650–666 1.000 84.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 648–664 1.000 84.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 668–684 1.000 84.1
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC CTTGAGGTCACGGGTTCAAA 228–232 1.000 86.5
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT CTTGAGGTCACGGGTTCAAA 229–233 1.000 86.5
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GGGTAGAGCAGTTTGGTAGC 264–268 1.000 85.6
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT GGGTAGAGCAGTTTGGTAGC 265–269 1.000 85.6
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GCAGTTTGGTAGCTTGCAAG 257–261 1.000 85.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Urera baccifera NC_064940.1 153215 View on NCBI ↗
Urera cameroonensis NC_064974.1 153212 View on NCBI ↗
Urera capitata NC_064973.1 153771 View on NCBI ↗
Urera cf. cordifolia Ur15 NC_064972.1 153214 View on NCBI ↗
Urera hypselodendron NC_064942.1 153212 View on NCBI ↗
Urera robusta NC_064943.1 153198 View on NCBI ↗